Author: "Department of Agriculture (US)" / Publication Year Range: Last 3 years - Searchworks@Jio Institute Digital Library Search Results

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63 results on '"Department of Agriculture (US)"'

1. A compendium of genetic regulatory effects across pig tissues

Author: National Natural Science Foundation of China, National Key Research and Development Program (China), Guangdong Province, National Supercomputer Center in Guangzhou, Earmarked Fund for China Agriculture Research System, Health Data Research UK, European Commission, Department of Agriculture (US), National Institute of Food and Agriculture (US), Agricultural Research Service (US), Medical Research Council (UK), Australian Research Council, Ballester, María [0000-0002-5413-4640], Crespo-Piazuelo, Daniel [0000-0001-7896-2507], Gòdia, Marta [0000-0002-0439-4014], Teng, Jinyan, Gao, Yahui, Yin, Hongwei, Bai, Zhonghao, Liu, Shuli, Zeng, Haonan, Bai, Lijing, Cai, Zexi, Zhao, Bingru, Li, Xiujin, Xu, Zhiting, Lin, Qing, Pan, Zhangyuan, Yang, Wenjing, Yu, Xiaoshan, Guan, Dailu, Hou, Yali, Keel, Brittney N., Rohrer, Gary A., Lindholm-Perry, Amanda K., Oliver, William T., Ballester, María, Crespo-Piazuelo, Daniel, Quintanilla, Raquel, Canela-Xandri, Oriol, Rawlik, Konrad, Xia, Charley, Yao, Yuelin, Zhao, Qianyi, Yao, Wenye, Yang, Liu, Li, Houcheng, Zhang, Huicong, Liao, Wang, Chen, Tianshuo, Karlskov-Mortensen, Peter, Fredholm, Merete, Amills, Marcel, Clop, Alex, Giuffra, Elisabetta, Wu, Jun, Cai, Xiaodian, Diao, Shuqi, Pan, Xiangchun, Wei, Chen, Li, Jinghui, Cheng, Hao, Wang, Sheng, Su, Guosheng, Sahana, Goutam, Lund, Mogens Sandø, Dekkers, Jack C. M., Kramer, Luke, Tuggle, Christopher K., Corbett, Ryan, Groenen, Martien A. M., Madsen, Ole, Gòdia, Marta, Rocha, Dominique, Charles, Mathieu, Li, Cong-Jun, Pausch, Hubert, Hu, Xiaoxiang, Frantz, Laurent, Luo, Yonglun, Lin, Lin, Zhou, Zhongyin, Zhang, Zhe, Chen, Zitao, Cui, Leilei, Xiang, Ruidong, Shen, Xia, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Zhao, Yunxiang, Yi, Guoqiang, Tang, Zhonglin, Jiang, Jicai, Zhao, Fuping, Yuan, Xiaolong, Liu, Xiaohong, Chen, Yaosheng, Xu, Xuewen, Zhao, Shuhong, Zhao, Pengju, Haley, Chris, Zhou, Huaijun, Wang, Qishan, Pan, Yuchun, Ding, Xiangdong, Ma, Li, Li, Jiaqi, Navarro, Pau, Zhang, Qin, Li, Bingjie, Tenesa, Albert, Li, Kui, Liu, George E., Fang, Lingzhao, National Natural Science Foundation of China, National Key Research and Development Program (China), Guangdong Province, National Supercomputer Center in Guangzhou, Earmarked Fund for China Agriculture Research System, Health Data Research UK, European Commission, Department of Agriculture (US), National Institute of Food and Agriculture (US), Agricultural Research Service (US), Medical Research Council (UK), Australian Research Council, Ballester, María [0000-0002-5413-4640], Crespo-Piazuelo, Daniel [0000-0001-7896-2507], Gòdia, Marta [0000-0002-0439-4014], Teng, Jinyan, Gao, Yahui, Yin, Hongwei, Bai, Zhonghao, Liu, Shuli, Zeng, Haonan, Bai, Lijing, Cai, Zexi, Zhao, Bingru, Li, Xiujin, Xu, Zhiting, Lin, Qing, Pan, Zhangyuan, Yang, Wenjing, Yu, Xiaoshan, Guan, Dailu, Hou, Yali, Keel, Brittney N., Rohrer, Gary A., Lindholm-Perry, Amanda K., Oliver, William T., Ballester, María, Crespo-Piazuelo, Daniel, Quintanilla, Raquel, Canela-Xandri, Oriol, Rawlik, Konrad, Xia, Charley, Yao, Yuelin, Zhao, Qianyi, Yao, Wenye, Yang, Liu, Li, Houcheng, Zhang, Huicong, Liao, Wang, Chen, Tianshuo, Karlskov-Mortensen, Peter, Fredholm, Merete, Amills, Marcel, Clop, Alex, Giuffra, Elisabetta, Wu, Jun, Cai, Xiaodian, Diao, Shuqi, Pan, Xiangchun, Wei, Chen, Li, Jinghui, Cheng, Hao, Wang, Sheng, Su, Guosheng, Sahana, Goutam, Lund, Mogens Sandø, Dekkers, Jack C. M., Kramer, Luke, Tuggle, Christopher K., Corbett, Ryan, Groenen, Martien A. M., Madsen, Ole, Gòdia, Marta, Rocha, Dominique, Charles, Mathieu, Li, Cong-Jun, Pausch, Hubert, Hu, Xiaoxiang, Frantz, Laurent, Luo, Yonglun, Lin, Lin, Zhou, Zhongyin, Zhang, Zhe, Chen, Zitao, Cui, Leilei, Xiang, Ruidong, Shen, Xia, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Zhao, Yunxiang, Yi, Guoqiang, Tang, Zhonglin, Jiang, Jicai, Zhao, Fuping, Yuan, Xiaolong, Liu, Xiaohong, Chen, Yaosheng, Xu, Xuewen, Zhao, Shuhong, Zhao, Pengju, Haley, Chris, Zhou, Huaijun, Wang, Qishan, Pan, Yuchun, Ding, Xiangdong, Ma, Li, Li, Jiaqi, Navarro, Pau, Zhang, Qin, Li, Bingjie, Tenesa, Albert, Li, Kui, Liu, George E., and Fang, Lingzhao
Abstract: The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.
Published: 2024

2. Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)

Author: Department of Agriculture (US), Animal and Plant Health Inspection Service (US), Wildlife Services (US), Ministry of Research, Innovation and Digitization (Romania), Amills, Marcel [0000-0002-8999-0770], Smyser, Timothy J., Pfaffelhuber, Peter, Giglio, Rachael M., DeSaix, Matthew G., Davis, Amy J., Bowden, Courtney F., Tabak, Michael A., Manunza, Arianna, Bâlteanu, Valentin Adrian, Amills, Marcel, Iacolina, Laura, Walker, Pamela, Lessard, Carl, Piaggio, Antoinette J., Department of Agriculture (US), Animal and Plant Health Inspection Service (US), Wildlife Services (US), Ministry of Research, Innovation and Digitization (Romania), Amills, Marcel [0000-0002-8999-0770], Smyser, Timothy J., Pfaffelhuber, Peter, Giglio, Rachael M., DeSaix, Matthew G., Davis, Amy J., Bowden, Courtney F., Tabak, Michael A., Manunza, Arianna, Bâlteanu, Valentin Adrian, Amills, Marcel, Iacolina, Laura, Walker, Pamela, Lessard, Carl, and Piaggio, Antoinette J.
Abstract: The rapid expansion of wild pigs (Sus scrofa) throughout the United States has been fueled by unlawful introductions, with invasive populations causing extensive crop losses, damaging native ecosystems, and serving as a reservoir for disease. Multiple states have passed laws prohibiting the possession or transport of wild pigs. However, genetic and phenotypic similarities between domestic pigs and invasive wild pigs—which overwhelmingly represent domestic pig and wild boar hybrids—pose a challenge for the enforcement of such regulations. We sought to exploit wild boar ancestry as a common attribute among the vast majority of invasive wild pigs as a means of genetically differentiating wild pigs from breeds of domestic pig found within the United States. We organized reference high-density single nucleotide polymorphism genotypes (1039 samples from 33 domestic breeds and 382 samples from 16 wild boar populations) into five genetically cohesive reference groups: mixed-commercial breeds, Durocs, heritage breeds, primitive breeds, and wild boar. Building upon well-established genetic clustering approaches, we structured the test statistic to describe the difference in the likelihood of a given genotype's ancestry vectors (sensu genetic clustering analysis) if derived strictly from the four described domestic pig reference groups versus allowing for admixture from the wild boar group. By fitting statistical distributions to test statistics of reference domestic pigs, we characterized the distribution of the null hypothesis that a given genotype descends strictly from domestic pig reference groups. We tested the approach with simulated genotypes and empirical data from an additional 29 breeds of domestic pig represented by 435 unique genotypes; all associated test statistics for simulated and empirical domestic pig challenge sets fell within the distribution of reference domestic pigs. We then evaluated 6566 invasive wild pigs sampled across the contiguous United States
Published: 2024

3. Heritable microbiome variation is correlated with source environment in locally adapted maize varieties

Author: German Research Foundation, University of Bonn, Ministry of Education of the People's Republic of China, Southwest University, Department of Agriculture (US), Wang. Danning [0000-0001-8395-1941], Jiang, Yong [0000-0002-2824-677X], Li, Meng [0000-0002-6411-3085], Delgado-Baquerizo, Manuel [0000-0002-6499-576X], McLaughlin, Chloee [0000-0002-6345-6764], Tandrón, Yudelsy A. [0000-0002-7511-0779], Von Wirén, Nicolaus [0000-0002-4966-425X], Deichmann, Marion [0000-0003-1691-6673], Schaaf, Gabriel [0000-0001-9022-4515], Yang, Zhikai [0000-0002-8372-704X], Yang, Jinliang [0000-0002-0999-3518], Vries, Franciska T. de [0000-0002-6822-8883], Sawer, Ruairidh J. H. [0000-0002-8945-3078], Reif, Jochen C. [0000-0002-6742-265X], Yu, Peng [0000-0003-1670-8428], He, Xiaoming, Wang. Danning, Jiang, Yong, Li, Meng, Delgado-Baquerizo, Manuel, McLaughlin, Chloee, Marcon, Caroline, Guo, Li, Baer, Marcel, Tandrón, Yudelsy A., Von Wirén, Nicolaus, Deichmann, Marion, Schaaf, Gabriel, Piepho, Hans-Peter, Yang, Zhikai, Yang, Jinliang, Yim, Bunlong, Smalla, Kornelia, Goormachtig, Sofie, Vries, Franciska T. de, Hüging, Hubert, Baer, Mareike, Sawer, Ruairidh J. H., Reif, Jochen C., Yu, Peng, German Research Foundation, University of Bonn, Ministry of Education of the People's Republic of China, Southwest University, Department of Agriculture (US), Wang. Danning [0000-0001-8395-1941], Jiang, Yong [0000-0002-2824-677X], Li, Meng [0000-0002-6411-3085], Delgado-Baquerizo, Manuel [0000-0002-6499-576X], McLaughlin, Chloee [0000-0002-6345-6764], Tandrón, Yudelsy A. [0000-0002-7511-0779], Von Wirén, Nicolaus [0000-0002-4966-425X], Deichmann, Marion [0000-0003-1691-6673], Schaaf, Gabriel [0000-0001-9022-4515], Yang, Zhikai [0000-0002-8372-704X], Yang, Jinliang [0000-0002-0999-3518], Vries, Franciska T. de [0000-0002-6822-8883], Sawer, Ruairidh J. H. [0000-0002-8945-3078], Reif, Jochen C. [0000-0002-6742-265X], Yu, Peng [0000-0003-1670-8428], He, Xiaoming, Wang. Danning, Jiang, Yong, Li, Meng, Delgado-Baquerizo, Manuel, McLaughlin, Chloee, Marcon, Caroline, Guo, Li, Baer, Marcel, Tandrón, Yudelsy A., Von Wirén, Nicolaus, Deichmann, Marion, Schaaf, Gabriel, Piepho, Hans-Peter, Yang, Zhikai, Yang, Jinliang, Yim, Bunlong, Smalla, Kornelia, Goormachtig, Sofie, Vries, Franciska T. de, Hüging, Hubert, Baer, Mareike, Sawer, Ruairidh J. H., Reif, Jochen C., and Yu, Peng
Abstract: Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant–microbiota interactions in the face of environmental stresses. Here we surveyed 3,168 root and rhizosphere microbiome samples from 129 accessions of locally adapted Zea, sourced from diverse habitats and grown under control and different stress conditions. We quantified stress treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome abundance. Genome-wide association analysis identified host genetic variants linked to both rhizosphere microbiome abundance and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone bacterium Massilia in our controlled experiments and total soil nitrogen in the source environment. Isolation and controlled inoculation of Massilia alone can contribute to root development, whole-plant biomass production and adaptation to low nitrogen availability. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.
Published: 2024

4. DNA barcoding, phylogeny and phylogeography of the cyst nematode species of the Schachtii group from the genus Heterodera (Tylenchida: Heteroderidae)

Author: Department of Agriculture (US), Palomares Rius, Juan E. [0000-0003-1776-8131], Castillo, Pablo [0000-0003-0256-876X], Subbotin, Sergei A., Roubtsova, Tatiana V., Bostock, Richard M., Tanha Maafi, Zahra, Chizhov, Vladimir N., Palomares Rius, Juan E., Castillo, Pablo, Department of Agriculture (US), Palomares Rius, Juan E. [0000-0003-1776-8131], Castillo, Pablo [0000-0003-0256-876X], Subbotin, Sergei A., Roubtsova, Tatiana V., Bostock, Richard M., Tanha Maafi, Zahra, Chizhov, Vladimir N., Palomares Rius, Juan E., and Castillo, Pablo
Abstract: Cyst-forming nematodes of the genus Heterodera are highly derived and economically important plant parasites. The Schachtii group of this genus is one of the largest ones with a total of 18 species parasitising dicotyledons. In this study, we provided comprehensive phylogenetic analyses of several hundred COI and ITS rRNA gene sequences of selected species from the Schachtii group, including H. betae, H. cajani, H. ciceri, H. galeopsidis, H. glycines, H. medicaginis, H. mediterranea, H. schachtii, H. sonchophila and H. trifolii, using Bayesian inference, maximum likelihood, and statistical parsimony. One hundred and twenty four new COI, 57 ITS rRNA and eight hsp90 gene sequences from 81 nematode populations collected in 19 countries were obtained in this study. Our study showed that the ITS rRNA gene has limited discrimination power compared to the COI gene. However, our analysis also revealed that partial COI gene sequences were identical for H. trifolii, H. betae and H. galeopsidis. Based on the results of phylogeographical analysis and age estimation of clades with a molecular clock approach, it was hypothesised that the majority of the Schachtii group species originated and diversified in the Mediterranean Basin biodiversity hotspot during the Pleistocene and then dispersed from this region across the world. The Sino-Japanese Floristic Region is likely one of the centres of diversification for the soybean cyst nematode, which showed distinct population structure. The possible role of hybridisation and polyploidisation in the evolution of species of the Schachtii group is discussed.
Published: 2024

5. Seedling root system adaptation to water availability during maize domestication and global expansion

Author: Deutsche Forschungsgemeinschaft, National Institute of Food and Agriculture (US), Consejo Nacional de Ciencia y Tecnología (México), Natural Science Foundation (US), National Key Research and Development Program (China), Chinese Academy of Agricultural Sciences, Southwest University, Department of Agriculture (US), European Commission, Ministerio de Ciencia e Innovación (España), German Research Foundation, Helmholtz Association, University of Bonn, Yu, Peng [0000-0003-1670-8428], Li, Meng [0000-0002-6411-3085], Wang. Danning [0000-0001-8395-1941], Chen, Xinping [0000-0002-6245-0133], Delgado-Baquerizo, Manuel [0000-0002-6499-576X], Plutenko, Iaroslav [0000-0002-1064-3531], Resende Jr., Marcio [0000-0002-2367-0766], Salvi, Silvio [0000-0002-0338-8894], Ahmed, Mutez Ali [0000-0002-7402-1571], Bauer, Felix M. [0000-0002-7441-9897], Schnepf, Andrea [0000-0003-2203-4466], Heymans, Adrien [0000-0003-3685-2240], Suresh, Kiran [0000-0002-7959-6323], McLaughlin, Chloee [0000-0002-6345-6764], Schön, Chris-Carolin [0000-0001-6067-7900], Bernau, Vivian [0000-0002-2393-8101], Von Wirén, Nicolaus [000-0002-4966-425X], Sawers, Ruairidh J. H. [000-0002-8945-3078], Wang, Tianyu [0000-0002-7254-7449], Hochholdinger, Frank [0000-0002-5155-0884], Yu, Peng, Li, Chunhui, Li, Meng, He, Xiaoming, Wang. Danning, Li, Hongjie, Marcon, Caroline, Li, Yu, Pérez-Limón, Sergio, Chen, Xinping, Delgado-Baquerizo, Manuel, Koller, Robert, Metzner, Ralf, Van Dusschoten, D., Pflugfelder, Daniel, Borisjuk, Ljudmilla, Plutenko, Iaroslav, Mahon, Audrey, Resende Jr., Marcio, Salvi, Silvio, Akale, Asegidew, Abdalla, Mohanned, Ahmed, Mutez Ali, Bauer, Felix M., Schnepf, Andrea, Lobet, Guillaume, Heymans, Adrien, Schreiber, Lukas, McLaughlin, Chloee, Li, Chunjian, Mayer, Manfred, Schön, Chris-Carolin, Bernau, Vivian, Von Wirén, Nicolaus, Sawers, Ruairidh J. H., Wang, Tianyu, Hochholdinger, Frank, Deutsche Forschungsgemeinschaft, National Institute of Food and Agriculture (US), Consejo Nacional de Ciencia y Tecnología (México), Natural Science Foundation (US), National Key Research and Development Program (China), Chinese Academy of Agricultural Sciences, Southwest University, Department of Agriculture (US), European Commission, Ministerio de Ciencia e Innovación (España), German Research Foundation, Helmholtz Association, University of Bonn, Yu, Peng [0000-0003-1670-8428], Li, Meng [0000-0002-6411-3085], Wang. Danning [0000-0001-8395-1941], Chen, Xinping [0000-0002-6245-0133], Delgado-Baquerizo, Manuel [0000-0002-6499-576X], Plutenko, Iaroslav [0000-0002-1064-3531], Resende Jr., Marcio [0000-0002-2367-0766], Salvi, Silvio [0000-0002-0338-8894], Ahmed, Mutez Ali [0000-0002-7402-1571], Bauer, Felix M. [0000-0002-7441-9897], Schnepf, Andrea [0000-0003-2203-4466], Heymans, Adrien [0000-0003-3685-2240], Suresh, Kiran [0000-0002-7959-6323], McLaughlin, Chloee [0000-0002-6345-6764], Schön, Chris-Carolin [0000-0001-6067-7900], Bernau, Vivian [0000-0002-2393-8101], Von Wirén, Nicolaus [000-0002-4966-425X], Sawers, Ruairidh J. H. [000-0002-8945-3078], Wang, Tianyu [0000-0002-7254-7449], Hochholdinger, Frank [0000-0002-5155-0884], Yu, Peng, Li, Chunhui, Li, Meng, He, Xiaoming, Wang. Danning, Li, Hongjie, Marcon, Caroline, Li, Yu, Pérez-Limón, Sergio, Chen, Xinping, Delgado-Baquerizo, Manuel, Koller, Robert, Metzner, Ralf, Van Dusschoten, D., Pflugfelder, Daniel, Borisjuk, Ljudmilla, Plutenko, Iaroslav, Mahon, Audrey, Resende Jr., Marcio, Salvi, Silvio, Akale, Asegidew, Abdalla, Mohanned, Ahmed, Mutez Ali, Bauer, Felix M., Schnepf, Andrea, Lobet, Guillaume, Heymans, Adrien, Schreiber, Lukas, McLaughlin, Chloee, Li, Chunjian, Mayer, Manfred, Schön, Chris-Carolin, Bernau, Vivian, Von Wirén, Nicolaus, Sawers, Ruairidh J. H., Wang, Tianyu, and Hochholdinger, Frank
Abstract: The maize root system has been reshaped by indirect selection during global adaptation to new agricultural environments. In this study, we characterized the root systems of more than 9,000 global maize accessions and its wild relatives, defining the geographical signature and genomic basis of variation in seminal root number. We demonstrate that seminal root number has increased during maize domestication followed by a decrease in response to limited water availability in locally adapted varieties. By combining environmental and phenotypic association analyses with linkage mapping, we identified genes linking environmental variation and seminal root number. Functional characterization of the transcription factor ZmHb77 and in silico root modeling provides evidence that reshaping root system architecture by reducing the number of seminal roots and promoting lateral root density is beneficial for the resilience of maize seedlings to drought.
Published: 2024

6. The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine

Author: Università degli Studi di Verona, National Science Foundation (US), Department of Agriculture (US), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, European Cooperation in Science and Technology, D’Incà, Erica, Foresti, Chiara, Orduña, Luis, Amato, Alessandra, Vandelle, Elodie, Santiago, Antonio, Botton, Alessandro, Cazzaniga, Stefano, Bertini, Edoardo, Pezzotti, Mario, Giovannoni, James, Vrebalov, Julia T., Matus, José Tomás, Tornielli, Giovanni Battista, Zenoni, Sara, Università degli Studi di Verona, National Science Foundation (US), Department of Agriculture (US), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, European Cooperation in Science and Technology, D’Incà, Erica, Foresti, Chiara, Orduña, Luis, Amato, Alessandra, Vandelle, Elodie, Santiago, Antonio, Botton, Alessandro, Cazzaniga, Stefano, Bertini, Edoardo, Pezzotti, Mario, Giovannoni, James, Vrebalov, Julia T., Matus, José Tomás, Tornielli, Giovanni Battista, and Zenoni, Sara
Abstract: Grapevine (Vitis vinifera L.) is one of the most widely cultivated fruit crops because the winemaking industry has huge economic relevance worldwide. Uncovering the molecular mechanisms controlling the developmental progression of plant organs will prove essential for maintaining high-quality grapes, expressly in the context of climate change, which impairs the ripening process. Through a deep inspection of transcriptomic data, we identified VviNAC60, a member of the NAC transcription factor family, as a putative regulator of grapevine organ maturation. We explored VviNAC60 binding landscapes through DNA affinity purification followed by sequencing and compared bound genes with transcriptomics datasets from grapevine plants stably and transiently overexpressing VviNAC60 to define a set of high-confidence targets. Among these, we identified key molecular markers associated with organ senescence and fruit ripening. Physiological, metabolic, and promoter activation analyses showed that VviNAC60 induces chlorophyll degradation and anthocyanin accumulation through the upregulation of STAY-GREEN PROTEIN 1 (VviSGR1) and VviMYBA1, respectively, with the latter being upregulated through a VviNAC60–VviNAC03 regulatory complex. Despite sharing a closer phylogenetic relationship with senescence-related homologs to the NAC transcription factor AtNAP, VviNAC60 complemented the nonripening(nor) mutant phenotype in tomato (Solanum lycopersicum), suggesting a dual role as an orchestrator of both ripening- and senescence-related processes. Our data support VviNAC60 as a regulator of processes initiated in the grapevine vegetative- to mature-phase organ transition and therefore as a potential target for enhancing the environmental resilience of grapevine by fine-tuning the duration of the vegetative phase.
Published: 2023

7. A multi-centre peptidomics investigation of food digesta: current state of the art in mass spectrometry analysis and data visualisation

Author: Department of Agriculture (US), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Ege University, European Commission, Agence Nationale de la Recherche (France), Aarhus University Research Foundation, Portmann, Reto, Jiménez-Barrios, Pablo, Jardin, Julien, Abbühl, Lychou, Barile, Daniela, Danielsen, Marianne, Huang, Yu-Ping, Kastrup Dalsgaard, Trine, Miralles, Beatriz, Briard-Bion, Valérie, Cattaneo, Stefano, Chambon, Christophe, Cudennec, Benoit, De Noni, Ivano, Deracinois, Barbara, Dupont, Didier, Duval, Angéline, Flahaut, Christophe, López-Nicolás, Rubén, Nehir El, Sedef, Pica, Valentina, Santé-Lhoutelier, Véronique, Stuknytė, Milda, Théron, Laëtitia, Sayd, Thierry, Recio, Isidra, Egger, Lotti, Department of Agriculture (US), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Ege University, European Commission, Agence Nationale de la Recherche (France), Aarhus University Research Foundation, Portmann, Reto, Jiménez-Barrios, Pablo, Jardin, Julien, Abbühl, Lychou, Barile, Daniela, Danielsen, Marianne, Huang, Yu-Ping, Kastrup Dalsgaard, Trine, Miralles, Beatriz, Briard-Bion, Valérie, Cattaneo, Stefano, Chambon, Christophe, Cudennec, Benoit, De Noni, Ivano, Deracinois, Barbara, Dupont, Didier, Duval, Angéline, Flahaut, Christophe, López-Nicolás, Rubén, Nehir El, Sedef, Pica, Valentina, Santé-Lhoutelier, Véronique, Stuknytė, Milda, Théron, Laëtitia, Sayd, Thierry, Recio, Isidra, and Egger, Lotti
Abstract: Mass spectrometry has become the technique of choice for the assessment of a high variety of molecules in complex food matrices. It is best suited for monitoring the evolution of digestive processes in vivo and in vitro. However, considering the variety of equipment available in different laboratories and the diversity of sample preparation methods, instrumental settings for data acquisition, statistical evaluations, and interpretations of results, it is difficult to predict a priori the ideal parameters for optimal results. The present work addressed this uncertainty by executing an inter-laboratory study with samples collected during in vitro digestion and presenting an overview of the state-of-the-art mass spectrometry applications and analytical capabilities available for studying food digestion. Three representative high-protein foods – skim milk powder (SMP), cooked chicken breast and tofu – were digested according to the static INFOGEST protocol with sample collection at five different time points during gastric and intestinal digestion. Ten laboratories analysed all digesta with their in-house equipment and applying theirconventional workflow., The compiled results demonstrate in general, that soy proteins had a slower gastric digestion and the presence of longer peptide sequences in the intestinal phase compared to SMP or chicken proteins, suggesting a higher resistance to the digestion of soy proteins. Differences in results among the various laboratories were attributed more to the peptide selection criteria than to the individual analytical platforms. Overall, the combination of mass spectrometry techniques with suitable methodological and statistical approaches is adequate for contributing to the characterisation of the recently defined digestome.
Published: 2023

8. Relationship between pre-trial milk fat concentration and milk fat response to marine oil diets that caused milk fat depression in sheep

Author: Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Department of Agriculture (US), Toral, Pablo G. [0000-0002-1913-7707], Hervás, Gonzalo [0000-0002-0013-7459], Frutos, Pilar [0000-0002-4919-5094], Della Badia, Antonella [0000-0002-2685-5328], Della Badia, Antonella, Toral, Pablo G., Hervás, Gonzalo, Matamoros, C., Frutos, Pilar, Harvatine, K.J., Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Department of Agriculture (US), Toral, Pablo G. [0000-0002-1913-7707], Hervás, Gonzalo [0000-0002-0013-7459], Frutos, Pilar [0000-0002-4919-5094], Della Badia, Antonella [0000-0002-2685-5328], Della Badia, Antonella, Toral, Pablo G., Hervás, Gonzalo, Matamoros, C., Frutos, Pilar, and Harvatine, K.J.
Published: 2023

9. Oxygen Nanobubble-Loaded Biochars Mitigate Copper Transfer from Copper-Contaminated Soil to Rice and Improve Rice Growth

Author: National Key Research and Development Program (China), Natural Science Foundation of Jiangsu Province, Agriculture Research System of China, China National Tobacco Corporation, Jiangsu Province, Department of Agriculture (US), Chu, Qingnan [0000-0003-0020-812X], Sha, Zhimin [0009-0008-2549-5579], Feng, Yanfang [0000-0001-6251-7660], Zhou, Dongmei [0000-0002-7917-7954], Xing, Baoshan [0000-0003-2028-1295], Chu, Qingnan, Sha, Zhimin, Li, Detian, Feng, Yanfang, Xue, Lihong, Zhou, Dongmei, Xing, Baoshan, National Key Research and Development Program (China), Natural Science Foundation of Jiangsu Province, Agriculture Research System of China, China National Tobacco Corporation, Jiangsu Province, Department of Agriculture (US), Chu, Qingnan [0000-0003-0020-812X], Sha, Zhimin [0009-0008-2549-5579], Feng, Yanfang [0000-0001-6251-7660], Zhou, Dongmei [0000-0002-7917-7954], Xing, Baoshan [0000-0003-2028-1295], Chu, Qingnan, Sha, Zhimin, Li, Detian, Feng, Yanfang, Xue, Lihong, Zhou, Dongmei, and Xing, Baoshan
Abstract: Copper (Cu)-contaminated paddy soil has caused substantial concerns for human health through biomagnification in the soil-rice-human chain. In this study, oxygen nanobubble-loaded biochars (ONBC), including pyrochars (NPC) and hydrochars (NHC), were used to amend Cu-contaminated paddy soils and reduce rice Cu toxicity. The ONBC amendment improved the rhizospheric redox potential and dissolved oxygen concentration via slow, continuous oxygen release, promoting root iron plaque formation and effectively inhibiting root Cu influx. Moreover, the ONBC amendment improved soil microbial diversity. The abundance of bacterial genes involved in cytosolic Cu complexation and Cu export to the periplasm space for Cu stabilization markedly improved. The sequestered Cu in root iron plaque and soil bacteria inhibited Cu influx into the shoots to avoid Cu overaccumulation in the edible parts. This was reflected by the Cu content decreasing by 1.91-fold and 2.38-fold in shoots under NPC and NHC treatments, respectively. Furthermore, the improved oxygen-enriched rhizosphere environment via the ONBC amendment promoted root activity and the abundance of bacterial genes involved in nutrients mineralization, further promoting shoot biomass by 1.46-fold and 2.29-fold under NPC and NHC treatments, respectively. This study proposes an environmentally friendly strategy to mitigate Cu transfer from soil to crops and improve crop productivity.
Published: 2023

10. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii

Author: Biotechnology and Biological Sciences Research Council (UK), Royal Society (UK), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Department of Agriculture (US), National Science Foundation (US), Department of Energy (US), Martin Del Campo, Julia S. [0000-0001-8914-2504], Bueno Batista, Marcelo [0000-0002-6642-6624], Mus, Florence [0000-0002-1655-1267], Rubio, Luis M. [0000-0003-1596-2475], Einsle, O. [0000-0001-8722-2893], Peters, John W. [0000-0001-9117-9568], Dixon, Ray [0000-0002-6348-639X], Dean, Dennis R. [0000-0001-8960-6196], Dos Santos, Patricia C. [0000-0002-3364-0931], Martin Del Campo, Julia S., Rigsbee, Jack, Bueno Batista, Marcelo, Mus, Florence, Rubio, Luis M., Einsle, O., Peters, John W., Dixon, Ray, Dean, Dennis R., Dos Santos, Patricia C., Biotechnology and Biological Sciences Research Council (UK), Royal Society (UK), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Department of Agriculture (US), National Science Foundation (US), Department of Energy (US), Martin Del Campo, Julia S. [0000-0001-8914-2504], Bueno Batista, Marcelo [0000-0002-6642-6624], Mus, Florence [0000-0002-1655-1267], Rubio, Luis M. [0000-0003-1596-2475], Einsle, O. [0000-0001-8722-2893], Peters, John W. [0000-0001-9117-9568], Dixon, Ray [0000-0002-6348-639X], Dean, Dennis R. [0000-0001-8960-6196], Dos Santos, Patricia C. [0000-0002-3364-0931], Martin Del Campo, Julia S., Rigsbee, Jack, Bueno Batista, Marcelo, Mus, Florence, Rubio, Luis M., Einsle, O., Peters, John W., Dixon, Ray, Dean, Dennis R., and Dos Santos, Patricia C.
Abstract: Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
Published: 2023

11. Integrative analysis of multimodal mass spectrometry data in MZmine 3

Author: Czech Science Foundation, European Commission, Department of Energy (US), National Science Foundation (US), National Institutes of Health (US), Department of Agriculture (US), Heuckeroth, Steffen [0000-0002-4928-2526], Dyrlund, Thomas S. [0000-0002-7159-6628], Bushuiev, Roman [0000-0003-1769-1509], Hoffmann, Nils [0000-0002-6540-6875], Fleischauer, Markus [0000-0001-7557-0831], Dührkop, Kai [0000-0002-9056-0540], Hoogstra, Shawn J. [0000-0003-2533-9310], Rudt, Edward [0000-0003-4351-3212], Fallon, Timothy R. [0000-0002-3048-7679], Schulze, Tobias [0000-0002-9744-8914], Bilbao, A. [0000-0003-2985-8249], Rivas-Ubach, Albert [0000-0003-1293-7127], Richter, Henning [0000-0003-3696-6993], Nothias, Louis-Félix [0000-0001-6711-6719], Orešič, Matej [0000-0002-2856-9165], Weng, Jing-Ke [0000-0003-3059-0075], Böcker, Sebastian [0000-0002-9304-8091], Hayen, Heiko [0000-0002-4074-8545], Karst, Uwe [0000-0002-1774-6787], Dorrestein, Pieter C. [0000-0002-3003-1030], Pluskal, Tomáš [0000-0002-6940-3006], Schmid, Robin, Heuckeroth, Steffen, Korf, Ansgar, Smirnov, Aleksandr, Myers, Owen, Dyrlund, Thomas S., Bushuiev, Roman, Murray, Kevin J, Hoffmann, Nils, Lu, Miaoshan, Sarvepalli, Abinesh, Zhang, Zheng, Fleischauer, Markus, Dührkop, Kai, Wesner, Mark, Hoogstra, Shawn J., Rudt, Edward, Mokshyna, Olena, Brungs, Corinna, Ponomarov, Kirill, Mutabdžija, Lana, Damiani, Tito, Pudney, Chris J, Earll, Mark, Helmer, Patrick O, Fallon, Timothy R., Schulze, Tobias, Rivas-Ubach, Albert, Bilbao, A., Richter, Henning, Nothias, Louis-Félix, Wang, Mingxun, Orešič, Matej, Weng, Jing-Ke, Böcker, Sebastian, Jeibmann, Astrid, Hayen, Heiko, Karst, Uwe, Dorrestein, Pieter C., Petras, Daniel, Du, Xiuxia, Pluskal, Tomáš, Czech Science Foundation, European Commission, Department of Energy (US), National Science Foundation (US), National Institutes of Health (US), Department of Agriculture (US), Heuckeroth, Steffen [0000-0002-4928-2526], Dyrlund, Thomas S. [0000-0002-7159-6628], Bushuiev, Roman [0000-0003-1769-1509], Hoffmann, Nils [0000-0002-6540-6875], Fleischauer, Markus [0000-0001-7557-0831], Dührkop, Kai [0000-0002-9056-0540], Hoogstra, Shawn J. [0000-0003-2533-9310], Rudt, Edward [0000-0003-4351-3212], Fallon, Timothy R. [0000-0002-3048-7679], Schulze, Tobias [0000-0002-9744-8914], Bilbao, A. [0000-0003-2985-8249], Rivas-Ubach, Albert [0000-0003-1293-7127], Richter, Henning [0000-0003-3696-6993], Nothias, Louis-Félix [0000-0001-6711-6719], Orešič, Matej [0000-0002-2856-9165], Weng, Jing-Ke [0000-0003-3059-0075], Böcker, Sebastian [0000-0002-9304-8091], Hayen, Heiko [0000-0002-4074-8545], Karst, Uwe [0000-0002-1774-6787], Dorrestein, Pieter C. [0000-0002-3003-1030], Pluskal, Tomáš [0000-0002-6940-3006], Schmid, Robin, Heuckeroth, Steffen, Korf, Ansgar, Smirnov, Aleksandr, Myers, Owen, Dyrlund, Thomas S., Bushuiev, Roman, Murray, Kevin J, Hoffmann, Nils, Lu, Miaoshan, Sarvepalli, Abinesh, Zhang, Zheng, Fleischauer, Markus, Dührkop, Kai, Wesner, Mark, Hoogstra, Shawn J., Rudt, Edward, Mokshyna, Olena, Brungs, Corinna, Ponomarov, Kirill, Mutabdžija, Lana, Damiani, Tito, Pudney, Chris J, Earll, Mark, Helmer, Patrick O, Fallon, Timothy R., Schulze, Tobias, Rivas-Ubach, Albert, Bilbao, A., Richter, Henning, Nothias, Louis-Félix, Wang, Mingxun, Orešič, Matej, Weng, Jing-Ke, Böcker, Sebastian, Jeibmann, Astrid, Hayen, Heiko, Karst, Uwe, Dorrestein, Pieter C., Petras, Daniel, Du, Xiuxia, and Pluskal, Tomáš
Published: 2023

12. Increasing crop rotational diversity can enhance cereal yields

Author: Department of Agriculture (US), Scottish Government, Swedish University of Agricultural Sciences, Biotechnology and Biological Sciences Research Council (UK), Agriculture and Agri-Food Canada, Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Vico, Giulia [0000-0002-7849-2653], Costa, Alessio [0000-0002-8647-4738], Bowles, Timothy [0000-0002-4840-3787], Gaudin, Amélie C.M. [0000-0003-4007-9991], Hallin, Sara [0000-0002-9069-9024], Alarcón Víllora, M. Remedios [0000-0003-0078-8363], Berti, Antonio [0000-0002-6377-2820], Blecharczyk, Andrzej [0000-0002-8688-3136], Culman, Steve [0000-0003-3985-257X], Deen, William [0000-0001-5966-6462], Drury, Craig F. [0000-0003-0986-0755], García y García, Axel [0000-0002-7263-530X], García-Díaz, Andrés [0000-0003-4270-0972], Hernández Plaza, María Eva [0000-0002-2378-2602], Jonczyk, Krzysztof [0000-0002-5262-8858], Jäck, Ortrud [0000-0002-9885-0008], Lehman, R. Michael [0000-0002-3391-3178], Montemurro, Francesco [0000-0003-3209-0189], Morari, Francesco [0000-0001-9081-868X], Onofri, Andrea [0000-0002-6603-329X], Osborne, Shannon L. [0000-0003-3458-3251], Tenorio, J. L. [0000-0001-7596-6676], Sandström, Boël [0000-0003-1316-8569], Santín Montanyá, Inés [0000-0003-1978-6560], Sawinska, Zuzanna [0000-0002-7030-3221], Schmer, Marty R. [0000-0002-3721-6177], Stalenga, Jaroslaw [0000-0002-3486-0995], Strock, Jeffrey [0000-0001-5357-0638], Tei, Francesco [0000-0003-0857-9662], Topp, Cairistiona F.E. [0000-0002-7064-638X], Walker, Robin L. [0000-0002-8008-4413], Bommarco, Riccardo [0000-0001-8888-0476], Smith, Monique E., Vico, Giulia, Costa, Alessio, Bowles, Timothy, Gaudin, Amélie C.M., Hallin, Sara, Watson, Christine A., Alarcòn, Remedios, Berti, Antonio, Blecharczyk, Andrzej, Calderon, Francisco J., Culman, Steve, Deen, William, Drury, Craig F., García y García, Axel, García-Díaz, Andrés, Hernández Plaza, María Eva, Jonczyk, Krzysztof, Jäck, Ortrud, Lehman, R. Michael, Montemurro, Francesco, Morari, Francesco, Onofri, Andrea, Osborne, Shannon L., Tenorio, J. L., Sandström, Boël, Santín Montanyá, Inés, Sawinska, Zuzanna, Schmer, Marty R., Stalenga, Jaroslaw, Strock, Jeffrey, Tei, Francesco, Topp, Cairistiona F.E., Ventrella, Domenico, Walker, Robin L., Bommarco, Riccardo, Department of Agriculture (US), Scottish Government, Swedish University of Agricultural Sciences, Biotechnology and Biological Sciences Research Council (UK), Agriculture and Agri-Food Canada, Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Vico, Giulia [0000-0002-7849-2653], Costa, Alessio [0000-0002-8647-4738], Bowles, Timothy [0000-0002-4840-3787], Gaudin, Amélie C.M. [0000-0003-4007-9991], Hallin, Sara [0000-0002-9069-9024], Alarcón Víllora, M. Remedios [0000-0003-0078-8363], Berti, Antonio [0000-0002-6377-2820], Blecharczyk, Andrzej [0000-0002-8688-3136], Culman, Steve [0000-0003-3985-257X], Deen, William [0000-0001-5966-6462], Drury, Craig F. [0000-0003-0986-0755], García y García, Axel [0000-0002-7263-530X], García-Díaz, Andrés [0000-0003-4270-0972], Hernández Plaza, María Eva [0000-0002-2378-2602], Jonczyk, Krzysztof [0000-0002-5262-8858], Jäck, Ortrud [0000-0002-9885-0008], Lehman, R. Michael [0000-0002-3391-3178], Montemurro, Francesco [0000-0003-3209-0189], Morari, Francesco [0000-0001-9081-868X], Onofri, Andrea [0000-0002-6603-329X], Osborne, Shannon L. [0000-0003-3458-3251], Tenorio, J. L. [0000-0001-7596-6676], Sandström, Boël [0000-0003-1316-8569], Santín Montanyá, Inés [0000-0003-1978-6560], Sawinska, Zuzanna [0000-0002-7030-3221], Schmer, Marty R. [0000-0002-3721-6177], Stalenga, Jaroslaw [0000-0002-3486-0995], Strock, Jeffrey [0000-0001-5357-0638], Tei, Francesco [0000-0003-0857-9662], Topp, Cairistiona F.E. [0000-0002-7064-638X], Walker, Robin L. [0000-0002-8008-4413], Bommarco, Riccardo [0000-0001-8888-0476], Smith, Monique E., Vico, Giulia, Costa, Alessio, Bowles, Timothy, Gaudin, Amélie C.M., Hallin, Sara, Watson, Christine A., Alarcòn, Remedios, Berti, Antonio, Blecharczyk, Andrzej, Calderon, Francisco J., Culman, Steve, Deen, William, Drury, Craig F., García y García, Axel, García-Díaz, Andrés, Hernández Plaza, María Eva, Jonczyk, Krzysztof, Jäck, Ortrud, Lehman, R. Michael, Montemurro, Francesco, Morari, Francesco, Onofri, Andrea, Osborne, Shannon L., Tenorio, J. L., Sandström, Boël, Santín Montanyá, Inés, Sawinska, Zuzanna, Schmer, Marty R., Stalenga, Jaroslaw, Strock, Jeffrey, Tei, Francesco, Topp, Cairistiona F.E., Ventrella, Domenico, Walker, Robin L., and Bommarco, Riccardo
Abstract: Diversifying agriculture by rotating a greater number of crop species in sequence is a promising practice to reduce negative impacts of crop production on the environment and maintain yields. However, it is unclear to what extent cereal yields change with crop rotation diversity and external nitrogen fertilization level over time, and which functional groups of crops provide the most yield benefit. Here, using grain yield data of small grain cereals and maize from 32 long-term (10–63 years) experiments across Europe and North America, we show that crop rotational diversity, measured as crop species diversity and functional richness, enhanced grain yields. This yield benefit increased over time. Only the yields of winter-sown small grain cereals showed a decline at the highest level of species diversity. Diversification was beneficial to all cereals with a low external nitrogen input, particularly maize, enabling a lower dependence on nitrogen fertilisers and ultimately reducing greenhouse gas emissions and nitrogen pollution. The results suggest that increasing crop functional richness rather than species diversity can be a strategy for supporting grain yields across many environments.
Published: 2023

13. Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

Author: National Institute of Allergy and Infectious Diseases (US), Antiviral Countermeasures Development Center (US), Department of Agriculture (US), Department of the Army (US), Department of Health and Human Services (US), US Department of Homeland Security, Federal Government of the United States, Kuhn, Jens H. [0000-0002-7800-6045], Abe, Junya [0000-0003-3627-7071], Adkins, Scott [0000-0003-0095-8414], Alkhovsky, Sergey V. [0000-0001-6913-5841], Avsic-Zupanc, Tatjana [0000-0001-6243-0688], Ayllón, María A. [0000-0001-7893-6106], Bahl, Justin [0000-0001-7572-4300], Balkema-Buschmann, A. [0000-0001-7613-9592], Ballinger, Matthew J. [0000-0001-7453-8725], Bejerman, Nicolas [0000-0002-7851-3506], Biedenkopf, Nadine [0000-0002-6061-8019], Blair, Carol D.[0000-0002-2803-0354], Blasdell, Kim R.[0000-0003-2121-0376], Bradfute, Steven B.[0000-0002-1985-751X], Briese, Thomas [0000-0002-4819-8963], Buchholz, Ursula J. [0000-0002-2329-3198], Buchmeier, Michael J.[0000-0002-2387-9287], Bukreyev, Alexander [0000-0002-0342-4824], Burt, Felicity [0000-0002-7238-7799], Büttner, Carmen [0000-0002-2086-2594], Calisher, Charles H. [0000-0003-0213-294X], Cao, Mengji [0000-0003-0396-262X], Casas, Inmaculada [0000-0003-1840-1198], Chandran, Kartik [0000-0003-0232-7077], Charrel, Rémi N.[0000-0002-7675-8251], Chaturvedi, Krishna Kumar [0000-0002-6529-5466], Crane, Anya [0000-0002-2060-2469], De Swart, Rik L.[0000-0003-3599-8969], Debat, Humberto [0000-0003-3056-3739], Dheilly, Nolwenn M.[0000-0002-3675-5013], Di Paola, Nicholas [0000-0002-9694-3913], Di Serio, Francesco [0000-0003-2822-704X], Dietzgen, Ralf G.[0000-0002-7772-2250], Digiaro, Michele [0009-0006-3089-3606], Drexler, J. Felix [0000-0002-3509-0232], Duprex, W. Paul [0000-0003-1716-6376], Elbeaino, Toufic [0000-0003-2211-7907], Ergünay, Koray [0000-0001-5422-1982], Feng, Guozhong [0000-0002-9489-9322], Fooks, Anthony R.[0000-0002-3243-6154], Formenty, Pierre B.H.[0000-0002-9482-5411], Freitas-Astúa, Juliana [0000-0002-0506-6880], Gago-Zachert, Selma [0000-0002-1084-2119], García, María Laura [0000-0001-6468-6943], Garrison, Aura R.[0000-0003-3034-6400], Gaskin, Thomas R. [0000-0002-5644-4431], Gouy de Bellocq, Joelle [0000-0001-5831-6284], Griffiths, Anthony [0000-0001-5435-8364], Groschup, M. H.[0000-0003-0215-185X], Günther, Stephan [0000-0002-6562-0230], Hayashi, Kazusa [0009-0002-9395-0066], Hepojoki, Jussi [0000-0001-5699-214X], Higgins, Colleen M. [0000-0001-9016-2940], Horie, Masayuki [0000-0003-4682-7698], Hughes, Holly R.[0000-0003-1380-8263], Hyndman, Timothy [0000-0002-7047-5023], Jiāng, Dàohóng [0000-0002-3862-7461], Jonson, Gilda B.[0000-0003-0097-8634], Junglen, Sandra [0000-0002-3799-6011], Klempa, B.[0000-0002-6931-1224], Klingström, Jonas [0000-0001-9076-1441], Kondō, Hideki [0000-0001-9220-5350], Koonin, Eugene V. [0000-0003-3943-8299], Krupovic, Mart [0000-0001-5486-0098], Kurath, Gael [0000-0003-3294-560X], Laenen, Lies [0000-0001-9118-8608], Li, Jianrong [0000-0002-7130-1084], Lukashevich, Igor S.[0000-0001-6523-5116], MacDiarmid, Robin M.[0000-0002-7057-2018], Maes, Piet [0000-0002-4571-5232], Marklewitz, Marco [0000-0003-1828-8770], Marshall, Sergio H.[0000-0003-0438-8252], Marzano, Shin-Yi L. [0000-0003-0548-3761], Mühlberger, Elke [0000-0003-3547-9376], Nabeshima, Tomoyuki [0000-0002-6570-096X], Naidu, Rayapati [0000-0002-7273-5116], Natsuaki, Tomohide [0000-0003-1823-7308], Navarro, José A. [0000-0002-0536-6074], Neriya, Yutaro [0000-0002-1385-0050], Netesov, Sergey V. [0000-0002-7786-2464], Neumann, Gabriele [0000-0001-7054-1775], Nowotny, N. [0000-0002-3548-571X], Ochoa-Corona, Francisco M. [0000-0002-4112-8209], Pallás, Vicente [0000-0003-4954-989X], Papa, Anna [0000-0002-6643-3322], Paraskevopoulou, Sofia [0000-0003-2608-2596], Parrish, Colin R. [0000-0002-1836-6655], Pauvolid-Corrêa, Alex [0000-0002-6924-157X], Pawęska, Janusz T. [0000-0001-8776-7519], Pérez, Daniel R. [0000-0002-6569-5689], Pfaff, Florian [0000-0003-0178-6183], Plemper, Richard K. [0000-0003-2034-2107], Postler, Thomas S. [0000-0002-3558-9084], Rabbidge, Lee O. [0009-0001-7962-4881], Radoshitzky, Sheli R. [0000-0001-8976-8056], Ramos-González, Pedro L. [0000-0002-9640-6587], Rehanek, Marius [0000-0002-5710-5060], Resende, Renato O. [0000-0003-3852-1576], Romanowski, Víctor [0000-0001-6378-7929], Rubbenstroth, Dennis [0000-0002-8209-6274], Rubino, Luisa [0000-0002-2073-2415], Runstadler, Jonathan A. [0000-0002-6747-7765], Sabanadzovic, Sead [0000-0002-2995-2633], Salvato, Maria S. [0000-0002-3357-5391], Sasaya, Takahide [0000-0002-5020-9377], Schwemmle, Martin [0000-0002-2972-6855], Shi, Mang [0000-0002-6154-4437], Shimomoto, Yoshifumi [0000-0002-0796-7068], Kavi Sidharthan, Venkidusamy [0000-0003-1561-549X], Sironi, Manuela [0000-0002-2267-5266], Smither, Sophie [0000-0002-7835-3581], Spann, Kirsten [0000-0003-0567-8382], Spengler, Jessica R. [0000-0002-5383-0513], Stenglein, Mark D. [0000-0002-0993-813X], Takada, Ayato [0000-0003-2464-6642], Takeyama, Sawana [0009-0000-3771-5999], Tesh, Robert B. [0000-0002-9226-397X], Thornburg, Natalie J. [0000-0003-3523-3616], Tischler, Nicole D. [0000-0002-4578-4780], Tomitaka, Yasuhiro [0000-0002-6914-4016], Tomonaga, Keizō [0000-0003-0405-7103], Tordo, Noël [0000-0001-5873-059X], Tu, Changchun [0000-0002-8134-7502], Turina, Massimo [0000-0002-9659-9470], Tzanetakis, Ioannis E. [0000-0002-5970-1763], Vaira, Anna Maria [0000-0003-2526-4419], Van den Hoogen, Bernadette [0000-0003-1996-8559], Vanmechelen, Bert [0000-0002-8350-4356], Verbeek, Martin [0000-0002-8973-3803], Von Bargen, Susanne [0000-0001-8321-1572], Wada, Jiro [0000-0001-9846-0846], Wahl, Victoria [0000-0002-6588-4308], Walker, Peter J. [0000-0003-1851-642X], Waltzek, Thomas B. [0000-0001-6383-5978], Whitfield, Anna E. [0000-0002-3538-015X], Wolf, Yuri I. [0000-0002-0247-8708], Xylogianni, Evanthia [0009-0001-8768-0939], Yanagisawa, Hironobu [0000-0002-6729-466X], Ye, Gongyin [0000-0003-4937-8867], Yuan, Zhiming [0000-0002-3234-9616], Zerbini, F. Murilo [0000-0001-8617-0200], Okland, Arnfinn Lodden [0000-0003-3062-4386], Kuhn, Jens H., Abe, Junya, Adkins, Scott, Alkhovsky, Sergey V., Avsic-Zupanc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, A., Ballinger, Matthew J., Kumar Baranwal, Virendra, Beer, Martin, Bejerman, Nicolas, Bergeron, Éric, Biedenkopf, Nadine, Blair, Carol D., Blasdell, Kim R., Blouin, Arnaud G., Bradfute, Steven B., Briese, Thomas, Brown, Paul A., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Chaturvedi, Krishna Kumar, Chooi, Kar Mun, Crane, Anya, Dal Bó, Elena, de la Torre, J. C., de Souza, William Marciel, De Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Drexler, J. Felix, Duprex, W. Paul, Dürrwald, Ralf, Easton, Andrew J., Elbeaino, Toufic, Ergünay, Koray, Feng, Guozhong, Firth, Andrew E., Fooks, Anthony R., Formenty, Pierre B.H., Freitas-Astúa, Juliana, Gago-Zachert, Selma, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas R., Gong, Wenjie, Gonzalez, Jean-Paul J., Gouy de Bellocq, Joelle, Griffiths, Anthony, Groschup, M. H., Günther, Ines, Günther, Stephan, Hammond, John, Hasegawa, Yusuke, Hayashi, Kazusa, Hepojoki, Jussi, Higgins, Colleen M., Hongo, Seiji, Horie, Masayuki, Hughes, Holly R., Hume, Adam J., Hyndman, Timothy, Ikeda, Kenichi, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Klempa, B., Klingström, Jonas, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Li, Jianrong, Li, Jun-Min, Liu, Ran, Lukashevich, Igor S., MacDiarmid, Robin M, Maes, Piet, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., McCauley, John W., Mirazimi, Ali, Mühlberger, Elke, Nabeshima, Tomoyuki, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Neriya, Yutaro, Netesov, Sergey V., Neumann, Gabriele, Nowotny, N., Nunes, Márcio R.T., Ochoa-Corona, Francisco M., Okada, Tomoyuki, Palacios, Gustavo, Pallás, Vicente, Papa, Anna, Paraskevopoulou, Sofia, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Pérez, Daniel R., Pfaff, Florian, Plemper, Richard K., Postler, Thomas S., Rabbidge, Lee O., Radoshitzky, Sheli R., Ramos-González, Pedro L., Rehanek, Marius, Resende, Renato O., Reyes, Carina A., Rodrigues, Thaís C.S., Romanowski, Víctor, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sadiq, Sabrina, Salvato, Maria S., Sasaya, Takahide, Schwemmle, Martin, Sharpe, Stephen R., Shi, Mang, Shimomoto, Yoshifumi, Kavi Sidharthan, Venkidusamy, Sironi, Manuela, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Takada, Ayato, Takeyama, Sawana, Tatara, Akio, Tesh, Robert B., Thornburg, Natalie J., Tian, Xin, Tischler, Nicole D., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Vaira, Anna Maria, Van den Hoogen, Bernadette, Vanmechelen, Bert, Vasilakis, Nikos, Verbeek, Martin, Von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Waltzek, Thomas B., Whitfield, Anna E., Wolf, Yuri I., Xia, Han, Xylogianni, Evanthia, Yanagisawa, Hironobu, Yano, Kazutaka, Ye, Gongyin, Yuan, Zhiming, Zerbini, F. Murilo, Zhang, Guilin, Zhang, Song, Zhang, Yong-Zhen, Zhao, Lu, Okland, Arnfinn Lodden, National Institute of Allergy and Infectious Diseases (US), Antiviral Countermeasures Development Center (US), Department of Agriculture (US), Department of the Army (US), Department of Health and Human Services (US), US Department of Homeland Security, Federal Government of the United States, Kuhn, Jens H. [0000-0002-7800-6045], Abe, Junya [0000-0003-3627-7071], Adkins, Scott [0000-0003-0095-8414], Alkhovsky, Sergey V. [0000-0001-6913-5841], Avsic-Zupanc, Tatjana [0000-0001-6243-0688], Ayllón, María A. [0000-0001-7893-6106], Bahl, Justin [0000-0001-7572-4300], Balkema-Buschmann, A. [0000-0001-7613-9592], Ballinger, Matthew J. [0000-0001-7453-8725], Bejerman, Nicolas [0000-0002-7851-3506], Biedenkopf, Nadine [0000-0002-6061-8019], Blair, Carol D.[0000-0002-2803-0354], Blasdell, Kim R.[0000-0003-2121-0376], Bradfute, Steven B.[0000-0002-1985-751X], Briese, Thomas [0000-0002-4819-8963], Buchholz, Ursula J. [0000-0002-2329-3198], Buchmeier, Michael J.[0000-0002-2387-9287], Bukreyev, Alexander [0000-0002-0342-4824], Burt, Felicity [0000-0002-7238-7799], Büttner, Carmen [0000-0002-2086-2594], Calisher, Charles H. [0000-0003-0213-294X], Cao, Mengji [0000-0003-0396-262X], Casas, Inmaculada [0000-0003-1840-1198], Chandran, Kartik [0000-0003-0232-7077], Charrel, Rémi N.[0000-0002-7675-8251], Chaturvedi, Krishna Kumar [0000-0002-6529-5466], Crane, Anya [0000-0002-2060-2469], De Swart, Rik L.[0000-0003-3599-8969], Debat, Humberto [0000-0003-3056-3739], Dheilly, Nolwenn M.[0000-0002-3675-5013], Di Paola, Nicholas [0000-0002-9694-3913], Di Serio, Francesco [0000-0003-2822-704X], Dietzgen, Ralf G.[0000-0002-7772-2250], Digiaro, Michele [0009-0006-3089-3606], Drexler, J. Felix [0000-0002-3509-0232], Duprex, W. Paul [0000-0003-1716-6376], Elbeaino, Toufic [0000-0003-2211-7907], Ergünay, Koray [0000-0001-5422-1982], Feng, Guozhong [0000-0002-9489-9322], Fooks, Anthony R.[0000-0002-3243-6154], Formenty, Pierre B.H.[0000-0002-9482-5411], Freitas-Astúa, Juliana [0000-0002-0506-6880], Gago-Zachert, Selma [0000-0002-1084-2119], García, María Laura [0000-0001-6468-6943], Garrison, Aura R.[0000-0003-3034-6400], Gaskin, Thomas R. [0000-0002-5644-4431], Gouy de Bellocq, Joelle [0000-0001-5831-6284], Griffiths, Anthony [0000-0001-5435-8364], Groschup, M. H.[0000-0003-0215-185X], Günther, Stephan [0000-0002-6562-0230], Hayashi, Kazusa [0009-0002-9395-0066], Hepojoki, Jussi [0000-0001-5699-214X], Higgins, Colleen M. [0000-0001-9016-2940], Horie, Masayuki [0000-0003-4682-7698], Hughes, Holly R.[0000-0003-1380-8263], Hyndman, Timothy [0000-0002-7047-5023], Jiāng, Dàohóng [0000-0002-3862-7461], Jonson, Gilda B.[0000-0003-0097-8634], Junglen, Sandra [0000-0002-3799-6011], Klempa, B.[0000-0002-6931-1224], Klingström, Jonas [0000-0001-9076-1441], Kondō, Hideki [0000-0001-9220-5350], Koonin, Eugene V. [0000-0003-3943-8299], Krupovic, Mart [0000-0001-5486-0098], Kurath, Gael [0000-0003-3294-560X], Laenen, Lies [0000-0001-9118-8608], Li, Jianrong [0000-0002-7130-1084], Lukashevich, Igor S.[0000-0001-6523-5116], MacDiarmid, Robin M.[0000-0002-7057-2018], Maes, Piet [0000-0002-4571-5232], Marklewitz, Marco [0000-0003-1828-8770], Marshall, Sergio H.[0000-0003-0438-8252], Marzano, Shin-Yi L. [0000-0003-0548-3761], Mühlberger, Elke [0000-0003-3547-9376], Nabeshima, Tomoyuki [0000-0002-6570-096X], Naidu, Rayapati [0000-0002-7273-5116], Natsuaki, Tomohide [0000-0003-1823-7308], Navarro, José A. [0000-0002-0536-6074], Neriya, Yutaro [0000-0002-1385-0050], Netesov, Sergey V. [0000-0002-7786-2464], Neumann, Gabriele [0000-0001-7054-1775], Nowotny, N. [0000-0002-3548-571X], Ochoa-Corona, Francisco M. [0000-0002-4112-8209], Pallás, Vicente [0000-0003-4954-989X], Papa, Anna [0000-0002-6643-3322], Paraskevopoulou, Sofia [0000-0003-2608-2596], Parrish, Colin R. [0000-0002-1836-6655], Pauvolid-Corrêa, Alex [0000-0002-6924-157X], Pawęska, Janusz T. [0000-0001-8776-7519], Pérez, Daniel R. [0000-0002-6569-5689], Pfaff, Florian [0000-0003-0178-6183], Plemper, Richard K. [0000-0003-2034-2107], Postler, Thomas S. [0000-0002-3558-9084], Rabbidge, Lee O. [0009-0001-7962-4881], Radoshitzky, Sheli R. [0000-0001-8976-8056], Ramos-González, Pedro L. [0000-0002-9640-6587], Rehanek, Marius [0000-0002-5710-5060], Resende, Renato O. [0000-0003-3852-1576], Romanowski, Víctor [0000-0001-6378-7929], Rubbenstroth, Dennis [0000-0002-8209-6274], Rubino, Luisa [0000-0002-2073-2415], Runstadler, Jonathan A. [0000-0002-6747-7765], Sabanadzovic, Sead [0000-0002-2995-2633], Salvato, Maria S. [0000-0002-3357-5391], Sasaya, Takahide [0000-0002-5020-9377], Schwemmle, Martin [0000-0002-2972-6855], Shi, Mang [0000-0002-6154-4437], Shimomoto, Yoshifumi [0000-0002-0796-7068], Kavi Sidharthan, Venkidusamy [0000-0003-1561-549X], Sironi, Manuela [0000-0002-2267-5266], Smither, Sophie [0000-0002-7835-3581], Spann, Kirsten [0000-0003-0567-8382], Spengler, Jessica R. [0000-0002-5383-0513], Stenglein, Mark D. [0000-0002-0993-813X], Takada, Ayato [0000-0003-2464-6642], Takeyama, Sawana [0009-0000-3771-5999], Tesh, Robert B. [0000-0002-9226-397X], Thornburg, Natalie J. [0000-0003-3523-3616], Tischler, Nicole D. [0000-0002-4578-4780], Tomitaka, Yasuhiro [0000-0002-6914-4016], Tomonaga, Keizō [0000-0003-0405-7103], Tordo, Noël [0000-0001-5873-059X], Tu, Changchun [0000-0002-8134-7502], Turina, Massimo [0000-0002-9659-9470], Tzanetakis, Ioannis E. [0000-0002-5970-1763], Vaira, Anna Maria [0000-0003-2526-4419], Van den Hoogen, Bernadette [0000-0003-1996-8559], Vanmechelen, Bert [0000-0002-8350-4356], Verbeek, Martin [0000-0002-8973-3803], Von Bargen, Susanne [0000-0001-8321-1572], Wada, Jiro [0000-0001-9846-0846], Wahl, Victoria [0000-0002-6588-4308], Walker, Peter J. [0000-0003-1851-642X], Waltzek, Thomas B. [0000-0001-6383-5978], Whitfield, Anna E. [0000-0002-3538-015X], Wolf, Yuri I. [0000-0002-0247-8708], Xylogianni, Evanthia [0009-0001-8768-0939], Yanagisawa, Hironobu [0000-0002-6729-466X], Ye, Gongyin [0000-0003-4937-8867], Yuan, Zhiming [0000-0002-3234-9616], Zerbini, F. Murilo [0000-0001-8617-0200], Okland, Arnfinn Lodden [0000-0003-3062-4386], Kuhn, Jens H., Abe, Junya, Adkins, Scott, Alkhovsky, Sergey V., Avsic-Zupanc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, A., Ballinger, Matthew J., Kumar Baranwal, Virendra, Beer, Martin, Bejerman, Nicolas, Bergeron, Éric, Biedenkopf, Nadine, Blair, Carol D., Blasdell, Kim R., Blouin, Arnaud G., Bradfute, Steven B., Briese, Thomas, Brown, Paul A., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Chaturvedi, Krishna Kumar, Chooi, Kar Mun, Crane, Anya, Dal Bó, Elena, de la Torre, J. C., de Souza, William Marciel, De Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Drexler, J. Felix, Duprex, W. Paul, Dürrwald, Ralf, Easton, Andrew J., Elbeaino, Toufic, Ergünay, Koray, Feng, Guozhong, Firth, Andrew E., Fooks, Anthony R., Formenty, Pierre B.H., Freitas-Astúa, Juliana, Gago-Zachert, Selma, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas R., Gong, Wenjie, Gonzalez, Jean-Paul J., Gouy de Bellocq, Joelle, Griffiths, Anthony, Groschup, M. H., Günther, Ines, Günther, Stephan, Hammond, John, Hasegawa, Yusuke, Hayashi, Kazusa, Hepojoki, Jussi, Higgins, Colleen M., Hongo, Seiji, Horie, Masayuki, Hughes, Holly R., Hume, Adam J., Hyndman, Timothy, Ikeda, Kenichi, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Klempa, B., Klingström, Jonas, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Li, Jianrong, Li, Jun-Min, Liu, Ran, Lukashevich, Igor S., MacDiarmid, Robin M, Maes, Piet, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., McCauley, John W., Mirazimi, Ali, Mühlberger, Elke, Nabeshima, Tomoyuki, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Neriya, Yutaro, Netesov, Sergey V., Neumann, Gabriele, Nowotny, N., Nunes, Márcio R.T., Ochoa-Corona, Francisco M., Okada, Tomoyuki, Palacios, Gustavo, Pallás, Vicente, Papa, Anna, Paraskevopoulou, Sofia, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Pérez, Daniel R., Pfaff, Florian, Plemper, Richard K., Postler, Thomas S., Rabbidge, Lee O., Radoshitzky, Sheli R., Ramos-González, Pedro L., Rehanek, Marius, Resende, Renato O., Reyes, Carina A., Rodrigues, Thaís C.S., Romanowski, Víctor, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sadiq, Sabrina, Salvato, Maria S., Sasaya, Takahide, Schwemmle, Martin, Sharpe, Stephen R., Shi, Mang, Shimomoto, Yoshifumi, Kavi Sidharthan, Venkidusamy, Sironi, Manuela, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Takada, Ayato, Takeyama, Sawana, Tatara, Akio, Tesh, Robert B., Thornburg, Natalie J., Tian, Xin, Tischler, Nicole D., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Vaira, Anna Maria, Van den Hoogen, Bernadette, Vanmechelen, Bert, Vasilakis, Nikos, Verbeek, Martin, Von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Waltzek, Thomas B., Whitfield, Anna E., Wolf, Yuri I., Xia, Han, Xylogianni, Evanthia, Yanagisawa, Hironobu, Yano, Kazutaka, Ye, Gongyin, Yuan, Zhiming, Zerbini, F. Murilo, Zhang, Guilin, Zhang, Song, Zhang, Yong-Zhen, Zhao, Lu, and Okland, Arnfinn Lodden
Abstract: In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Published: 2023

14. Antioxidant, immunostimulatory, and anticancer properties of hydrolyzed wheat bran mediated through macrophages stimulation

Author: Department of Agriculture (US), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Tomé-Sánchez, Irene, Martínez-Villaluenga, Cristina, Martín Diana, Ana Belén, Rico, Daniel, Jiménez-Pulido, Iván J., Frías, Juana, Dia, Vermont P., Department of Agriculture (US), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Tomé-Sánchez, Irene, Martínez-Villaluenga, Cristina, Martín Diana, Ana Belén, Rico, Daniel, Jiménez-Pulido, Iván J., Frías, Juana, and Dia, Vermont P.
Abstract: Previous studies demonstrated that enzymatic hydrolysis enhances wheat bran (WB) biological properties. This study evaluated the immunostimulatory effect of a WB hydrolysate (HYD) and a mousse enriched with HYD (MH) before and after in vitro digestion on murine and human macrophages. The antiproliferative activity of the harvested macrophage supernatant on colorectal cancer (CRC) cells was also analyzed. MH showed significantly higher content than control mousse (M) in soluble poly- and oligosaccharides (OLSC), as well as total soluble phenolic compounds (TSPC). Although in vitro gastrointestinal digestion slightly reduced the TSPC bioaccessibility of MH, ferulic acid (FA) levels remained stable. HYD showed the highest antioxidant activity followed by MH, which demonstrated a greater antioxidant activity before and after digestion as compared with M. RAW264.7 and THP-1 cells released the highest amounts of pro-inflammatory cytokines after being treated with 0.5 mg/mL of digested WB samples. Treatment with digested HYD-stimulated RAW264.7 supernatant for 96 h showed the most anticancer effect, and spent medium reduced cancer cell colonies more than direct WB sample treatments. Although a lack of inner mitochondrial membrane potential alteration was found, increased Bax:Bcl-2 ratio and caspase-3 expression suggested activation of the mitochondrial apoptotic pathway when CRC cells were treated with macrophage supernatants. Intracellular reactive oxygen species (ROS) were positively correlated with the cell viability in CRC cells exposed to RAW264.7 supernatants (r = 0.78, p < 0.05) but was not correlated in CRC cells treated with THP-1 conditioned media. Supernatant from WB-stimulated THP-1 cells may be able to stimulate ROS production in HT-29 cells, leading to a decrease of viable cells in a time-dependent manner. Therefore, our present study revealed a novel anti-tumour mechanism of HYD through the stimulation of cytokine production in macrophages and the indirect i
Published: 2023

15. Distribution of Bacterial Endosymbionts of the Cardinium Clade in Plant-Parasitic Nematodes

Author: Department of Agriculture (US), Animal and Plant Health Inspection Service (US), Ministry of Science and Higher Education of the Russian Federation, Russian Science Foundation, Castillo, Pablo [0000-0003-0256-876X], Tarlachkov, Sergey V., Efeykin, Boris D., Castillo, Pablo, Evtushenko, Lyudmila I., Subbotin, Sergei A., Department of Agriculture (US), Animal and Plant Health Inspection Service (US), Ministry of Science and Higher Education of the Russian Federation, Russian Science Foundation, Castillo, Pablo [0000-0003-0256-876X], Tarlachkov, Sergey V., Efeykin, Boris D., Castillo, Pablo, Evtushenko, Lyudmila I., and Subbotin, Sergei A.
Abstract: Bacteria of the genus "Candidatus Cardinium" and related organisms composing the Cardinium clade are intracellular endosymbionts frequently occurring in several arthropod groups, freshwater mussels and plant-parasitic nematodes. Phylogenetic analyses based on two gene sequences (16S rRNA and gyrB) showed that the Cardinium clade comprised at least five groups: A, B, C, D and E. In this study, a screening of 142 samples of plant-parasitic nematodes belonging to 93 species from 12 families and two orders using PCR with specific primers and sequencing, revealed bacteria of Cardinium clade in 14 nematode samples belonging to 12 species of cyst nematodes of the family Heteroderidae. Furthermore, in this study, the genome of the Cardinium cHhum from the hop cyst nematode, Heterodera humuli, was also amplified, sequenced and analyzed. The comparisons of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values for the strain Cardinium cHhum with regard to related organisms with available genomes, combined with the data on 16S rRNA and gyrB gene sequence identities, showed that this strain represents a new candidate species within the genus "Candidatus Paenicardinium". The phylogenetic position of endosymbionts of the Cardinium clade detected in nematode hosts was also compared to known representatives of this clade from other metazoans. Phylogenetic reconstructions based on analysis of 16S rRNA, gyrB, sufB, gloEL, fusA, infB genes and genomes and estimates of genetic distances both indicate that the endosymbiont of the root-lesion nematode Pratylenchus penetrans represented a separate lineage and is designated herein as a new group F. The phylogenetic analysis also confirmed that endosymbionts of ostracods represent the novel group G. Evolutionary relationships of bacterial endosymbionts of the Cardinium clade within invertebrates are presented and discussed.
Published: 2023

16. Phenolic acid-induced phase separation and translation inhibition mediate plant interspecific competition

Author: National Natural Science Foundation of China, Department of Agriculture (US), European Commission, Natural Science Foundation of Fujian Province, Zhao, Shuai [0000-0002-8482-452X], Shi, Yabo [0000-0002-0062-7909], Chen, Xiaoyuan [0009-0009-1665-8900], Wang, Xingwei [0000-0002-6437-7187], Gutierrez-Beltran, Emilio [0000-0001-7978-3164], Bozhkov, Peter V [0000-0002-8819-3884], Qian, Weiqiang [0000-0002-3135-6689], Zhou, Mian [0000-0002-9332-0147], Wang, Wei [0000-0002-3780-5158], Xie, Zhouli, Zhao, Shuai, Li, Ying, Deng, Yuhua, Shi, Yabo, Chen, Xiaoyuan, Li, Yue, Li, Haiwei, Chen, Changtian, Wang, Xingwei, Liu, Enhui, Tu, Yuchen, Shi, Peng, Tong, Jinjin, Gutierrez-Beltran, Emilio, Li, Jiayu, Bozhkov, Peter V, Qian, Weiqiang, Zhou, Mian, Wang, Wei, National Natural Science Foundation of China, Department of Agriculture (US), European Commission, Natural Science Foundation of Fujian Province, Zhao, Shuai [0000-0002-8482-452X], Shi, Yabo [0000-0002-0062-7909], Chen, Xiaoyuan [0009-0009-1665-8900], Wang, Xingwei [0000-0002-6437-7187], Gutierrez-Beltran, Emilio [0000-0001-7978-3164], Bozhkov, Peter V [0000-0002-8819-3884], Qian, Weiqiang [0000-0002-3135-6689], Zhou, Mian [0000-0002-9332-0147], Wang, Wei [0000-0002-3780-5158], Xie, Zhouli, Zhao, Shuai, Li, Ying, Deng, Yuhua, Shi, Yabo, Chen, Xiaoyuan, Li, Yue, Li, Haiwei, Chen, Changtian, Wang, Xingwei, Liu, Enhui, Tu, Yuchen, Shi, Peng, Tong, Jinjin, Gutierrez-Beltran, Emilio, Li, Jiayu, Bozhkov, Peter V, Qian, Weiqiang, Zhou, Mian, and Wang, Wei
Abstract: Phenolic acids (PAs) secreted by donor plants suppress the growth of their susceptible plant neighbours. However, how structurally diverse ensembles of PAs are perceived by plants to mediate interspecific competition remains a mystery. Here we show that a plant stress granule (SG) marker, RNA-BINDING PROTEIN 47B (RBP47B), is a sensor of PAs in Arabidopsis. PAs, including salicylic acid, 4-hydroxybenzoic acid, protocatechuic acid and so on, directly bind RBP47B, promote its phase separation and trigger SG formation accompanied by global translation inhibition. Salicylic acid-induced global translation inhibition depends on RBP47 family members. RBP47s regulate the proteome rather than the absolute quantity of SG. The rbp47 quadruple mutant shows a reduced sensitivity to the inhibitory effect of the PA mixture as well as to that of PA-rich rice when tested in a co-culturing ecosystem. In this Article, we identified the long sought-after PA sensor as RBP47B and illustrated that PA-induced SG-mediated translational inhibition was one of the PA perception mechanisms.
Published: 2023

17. Pollination supply models from a local to global scale

Author: Agencia Estatal de Investigación (España), Eusko Jaurlaritza, Comunidad de Madrid, European Commission, Universidad Politécnica de Madrid, Research Foundation - Flanders, Ministerio de Economía y Competitividad (España), Ministerio de Universidades (España), Fundação para a Ciência e a Tecnologia (Portugal), Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Department of Agriculture (US), German Research Foundation, Irish Research Council, Swedish Research Council, Giménez-García, Ángel, Allen-Perkins, Alfonso, Bartomeus, Ignasi, Balbi, Stefano, Knapp, Jessica L., Hevia, Violeta, Woodcock, Ben Alex, Smagghe, Guy, Miñarro, Marcos, Eeraerts, Maxime, Colville, Jonathan F., Hipólito, Juliana, Cavigliasso, Pablo, Nates-Parra, Guiomar, Herrera, José M., Cusser, Sarah, Simmons, Benno I., Wolters, Volkmar, Jha, Shalene, Freitas, Breno M., Horgan, Finbarr G., Artz, Derek R., Sidhu, C. Sheena, Otieno, Mark, Boreux, Virginie, Biddinger, David J., Klein, Alexandra Maria, Joshi, Neelendra K., Stewart, Rebecca I.A., Albrecht, Matthias, Nicholson, Charlie C., O'Reilly, Alison D., Crowder, David William, Burns, Katherine L.W., Nabaes Jodar, Diego Nicolás, Garibaldi, Lucas Alejandro, Sutter, Louis, Dupont, Yoko L., Dalsgaard, Bo, Da Encarnação Coutinho, Jeferson Gabriel, Lázaro, Amparo, Andersson, Georg K. S., Raine, Nigel E., Krishnan, Smitha, Dainese, Matteo, Van Der Werf, Wopke, Smith, Henrik G., Magrach, Ainhoa, Agencia Estatal de Investigación (España), Eusko Jaurlaritza, Comunidad de Madrid, European Commission, Universidad Politécnica de Madrid, Research Foundation - Flanders, Ministerio de Economía y Competitividad (España), Ministerio de Universidades (España), Fundação para a Ciência e a Tecnologia (Portugal), Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Department of Agriculture (US), German Research Foundation, Irish Research Council, Swedish Research Council, Giménez-García, Ángel, Allen-Perkins, Alfonso, Bartomeus, Ignasi, Balbi, Stefano, Knapp, Jessica L., Hevia, Violeta, Woodcock, Ben Alex, Smagghe, Guy, Miñarro, Marcos, Eeraerts, Maxime, Colville, Jonathan F., Hipólito, Juliana, Cavigliasso, Pablo, Nates-Parra, Guiomar, Herrera, José M., Cusser, Sarah, Simmons, Benno I., Wolters, Volkmar, Jha, Shalene, Freitas, Breno M., Horgan, Finbarr G., Artz, Derek R., Sidhu, C. Sheena, Otieno, Mark, Boreux, Virginie, Biddinger, David J., Klein, Alexandra Maria, Joshi, Neelendra K., Stewart, Rebecca I.A., Albrecht, Matthias, Nicholson, Charlie C., O'Reilly, Alison D., Crowder, David William, Burns, Katherine L.W., Nabaes Jodar, Diego Nicolás, Garibaldi, Lucas Alejandro, Sutter, Louis, Dupont, Yoko L., Dalsgaard, Bo, Da Encarnação Coutinho, Jeferson Gabriel, Lázaro, Amparo, Andersson, Georg K. S., Raine, Nigel E., Krishnan, Smitha, Dainese, Matteo, Van Der Werf, Wopke, Smith, Henrik G., and Magrach, Ainhoa
Abstract: Ecological intensification has been embraced with great interest by the academic sector but is still rarely taken up by farmers because monitoring the state of different ecological functions is not straightforward. Modelling tools can represent a more accessible alternative of measuring ecological functions, which could help promote their use amongst farmers and other decision-makers. In the case of crop pollination, modelling has traditionally followed either a mechanistic or a data-driven approach. Mechanistic models simulate the habitat preferences and foraging behaviour of pollinators, while data-driven models associate georeferenced variables with real observations. Here, we test these two approaches to predict pollination supply and validate these predictions using data from a newly released global dataset on pollinator visitation rates to different crops. We use one of the most extensively used models for the mechanistic approach, while for the data-driven approach, we select from among a comprehensive set of state-of-The-Art machine-learning models. Moreover, we explore a mixed approach, where data-derived inputs, rather than expert assessment, inform the mechanistic model. We find that, at a global scale, machine-learning models work best, offering a rank correlation coefficient between predictions and observations of pollinator visitation rates of 0.56. In turn, the mechanistic model works moderately well at a global scale for wild bees other than bumblebees. Biomes characterized by temperate or Mediterranean forests show a better agreement between mechanistic model predictions and observations, probably due to more comprehensive ecological knowledge and therefore better parameterization of input variables for these biomes. This study highlights the challenges of transferring input variables across multiple biomes, as expected given the different composition of species in different biomes. Our results provide clear guidance on which pollination supply mode
Published: 2023

18. Genome-wide association studies for resumption of postpartum ovarian cyclicity trait in seasonal anestrus in Spanish Merino sheep breed

Author: Department of Agriculture (US), Calvo, Jorge Hugo [0000-0001-9513-0219], Lakhssassi, Kenza [0000-0002-9793-7494], Lahoz, Belén [0000-0001-9394-5027], Serrano Noreña, Magdalena [0000-0002-1621-3102], Alabart, José Luis [0000-0001-5015-8103], Calvo, Jorge Hugo, Martí, J. I., Lakhssassi, Kenza, García-Méndez, M.S., Sarto, María Pilar, Lahoz, Belén, Bravo-Fernández, J. A., Domingo, A., Serrano Noreña, Magdalena, Alabart, José Luis, Department of Agriculture (US), Calvo, Jorge Hugo [0000-0001-9513-0219], Lakhssassi, Kenza [0000-0002-9793-7494], Lahoz, Belén [0000-0001-9394-5027], Serrano Noreña, Magdalena [0000-0002-1621-3102], Alabart, José Luis [0000-0001-5015-8103], Calvo, Jorge Hugo, Martí, J. I., Lakhssassi, Kenza, García-Méndez, M.S., Sarto, María Pilar, Lahoz, Belén, Bravo-Fernández, J. A., Domingo, A., Serrano Noreña, Magdalena, and Alabart, José Luis
Abstract: To elucidate the genetic basis of reproductive seasonality in Spanish Merino sheep breed, a genome-wide association study (GWAS) in order to detect single nucleotide polymorphisms (SNPs) or regions associated with resumption of ovarian cyclicity during the postpartum period in conjunction with the seasonal anestrus was performed. In total, 169 multiparous Merino ewes which lambed in February were genotyped using the 50k Illumina Ovine Beadchip. After of lambing, blood samples were obtained weekly for measurement of peripheral progesterone concentrations from day 45 to 120. At 72 days of age, lambs were weaned. Live weight, and body condition score of the ewes were also measured. The days from lambing to ovarian activation trait was used for GWAS. An ewe was considered cyclic when the progesterone concentration was higher than or equal to the threshold of 0.5 ng/mL. GCTA software was used for GWAS analysis. Only one SNP (rs161969506) overcame the genome-wide significance level (p_Bonferroni < 0.05) on chromosome 3. Six potential SNPs overcame the chromosome-wise significance level (p_FDR < 0.05). The SNP rs161969506 was located in intron 7 of the KDM3A candidate gene in Oar_Rambouillet 1.0. KDM3A is a demethylase enzyme that has been identified as key regulator of a number of transcription factors, including androgen receptors in the ovary. This gene was partial isolated and Sanger-sequenced, and 5 SNPs were found: 1 SNP in promoter region and 4 nonsynonymous polymorphisms in exons 10 and 17. One and 2 SNPs in promoter and exon 10, respectively, were associated with the studied phenotype in the GWAS population. Haplotype association analysis confirmed the implication of this gene in the studied trait.
Published: 2023

19. Molecular diagnostics of the Mediterranean olive cyst nematode, Heterodera mediterranea Vovlas, Inserra & Stone, 1981 using conventional and real-time PCR

Author: Department of Agriculture (US), Subbotin, Sergei A., Burbridge, Julie, Palomares Rius, Juan E., Castillo, Pablo, Department of Agriculture (US), Subbotin, Sergei A., Burbridge, Julie, Palomares Rius, Juan E., and Castillo, Pablo
Abstract: The Mediterranean olive cyst nematode, Heterodera mediterranea, is a pest of olive trees that is found in Spain, Italy, and Tunisia. In this paper, conventional and real-time PCR assays for the identification of H. mediterranea was developed. The hsp90 gene fragment was used to design a species-specific primer and a TaqMan probe. The specificity of the primer/probe set was tested in singleplex or multiplex reactions against Mediterranean olive cyst nematode and non-target nematodes. In multiplex real-time PCR experiments with the specific and universal primer/probe sets, fluorescent signals were simultaneously monitored for hsp90 and D3 of 28S rRNA target genes. The results of the experiments showed that the assays with species-specific primer/probe were sensitive enough to detect the DNA from 0.03 of a second-stage juvenile (J2) H. mediterranea in a reaction tube.
Published: 2023

20. Differential gene expression during floral transition in pineapple

Author: Department of Agriculture (US), National Institute of Food and Agriculture (US), Ksouri, Najla [0000-0001-8956-2920], Paull, Robert E., Ksouri, Najla, Kantar, Michael, Zerpa-Catanho, Dessireé, Chen, Nancy Jung, Uruu, Gail, Yue, Jingjing, Guo, Shiyong, Zheng, Yun, Wai, Ching Man Jennifer, Ming, Ray, Department of Agriculture (US), National Institute of Food and Agriculture (US), Ksouri, Najla [0000-0001-8956-2920], Paull, Robert E., Ksouri, Najla, Kantar, Michael, Zerpa-Catanho, Dessireé, Chen, Nancy Jung, Uruu, Gail, Yue, Jingjing, Guo, Shiyong, Zheng, Yun, Wai, Ching Man Jennifer, and Ming, Ray
Abstract: Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 h to 8 days after treatment, 7961 genes were found to exhibit differential expression (DE) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up-regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS-like 3 (CO), a WUSCHEL gene, two APETALA1/FRUITFULL (AP1/FUL) genes, an epidermal patterning gene, and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up-regulated within a day of treatment, their predicted targets being the up-regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS-like APETELAR (AP2), and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up-regulated at the apex and not at the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads act directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP, and AP2. A model based on AP2/ERTF DE and predicted
Published: 2023

21. Evidence for the efficacy of pre-harvest agricultural practices in mitigating food-safety risks to fresh produce in North America

Author: Center for Produce Safety (US), Department of Agriculture (US), Agricultural Research Service (US), Allende, Ana [0000-0002-5622-4332], Devarajan, Naresh, Weller, Daniel L., Jones, Matthew, Adell, Aiko D., Adhikari, Achyut, Allende, Ana, Baur, Arnold Patrick, Beno, Sarah M., Clements, Donna, Critzer, Faith, Green, Hyatt, Gorski, Lisa, Ferelli Gruber, Angela, Kovac, Jasna, McGarvey, Jeffery, M. Murphy, Claire, Murphy, Sarah I., Navarro-Gonzalez, Nora, Owen, Jeb P., Pires, Alda F. A., Richard, Nicole, Samaddar, Sandipan, Schmidt, Radomir, Scow, Kate, Shariat, Nikki W., Smith, Olivia M., Spence, Austin R., Stoeckel, Don, Tran, Thao D. H., Wall, Gretchen, Daniel S. Karp, Center for Produce Safety (US), Department of Agriculture (US), Agricultural Research Service (US), Allende, Ana [0000-0002-5622-4332], Devarajan, Naresh, Weller, Daniel L., Jones, Matthew, Adell, Aiko D., Adhikari, Achyut, Allende, Ana, Baur, Arnold Patrick, Beno, Sarah M., Clements, Donna, Critzer, Faith, Green, Hyatt, Gorski, Lisa, Ferelli Gruber, Angela, Kovac, Jasna, McGarvey, Jeffery, M. Murphy, Claire, Murphy, Sarah I., Navarro-Gonzalez, Nora, Owen, Jeb P., Pires, Alda F. A., Richard, Nicole, Samaddar, Sandipan, Schmidt, Radomir, Scow, Kate, Shariat, Nikki W., Smith, Olivia M., Spence, Austin R., Stoeckel, Don, Tran, Thao D. H., Wall, Gretchen, and Daniel S. Karp
Abstract: Consumption of contaminated produce remains a leading cause of foodborne illness. Increasingly, growers are altering agricultural practices and farm environments to manage food-safety hazards, but these changes often result in substantial economic, social, and environmental costs. Here, we present a comprehensive evidence synthesis evaluating the efficacy of soil, non-crop vegetation, animal, landscape, and irrigation water management strategies aimed at reducing produce-safety risk in North America. We systematically summarized findings from 78 peer-reviewed papers on the effect of 21 management practices on the prevalence, abundance, or survival of four foodborne pathogens (i.e., E. coli, Salmonella spp., Listeria spp., and Campylobacter spp.), resulting in 113 summaries. We then organized a 30-member expert panel, who used these summaries to evaluate the impact of each practice on food-safety outcomes. While more than half of the practices were too understudied to confidently evaluate their impact on food safety, the panel did identify several practices that were associated with reduced preharvest food-safety risks, including not using raw manure, separating crop and livestock production, and choosing low-risk irrigation sources. The panel also identified practices that appear ineffective at reducing food-safety risks, such as the removal of non-crop vegetation. Overall, these findings provide insights into the food-safety impacts of agricultural and land management practices that growers, auditors, and extension personnel can use to co-manage produce preharvest environments for food safety and other aims
Published: 2023

22. Enriched root bacterial microbiome in invaded vs native ranges of the model grass allotetraploid Brachypodium hybridum

Author: National Institute of Food and Agriculture (US), Department of Agriculture (US), Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Gobierno de Aragón, European Commission, Pickett, Brooke, Carey, Chelsea J., Arogyaswamy, Keshav, Botthoff, Jon, Maltz, Mia, Catalán, Pilar, Aronson, Emma L., National Institute of Food and Agriculture (US), Department of Agriculture (US), Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Gobierno de Aragón, European Commission, Pickett, Brooke, Carey, Chelsea J., Arogyaswamy, Keshav, Botthoff, Jon, Maltz, Mia, Catalán, Pilar, and Aronson, Emma L.
Abstract: Invasive species can shift the composition of key soil microbial groups, thus creating novel soil microbial communities. To better understand the biological drivers of invasion, we studied plant-microbial interactions in species of the Brachypodium distachyon complex, a model system for functional genomic studies of temperate grasses and bioenergy crops. While Brachypodium hybridum invasion in California is in an incipient stage, threatening natural and agricultural systems, its diploid progenitor species B. distachyon is not invasive in California. We investigated the root, soil, and rhizosphere bacterial composition of Brachypodium hybridum in both its native and invaded range, and of B. distachyon in the native range. We used high-throughput, amplicon sequencing to evaluate if the bacteria associated with these plants differ, and whether biotic controls may be driving B. hybridum invasion. Bacterial community composition of B. hybridum differed based on provenance (native or invaded range) for root, rhizosphere, and bulk soils, as did the abundance of dominant bacterial taxa. Bacteroidetes, Cyanobacteria and Bacillus spp. (species) were significantly more abundant in B. hybridum roots from the invaded range, whereas Proteobacteria, Firmicutes, Erwinia and Pseudomonas were more abundant in the native range roots. Brachypodium hybridum forms novel biotic interactions with a diverse suite of rhizosphere microbes from the invaded range, which may not exert a similar influence within its native range, ostensibly contributing to B. hybridum’s invasiveness. These associated plant microbiomes could inform future management approaches for B. hybridum in its invaded range and could be key to understanding, predicting, and preventing future plant invasions.
Published: 2022

23. Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon

Author: Department of Agriculture (US), Ministerio de Ciencia e Innovación (España), Universidad de Zaragoza, Joint Genome Institute (US), Ministerio de Economía y Competitividad (España), Ibercaja, Instituto de Estudios Altoaragoneses, ARAID Foundation, Contreras-Moreira, Bruno [0000-0002-5462-907X], Sancho Cohen, Rubén, Catalán, Pilar, Contreras-Moreira, Bruno, Juenger, Thomas E., Des Marais, David L., Department of Agriculture (US), Ministerio de Ciencia e Innovación (España), Universidad de Zaragoza, Joint Genome Institute (US), Ministerio de Economía y Competitividad (España), Ibercaja, Instituto de Estudios Altoaragoneses, ARAID Foundation, Contreras-Moreira, Bruno [0000-0002-5462-907X], Sancho Cohen, Rubén, Catalán, Pilar, Contreras-Moreira, Bruno, Juenger, Thomas E., and Des Marais, David L.
Abstract: Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable “occupancy” in the pan-genome – genes which are either present in all studied genotypes or missing in some genotypes – show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.
Published: 2022

24. Capturing Wheat Phenotypes at the Genome Level

Author: Department of Agriculture (US), National Institute of Food and Agriculture (US), National Science Foundation (US), Junta de Andalucía, European Commission, Biotechnology and Biological Sciences Research Council (UK), Two Blades Foundation, Grains Research and Development Corporation (Australia), Ministry of Science and Higher Education of the Russian Federation, German Research Foundation, Czech Science Foundation, Government of Norway, Hussain, Babar, Akpınar, Bala Anı, Alaux, Michael, Algharib, Ahmed M., Sehgal, Deepmala, Ali, Zulfiqar, Aradottir, Gudbjorg I., Batley, Jacqueline, Bellec, Arnaud, Bentley, Alison R., Cagirici, Halise B., Cattivelli, Luigi, Choulet, Fred, Cockram, James, Desiderio, Francesca, Devaux, Pierre, Dogramaci, Munevver, Dorado, Gabriel, Dreisigacker, Susanne, Edwards, David, El-Hassouni, Khaoula, Eversole, Kellye, Fahima, Tzion, Figueroa, Melania, Gálvez, Sergio, Gill, Kulvinder S., Govta, Liubov, Gul, Alvina, Hensel, Goetz, Hernández Molina, Pilar, Crespo-Herrera, Leonardo Abdiel, Ibrahim, Amir, Kilian, Benjamin, Korzun, Viktor, Krugman, Tamar, Li, Yinghui, Liu, Shuyu, Mahmoud, Amer F., Morgounov, Alexey, Muslu, Tugdem, Naseer, Faiza, Ordon, Frank, Paux, Etienne, Perovic, Dragan, Reddy, Gadi V. P., Reif, Jochen C., Reynolds, Matthew, Roychowdhury, Rajib, Rudd, Jackie, Sen, Taner Z., Sukumaran, Sivakumar, Özdemir, Bahar Soğutmaz, Tiwari, Vijay Kumar, Ullah, Naimat, Unver, Turgay, Yazar, Selami, Appels, Rudi, Budak, Hikmet, Department of Agriculture (US), National Institute of Food and Agriculture (US), National Science Foundation (US), Junta de Andalucía, European Commission, Biotechnology and Biological Sciences Research Council (UK), Two Blades Foundation, Grains Research and Development Corporation (Australia), Ministry of Science and Higher Education of the Russian Federation, German Research Foundation, Czech Science Foundation, Government of Norway, Hussain, Babar, Akpınar, Bala Anı, Alaux, Michael, Algharib, Ahmed M., Sehgal, Deepmala, Ali, Zulfiqar, Aradottir, Gudbjorg I., Batley, Jacqueline, Bellec, Arnaud, Bentley, Alison R., Cagirici, Halise B., Cattivelli, Luigi, Choulet, Fred, Cockram, James, Desiderio, Francesca, Devaux, Pierre, Dogramaci, Munevver, Dorado, Gabriel, Dreisigacker, Susanne, Edwards, David, El-Hassouni, Khaoula, Eversole, Kellye, Fahima, Tzion, Figueroa, Melania, Gálvez, Sergio, Gill, Kulvinder S., Govta, Liubov, Gul, Alvina, Hensel, Goetz, Hernández Molina, Pilar, Crespo-Herrera, Leonardo Abdiel, Ibrahim, Amir, Kilian, Benjamin, Korzun, Viktor, Krugman, Tamar, Li, Yinghui, Liu, Shuyu, Mahmoud, Amer F., Morgounov, Alexey, Muslu, Tugdem, Naseer, Faiza, Ordon, Frank, Paux, Etienne, Perovic, Dragan, Reddy, Gadi V. P., Reif, Jochen C., Reynolds, Matthew, Roychowdhury, Rajib, Rudd, Jackie, Sen, Taner Z., Sukumaran, Sivakumar, Özdemir, Bahar Soğutmaz, Tiwari, Vijay Kumar, Ullah, Naimat, Unver, Turgay, Yazar, Selami, Appels, Rudi, and Budak, Hikmet
Abstract: Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, provi
Published: 2022

25. Evaluating different metrics from the thermal-based two-source energy balance model for monitoring grapevine water stress

Author: National Aeronautics and Space Administration (US), Department of Agriculture (US), Agricultural Research Service (US), Conferencia de Rectores de las Universidades Españolas, Consejo Superior de Investigaciones Científicas (España), Nieto, Héctor [0000-0003-4250-6424], Nieto, Héctor, Alsina, María Mar, Kustas, William P., García-Tejera, Omar, Chen, Fan, Bambach, Nicolas, Gao, Feng, Alfieri, Joseph G., Hipps, Lawrence E., Prueger, John H., McKee, Lynn G., Zahn, Einara, Bou-Zeid, Elie, McElrone, Andrew J., Castro, Sebastian J., Dokoozlian, Nick, National Aeronautics and Space Administration (US), Department of Agriculture (US), Agricultural Research Service (US), Conferencia de Rectores de las Universidades Españolas, Consejo Superior de Investigaciones Científicas (España), Nieto, Héctor [0000-0003-4250-6424], Nieto, Héctor, Alsina, María Mar, Kustas, William P., García-Tejera, Omar, Chen, Fan, Bambach, Nicolas, Gao, Feng, Alfieri, Joseph G., Hipps, Lawrence E., Prueger, John H., McKee, Lynn G., Zahn, Einara, Bou-Zeid, Elie, McElrone, Andrew J., Castro, Sebastian J., and Dokoozlian, Nick
Abstract: Precision irrigation management requires operational monitoring of crop water status. However, there is still some controversy on how to account for crop water stress. To address this question, several physiological, several physiological metrics have been proposed, such as the leaf/stem water potentials, stomatal conductance, or sap flow. On the other hand, thermal remote sensing has been shown to be a promising tool for efficiently evaluating crop stress at adequate spatial and temporal scales, via the Crop Water Stress Index (CWSI), one of the most common indices used for assessing plant stress. CWSI relates the actual crop evapotranspiration ET (related to the canopy radiometric temperature) to the potential ET (or minimum crop temperature). However, remotely sensed surface temperature from satellite sensors includes a mixture of plant canopy and soil/substrate temperatures, while what is required for accurate crop stress detection is more related to canopy metrics, such as transpiration, as the latter one avoids the influence of soil/substrate in determining crop water status or stress. The Two-Source Energy Balance (TSEB) model is one of the most widely used and robust evapotranspiration model for remote sensing. It has the capability of partitioning ET into the crop transpiration and soil evaporation components, which is required for accurate crop water stress estimates. This study aims at evaluating different TSEB metrics related to its retrievals of actual ET, transpiration and stomatal conductance, to track crop water stress in a vineyard in California, part of the GRAPEX experiment. Four eddy covariance towers were deployed in a Variable Rate Irrigation system in a Merlot vineyard that was subject to different stress periods. In addition, root-zone soil moisture, stomatal conductance and leaf/stem water potential were collected as proxy for in situ crop water stress. Results showed that the most robust variable for tracking water stress was the TSEB deriv
Published: 2022

26. Impact of advection on two-source energy balance (TSEB) canopy transpiration parameterization for vineyards in the California Central Valley

Author: E. & J. Gallo Winery, National Aeronautics and Space Administration (US), Department of Agriculture (US), Agricultural Research Service (US), Kustas, William P., Nieto, Héctor, García-Tejera, Omar, Bambach, Nicolas, McElrone, Andrew J., Gao, Feng, Alfieri, Joseph G., Hipps, Lawrence E., Prueger, John H., Torres-Rua, Alfonso, Anderson, Martha C., Knipper, Kyle, Alsina, Maria Mar, McKee, Lynn G., Zahn, Einara, Bou-Zeid, Elie, Dokoozlian, Nick, E. & J. Gallo Winery, National Aeronautics and Space Administration (US), Department of Agriculture (US), Agricultural Research Service (US), Kustas, William P., Nieto, Héctor, García-Tejera, Omar, Bambach, Nicolas, McElrone, Andrew J., Gao, Feng, Alfieri, Joseph G., Hipps, Lawrence E., Prueger, John H., Torres-Rua, Alfonso, Anderson, Martha C., Knipper, Kyle, Alsina, Maria Mar, McKee, Lynn G., Zahn, Einara, Bou-Zeid, Elie, and Dokoozlian, Nick
Abstract: Water conservation efforts for California’s agricultural industry are critical to its sustainability through severe droughts like the current one and others experienced over the last two decades. This is most critical for perennial crops, such as vineyards and orchards, which are costly to plant and maintain and constitute a significant fraction of the regional water use. It is no longer feasible to access groundwater for irrigation to replace deficit surface water resources during drought due to a significant overdraft of aquifers and new regulation limiting its use. To achieve significant water savings, the actual crop water use or evapotranspiration (ET) needs to be mapped from field to regional scales on a daily basis. This can only be achieved using remote sensing-based models, particularly thermal-based energy balance models that are sensitive to deficit irrigation conditions. The two-source energy balance (TSEB) model has been successfully applied over vineyards in California, but challenges still remain. In particular, much of the irrigated cropland in the California Central Valley is affected by advection of hot dry air masses from surrounding non-irrigated areas and the TSEB model appears to need modifications to adequately estimate ET under such conditions, as well as the partitioning between evaporation and transpiration. This study investigates the application of the TSEB model, using local observations in a vineyard having significant advection. Four versions of the transpiration algorithm in TSEB are applied and evaluated with tower eddy covariance measurements spanning 4 growing seasons. The results suggest the performance of the original transpiration algorithm based on Priestley–Taylor used in TSEB is satisfactory in all but the most extreme advective conditions, while a transpiration algorithm based on Shuttleworth–Wallace with a canopy resistance formula, which relates maximum stomata conductance to vapor pressure deficit (VPD), performs well in
Published: 2022

27. Complete Genome Resources for Xylella fastidiosa Strains AlmaEM3 and BB08-1 Reveal Prophage-Associated Structural Variation Among Blueberry-Infecting Strains

Author: Department of Agriculture (US), National Institutes of Health (US), O'Leary, Michael L, Arias-Giraldo, Luis F., Burbank, Lindsey P., Fuente, L. de la, Landa, Blanca B., Department of Agriculture (US), National Institutes of Health (US), O'Leary, Michael L, Arias-Giraldo, Luis F., Burbank, Lindsey P., Fuente, L. de la, and Landa, Blanca B.
Published: 2022

28. Standards recommendations for the Earth BioGenome Project

Author: National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen
Abstract: A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
Published: 2022

29. Brachyptery analysis in Alloxysta (Hymenoptera: Figitidae): Synonymy of A. curta Ferrer-Suay and Pujade Villar as the brachypterou of A. ramulifera (Thomson) in the nearctics male

Author: Universidad de Valencia, Ministerio de Economía, Industria y Competitividad (España), Ministerio de Economía y Competitividad (España), University of Minnesota, Department of Agriculture (US), Casiraghi, Alice, Dregni, Jonathan S., Pérez Hidalgo, Nicolás, Kaser, Joe M., Heimpel, George E., Selfa, Jesús, Ferrer-Suay, Mar, Universidad de Valencia, Ministerio de Economía, Industria y Competitividad (España), Ministerio de Economía y Competitividad (España), University of Minnesota, Department of Agriculture (US), Casiraghi, Alice, Dregni, Jonathan S., Pérez Hidalgo, Nicolás, Kaser, Joe M., Heimpel, George E., Selfa, Jesús, and Ferrer-Suay, Mar
Abstract: Eight brachypterous species have been described within the hymenopteran genus Alloxysta. Intraspecific wing polymorphism linked to sex has been previously hypothesized within this genus and the aim of this work was to confirm whether the phylogenetic relationships based on morphological characters between brachypterous and macropterous species are correct using molecular analyses. This study used material collected from Minnesota (USA), with 278 specimens identified as Alloxysta brachyptera (Hartig, 1840), A. curta Ferrer-Suay and Pujade-Villar, 2017 (Ferrer-suay et al. 2017), A. brevis (Thomson, 1862), or A. ramulifera (Thomson, 1862). Twenty-three of these specimens were subjected to sequencing of the barcoding gene, Cytochrome Oxidase I. Previous analyses had identified A. curta as a distinct species from A. ramulifera based in part on shorter wing length and our current sampling from Minnesota identified only male A. curta. However, our molecular analyses (COI) showed that A. curta should instead be considered a phenotypic variant of A. ramulifera exhibiting male brachyptery, and we establish this new synonymy here. Alloxysta brevis and A. brachyptera remain as valid species. These results suggest that some brachypterous taxa within the figitid subfamily Charipinae, which have been described as valid species, are actually sexually dimorphic forms from the same species with different wing morphology.
Published: 2022

30. Variation in leaf transcriptome responses to elevated ozone corresponds with physiological sensitivity to ozone across maize inbred lines

Author: National Science Foundation (US), National Institute of General Medical Sciences (US), National Cancer Institute (US), Department of Agriculture (US), Nanni, Adalena V. [0000-0001-7316-0951], Morse, Alison M. [0000-0003-4286-6489], Newman, Jeremy R. B. [0000-0001-8486-2801], Wedow, Jessica M. [0000-0001-5410-9026], Leakey, Andrew D. B. [0000-0001-6251-024X], Conesa, Ana [0000-0001-9597-311X], Ainsworth, Elizabeth A. [0000-0002-3199-8999], McIntyre, Lauren M. [0000-0002-0077-3359], Nanni, Adalena V., Morse, Alison M., Newman, Jeremy R. B., Choquette, Nicole E., Wedow, Jessica M., Liu, Zihao, Leakey, Andrew D. B., Conesa, Ana, Ainsworth, Elizabeth A., McIntyre, Lauren M., National Science Foundation (US), National Institute of General Medical Sciences (US), National Cancer Institute (US), Department of Agriculture (US), Nanni, Adalena V. [0000-0001-7316-0951], Morse, Alison M. [0000-0003-4286-6489], Newman, Jeremy R. B. [0000-0001-8486-2801], Wedow, Jessica M. [0000-0001-5410-9026], Leakey, Andrew D. B. [0000-0001-6251-024X], Conesa, Ana [0000-0001-9597-311X], Ainsworth, Elizabeth A. [0000-0002-3199-8999], McIntyre, Lauren M. [0000-0002-0077-3359], Nanni, Adalena V., Morse, Alison M., Newman, Jeremy R. B., Choquette, Nicole E., Wedow, Jessica M., Liu, Zihao, Leakey, Andrew D. B., Conesa, Ana, Ainsworth, Elizabeth A., and McIntyre, Lauren M.
Abstract: We examine the impact of sustained elevated ozone concentration on the leaf transcriptome of 5 diverse maize inbred genotypes, which vary in physiological sensitivity to ozone (B73, Mo17, Hp301, C123, and NC338), using long reads to assemble transcripts and short reads to quantify expression of these transcripts. More than 99% of the long reads, 99% of the assembled transcripts, and 97% of the short reads map to both B73 and Mo17 reference genomes. Approximately 95% of the genes with assembled transcripts belong to known B73–Mo17 syntenic loci and 94% of genes with assembled transcripts are present in all temperate lines in the nested association mapping pan-genome. While there is limited evidence for alternative splicing in response to ozone stress, there is a difference in the magnitude of differential expression among the 5 genotypes. The transcriptional response to sustained ozone stress in the ozone resistant B73 genotype (151 genes) was modest, while more than 3,300 genes were significantly differentially expressed in the more sensitive NC338 genotype. There is the potential for tandem duplication in 30% of genes with assembled transcripts, but there is no obvious association between potential tandem duplication and differential expression. Genes with a common response across the 5 genotypes (83 genes) were associated with photosynthesis, in particular photosystem I. The functional annotation of genes not differentially expressed in B73 but responsive in the other 4 genotypes (789) identifies reactive oxygen species. This suggests that B73 has a different response to long-term ozone exposure than the other 4 genotypes. The relative magnitude of the genotypic response to ozone, and the enrichment analyses are consistent regardless of whether aligning short reads to: long read assembled transcripts; the B73 reference; the Mo17 reference. We find that prolonged ozone exposure directly impacts the photosynthetic machinery of the leaf.
Published: 2022

31. Full adoption of the most effective strategies to mitigate methane emissions by ruminants can help meet the 1.5 °C target by 2030 but not 2050

Author: European Commission, Kravis Scientific Research Fund, Department of Agriculture (US), University of California, Davis, Deutsche Gesellschaft für Internationale Zusammenarbeit, Federal Ministry of Economic Cooperation and Development (Germany), Arndt, C., Hristov, A. N., Price, W.J., McClelland, S.C., Pelaez, A.M., Cueva, S.F., Oh, J., Dijkstra, J., Bannink, A., Bayat, A.R., Crompton, L. A., Eugène, M. A., Enahoro, D., Kebreab, E., Kreuzer, M., McGee, M., Martin, C., Newbold, C.J., Reynolds, C.K., Schwarm, A., Shingfield, K.J, Veneman, J.B., Yáñez Ruiz, David R., European Commission, Kravis Scientific Research Fund, Department of Agriculture (US), University of California, Davis, Deutsche Gesellschaft für Internationale Zusammenarbeit, Federal Ministry of Economic Cooperation and Development (Germany), Arndt, C., Hristov, A. N., Price, W.J., McClelland, S.C., Pelaez, A.M., Cueva, S.F., Oh, J., Dijkstra, J., Bannink, A., Bayat, A.R., Crompton, L. A., Eugène, M. A., Enahoro, D., Kebreab, E., Kreuzer, M., McGee, M., Martin, C., Newbold, C.J., Reynolds, C.K., Schwarm, A., Shingfield, K.J, Veneman, J.B., and Yáñez Ruiz, David R.
Abstract: To meet the 1.5 °C target, methane (CH) from ruminants must be reduced by 11 to 30% by 2030 and 24 to 47% by 2050 compared to 2010 levels. A meta-analysis identified strategies to decrease product-based (PB; CH per unit meat or milk) and absolute (ABS) enteric CH emissions while maintaining or increasing animal productivity (AP; weight gain or milk yield). Next, the potential of different adoption rates of one PB or one ABS strategy to contribute to the 1.5 °C target was estimated. The database included findings from 430 peer-reviewed studies, which reported 98 mitigation strategies that can be classified into three categories: animal and feed management, diet formulation, and rumen manipulation. A random-effects meta-analysis weighted by inverse variance was carried out. Three PB strategies—namely, increasing feeding level, decreasing grass maturity, and decreasing dietary forage-to-concentrate ratio—decreased CH per unit meat or milk by on average 12% and increased AP by a median of 17%. Five ABS strategies—namely CH inhibitors, tanniferous forages, electron sinks, oils and fats, and oilseeds—decreased daily methane by on average 21%. Globally, only 100% adoption of the most effective PB and ABS strategies can meet the 1.5 °C target by 2030 but not 2050, because mitigation effects are offset by projected increases in CH due to increasing milk and meat demand. Notably, by 2030 and 2050, low- and middle-income countries may not meet their contribution to the 1.5 °C target for this same reason, whereas high-income countries could meet their contributions due to only a minor projected increase in enteric CH emissions.
Published: 2022

32. Evaluation of Effective Class-Balancing Techniques for CNN-Based Assessment of Aphanomyces Root Rot Resistance in Pea (Pisum sativum L.)

Author: Department of Agriculture (US), National Institute of Food and Agriculture (US), College of Agricultural, Human, and Natural Resource Sciences (US), Divyanth, L. G., Marzougui, Afef, González-Bernal, María José, McGee, Rebecca, Rubiales, Diego, Sankaran, Sindhuja, Department of Agriculture (US), National Institute of Food and Agriculture (US), College of Agricultural, Human, and Natural Resource Sciences (US), Divyanth, L. G., Marzougui, Afef, González-Bernal, María José, McGee, Rebecca, Rubiales, Diego, and Sankaran, Sindhuja
Abstract: Aphanomyces root rot (ARR) is a devastating disease that affects the production of pea. The plants are prone to infection at any growth stage, and there are no chemical or cultural controls. Thus, the development of resistant pea cultivars is important. Phenomics technologies to support the selection of resistant cultivars through phenotyping can be valuable. One such approach is to couple imaging technologies with deep learning algorithms that are considered efficient for the assessment of disease resistance across a large number of plant genotypes. In this study, the resistance to ARR was evaluated through a CNN-based assessment of pea root images. The proposed model, DeepARRNet, was designed to classify the pea root images into three classes based on ARR severity scores, namely, resistant, intermediate, and susceptible classes. The dataset consisted of 1581 pea root images with a skewed distribution. Hence, three effective data-balancing techniques were identified to solve the prevalent problem of unbalanced datasets. Random oversampling with image transformations, generative adversarial network (GAN)-based image synthesis, and loss function with class-weighted ratio were implemented during the training process. The result indicated that the classification F1-score was 0.92 ± 0.03 when GAN-synthesized images were added, 0.91 ± 0.04 for random resampling, and 0.88 ± 0.05 when class-weighted loss function was implemented, which was higher than when an unbalanced dataset without these techniques were used (0.83 ± 0.03). The systematic approaches evaluated in this study can be applied to other image-based phenotyping datasets, which can aid the development of deep-learning models with improved performance.
Published: 2022

33. Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity

Author: National Institutes of Health (US), Department of Agriculture (US), National Institute of Food and Agriculture (US), National Science Foundation (US), Crohn's and Colitis Foundation of America, Independent Research Fund Denmark, German Research Foundation, Shaffer, Justin P. [0000-0002-9371-6336], Nothias, Louis-Félix [0000-0001-6711-6719], Thompson, Luke R. [0000-0002-3911-1280], Sanders, Jon G. [0000-0001-6077-4014], Couvillion, Sneha P. [0000-0003-0307-9343], Haiminen, Niina [0000-0002-8663-1019], Lutz, Holly L. [0000-0001-6454-809X], Zhu, Qiyun [0000-0002-3568-6271], Shaffer, Justin P., Nothias, Louis-Félix, Thompson, Luke R., Sanders, Jon G., Salido, Rodolfo A., Couvillion, Sneha P., Brejnrod, Asker D., Lejzerowicz, Franck, Haiminen, Niina, Huang, Shi, Lutz, Holly L., Zhu, Qiyun, Martino, Cameron, Morton, James T., Karthikeyan, Smruthi, Nothias-Esposito, Mélissa, Dührkop, Kai, Böcker, Sebastian, Kim, Hyun Woo, Aksenov, Alexander A., Bittremieux, Wout, Minich, Jeremiah J., Marotz, Clarisse, Bryant, MacKenzie M., Sanders, Karenina, Schwartz, Tara, Humphrey, Greg, Vásquez-Baeza, Yoshiki, Tripathi, Anupriya, Parida, Laxmi, Carrieri, Anna Paola, Beck, Kristen L., Das, Promi, González, Antonio, McDonald, Daniel, Ladau, Joshua, Karst, Søren M., Albertsen, Mads, Ackermann, Gail, DeReus, Jeff, Thomas, Torsten, Petras, Daniel, Shade, Ashley, Stegen, James, Song, Se Jin, Metz, Thomas O., Swafford, Austin D., Dorrestein, Pieter C., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, National Institutes of Health (US), Department of Agriculture (US), National Institute of Food and Agriculture (US), National Science Foundation (US), Crohn's and Colitis Foundation of America, Independent Research Fund Denmark, German Research Foundation, Shaffer, Justin P. [0000-0002-9371-6336], Nothias, Louis-Félix [0000-0001-6711-6719], Thompson, Luke R. [0000-0002-3911-1280], Sanders, Jon G. [0000-0001-6077-4014], Couvillion, Sneha P. [0000-0003-0307-9343], Haiminen, Niina [0000-0002-8663-1019], Lutz, Holly L. [0000-0001-6454-809X], Zhu, Qiyun [0000-0002-3568-6271], Shaffer, Justin P., Nothias, Louis-Félix, Thompson, Luke R., Sanders, Jon G., Salido, Rodolfo A., Couvillion, Sneha P., Brejnrod, Asker D., Lejzerowicz, Franck, Haiminen, Niina, Huang, Shi, Lutz, Holly L., Zhu, Qiyun, Martino, Cameron, Morton, James T., Karthikeyan, Smruthi, Nothias-Esposito, Mélissa, Dührkop, Kai, Böcker, Sebastian, Kim, Hyun Woo, Aksenov, Alexander A., Bittremieux, Wout, Minich, Jeremiah J., Marotz, Clarisse, Bryant, MacKenzie M., Sanders, Karenina, Schwartz, Tara, Humphrey, Greg, Vásquez-Baeza, Yoshiki, Tripathi, Anupriya, Parida, Laxmi, Carrieri, Anna Paola, Beck, Kristen L., Das, Promi, González, Antonio, McDonald, Daniel, Ladau, Joshua, Karst, Søren M., Albertsen, Mads, Ackermann, Gail, DeReus, Jeff, Thomas, Torsten, Petras, Daniel, Shade, Ashley, Stegen, James, Song, Se Jin, Metz, Thomas O., Swafford, Austin D., Dorrestein, Pieter C., Jansson, Janet K., Gilbert, Jack A., and Knight, Rob
Abstract: Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Ear
Published: 2022

34. Improved high-quality genome assembly and annotation of pineapple (Ananas comosus) cultivar md2 revealed extensive haplotype diversity and diversified frs/frf gene family

Author: Department of Agriculture (US), National Institute of Food and Agriculture (US), Yow, Ashley G., Bostan, Hamed, Castanera, Raúl, Ruggieri, Valentino, Mengist, Molla F., Curaba, Julien, Young, Roberto, Gillitt, Nicholas, Iorizzo, Massimo, Department of Agriculture (US), National Institute of Food and Agriculture (US), Yow, Ashley G., Bostan, Hamed, Castanera, Raúl, Ruggieri, Valentino, Mengist, Molla F., Curaba, Julien, Young, Roberto, Gillitt, Nicholas, and Iorizzo, Massimo
Abstract: Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple.
Published: 2022

35. The Role of Nanoengineered Biochar Activated with Fe for Sulfanilamide Removal from Soils and Water

Author: Ministerio de Ciencia e Innovación (España), European Commission, Agencia Estatal de Investigación (España), Junta de Andalucía, Department of Agriculture (US), Gámiz, B. [0000-0002-7244-778X], Velarde Muñoz, Pilar [0000-0003-3431-7543], Spokas, K. A. [0000-0002-5049-5959], Cox, L. [0000-0003-2113-4780], Gámiz, B., Velarde Muñoz, Pilar, Spokas, K. A., Cox, Lucía, Ministerio de Ciencia e Innovación (España), European Commission, Agencia Estatal de Investigación (España), Junta de Andalucía, Department of Agriculture (US), Gámiz, B. [0000-0002-7244-778X], Velarde Muñoz, Pilar [0000-0003-3431-7543], Spokas, K. A. [0000-0002-5049-5959], Cox, L. [0000-0003-2113-4780], Gámiz, B., Velarde Muñoz, Pilar, Spokas, K. A., and Cox, Lucía
Abstract: Biochar is a nanoengineered sorbent proposed to control the contamination derived from the presence of residual concentrations of sulfonamides in soil. In this work, we evaluated the sorption of sulfanilamide (SFA) in commercial biochar (BC) produced at 500 °C from oak hardwood (Quercus ilex) and its analog activated with 2% (w/w) Fe (BC-Fe). Subsequently, the effect on dissipation and transport of SFA in untreated soil and soil treated with BC and BC-Fe was also assessed. Laboratory batch studies revealed that BC-Fe increased the sorption of SFA as compared to the pristine BC with Kd of 278 and 98 L/kg, respectively. The dissipation of SFA in either untreated soil or soil treated with BC or BC-Fe was similar, displaying half-lives ranging between 4 and 6.4 days. Conversely, the concurrent determination of sorption during the incubation experiment showed that lower amounts of SFA in solution at the beginning of the experiments were bioavailable in BC-Fe-treated soil when compared to the rest of the treatments shortly after application. Leaching column studies confirmed the amendment’s capability to bind the SFA compound. Therefore, the decrease in bioavailability and movement of SFA in treated soils suggest that biochar soil application can reduce SFA soil and water contamination. According to our results, BC surface modification after Fe activation may be more appropriate for water decontamination than for soil since there were no significant differences between the two types of biochar when added to the soil. Therefore, these outcomes should be considered to optimize the SFA mitigation potential of biochar.
Published: 2022

36. Prevention of microbes-induced spoilage in sodium chloride-free cucumber fermentations employing preservatives

Author: Department of Agriculture (US), Pérez-Díaz, Ilenys M., Medina Pradas, Eduardo, Page, Clinton A, Johanningsmeier, Suzanne D, Daughtry, Katheryne V, Moeller, Lisa, Department of Agriculture (US), Pérez-Díaz, Ilenys M., Medina Pradas, Eduardo, Page, Clinton A, Johanningsmeier, Suzanne D, Daughtry, Katheryne V, and Moeller, Lisa
Abstract: This study evaluated preservatives to stabilize sodium chloride (NaCl)-free-cucumber fermentations. The brining of air-purged laboratory cucumber fermentations with 100.0 mM calcium chloride (CaCl2 ) and 25.0 mM acetic acid resulted in immediate rises in pH, the chemical reduction of the medium, and malodors. Supplementation with 3.0 mM sodium benzoate or 3.0 mM potassium sorbate enabled a decline in pH, a continuous oxidative state of the medium, and delayed rising pH spoilage. However, lactic and acetic acids eventually disappeared in fermentations supplemented with preservatives. The amount of preservatives needed to suppress growth of brined-cucumber-spoilage microbes was determined in Fermented Cucumber Juice Medium (FCJM). Supplementation of FCJM with 10.0 mM sodium benzoate was inhibitory for the spoilage yeasts, Issatchenkia occidentalis and Pichia manshurica, and the lactobacilli, Lentilactobacillus buchneri and Lentilactobacillus parafarraginis, but not of Zygosaccharomyces globiformis. Potassium sorbate inhibited the spoilage yeasts at 15.0 mM in FCJM but not the lactobacilli. Supplementation of FCJM with 20.0 mM fumaric acid had a bactericidal effect on the spoilage-associated lactobacilli. As expected, NaCl-free-commercial cucumber fermentations brined with 100 mM CaCl2 , no acetic acid, and 6 mM potassium sorbate resulted in complete fermentations, but supported rising pH, microbially induced spoilage during long-term storage. Post-fermentation supplementation with 12 mM sodium benzoate, 10 mM fumaric acid, a combination of the two, or 10 mM fumaric acid and 2 mM AITC prevented microbial activity during long-term bulk storage. PRACTICAL APPLICATION: Several preservative-based strategies for stabilizing NaCl-free cucumber fermentation in a commercial production setting were developed, enabling the implementation of a processing technology that reduces wastewater volumes and environmental impact.
Published: 2022

37. Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer

Author: Extreme Science and Engineering Discovery Environment (US), National Science Foundation (US), Great Lakes Bioenergy Research Center (US), Agencia Estatal de Investigación (España), European Commission, Junta de Andalucía, Department of Agriculture (US), Elder T. [0000-0003-3909-2152], Río Andrade, José Carlos del [0000-0002-3040-6787], Ralph, John [0000-0002-6093-4521], Rencoret, Jorge [0000-0003-2728-7331], Kim, Hoon [0000-0001-7425-7464], Elder T., Río Andrade, José Carlos del, Ralph, John, Rencoret, Jorge, Kim, Hoon, Extreme Science and Engineering Discovery Environment (US), National Science Foundation (US), Great Lakes Bioenergy Research Center (US), Agencia Estatal de Investigación (España), European Commission, Junta de Andalucía, Department of Agriculture (US), Elder T. [0000-0003-3909-2152], Río Andrade, José Carlos del [0000-0002-3040-6787], Ralph, John [0000-0002-6093-4521], Rencoret, Jorge [0000-0003-2728-7331], Kim, Hoon [0000-0001-7425-7464], Elder T., Río Andrade, José Carlos del, Ralph, John, Rencoret, Jorge, and Kim, Hoon
Abstract: Diferuloylputrescine has been found in a variety of plant species, and recent work has provided evidence of its covalent bonding into lignin. Results from nuclear magnetic resonance spectroscopy revealed the presence of bonding patterns consistent with homo-coupling of diferuloylputrescine and the possibility of cross-coupling with lignin. In the present work, density functional theory calculations have been applied to assess the energetics associated with radical coupling, rearomatization, and dehydrogenation for possible homo-coupled dimers of diferuloylputrescine and cross-coupled dimers of diferuloylputrescine and coniferyl alcohol. The values obtained for these reaction energetics are consistent with those reported for monolignols and other novel lignin monomers. As such, this study shows that there would be no thermodynamic impediment to the incorporation of diferuloylputrescine into the lignin polymer and its addition to the growing list of non-canonical lignin monomers.
Published: 2022

38. Application of a remote-sensing three-source energy balance model to improve evapotranspiration partitioning in vineyards

Author: E. & J. Gallo Winery, National Aeronautics and Space Administration (US), Agricultural Research Service (US), Department of Agriculture (US), Burchard-Levine, Vicente [0000-0003-0222-8706], Nieto, Héctor [0000-0003-4250-6424], Burchard-Levine, Vicente, Nieto, Héctor, Kustas, William P., Gao, Feng, Alfieri, Joseph G., Prueger, John H., Hipps, Lawrence E., Bambach, Nicolas, McElrone, Andrew J., Castro, Sebastian J., Alsina, María Mar, McKee, Lynn G., Zahn, Einara, Bou-Zeid, Elie, Dokoozlian, Nick, E. & J. Gallo Winery, National Aeronautics and Space Administration (US), Agricultural Research Service (US), Department of Agriculture (US), Burchard-Levine, Vicente [0000-0003-0222-8706], Nieto, Héctor [0000-0003-4250-6424], Burchard-Levine, Vicente, Nieto, Héctor, Kustas, William P., Gao, Feng, Alfieri, Joseph G., Prueger, John H., Hipps, Lawrence E., Bambach, Nicolas, McElrone, Andrew J., Castro, Sebastian J., Alsina, María Mar, McKee, Lynn G., Zahn, Einara, Bou-Zeid, Elie, and Dokoozlian, Nick
Abstract: Improved accuracy of evapotranspiration (ET) estimation, including its partitioning between transpiration (T) and surface evaporation (E), is key to monitor agricultural water use in vineyards, especially to enhance water use efficiency in semi-arid regions such as California, USA. Remote-sensing methods have shown great utility in retrieving ET from surface energy balance models based on thermal infrared data. Notably, the two-source energy balance (TSEB) has been widely and robustly applied in numerous landscapes, including vineyards. However, vineyards add an additional complexity where the landscape is essentially made up of two distinct zones: the grapevine and the interrow, which is often seasonally covered by an herbaceous cover crop. Therefore, it becomes more complex to disentangle the various contributions of the different vegetation elements to total ET, especially through TSEB, which assumes a single vegetation source over a soil layer. As such, a remote-sensing-based three-source energy balance (3SEB) model, which essentially adds a vegetation source to TSEB, was applied in an experimental vineyard located in California’s Central Valley to investigate whether it improves the depiction of the grapevine-interrow system. The model was applied in four different blocks in 2019 and 2020, where each block had an eddy-covariance (EC) tower collecting continuous flux, radiometric, and meteorological measurements. 3SEB’s latent and sensible heat flux retrievals were accurate with an overall RMSD ~ 50 W/m2 compared to EC measurements. 3SEB improved upon TSEB simulations, with the largest differences being concentrated in the spring season, when there is greater mixing between grapevine foliage and the cover crop. Additionally, 3SEB’s modeled ET partitioning (T/ET) compared well against an EC T/ET retrieval method, being only slightly underestimated. Overall, these promising results indicate 3SEB can be of great utility to vineyard irrigation management, especially
Published: 2022

39. Oxygen Nanobubble-Loaded Biochars Mitigate Copper Transfer from Copper-Contaminated Soil to Rice and Improve Rice Growth

Author: Qingnan Chu, Zhimin Sha, Detian Li, Yanfang Feng, Lihong Xue, Dongmei Zhou, Baoshan Xing, National Key Research and Development Program (China), Natural Science Foundation of Jiangsu Province, Agriculture Research System of China, China National Tobacco Corporation, Jiangsu Province, Department of Agriculture (US), Chu, Qingnan, Sha, Zhimin, Feng, Yanfang, Zhou, Dongmei, and Xing, Baoshan
Subjects: Paddy soil, Renewable Energy, Sustainability and the Environment, General Chemical Engineering, Copper contamination, Environmental Chemistry, Copper-transformed genes, General Chemistry, Redox potential, Hydrochar, Iron plaque
Abstract: 13 Pág., Copper (Cu)-contaminated paddy soil has caused substantial concerns for human health through biomagnification in the soil-rice-human chain. In this study, oxygen nanobubble-loaded biochars (ONBC), including pyrochars (NPC) and hydrochars (NHC), were used to amend Cu-contaminated paddy soils and reduce rice Cu toxicity. The ONBC amendment improved the rhizospheric redox potential and dissolved oxygen concentration via slow, continuous oxygen release, promoting root iron plaque formation and effectively inhibiting root Cu influx. Moreover, the ONBC amendment improved soil microbial diversity. The abundance of bacterial genes involved in cytosolic Cu complexation and Cu export to the periplasm space for Cu stabilization markedly improved. The sequestered Cu in root iron plaque and soil bacteria inhibited Cu influx into the shoots to avoid Cu overaccumulation in the edible parts. This was reflected by the Cu content decreasing by 1.91-fold and 2.38-fold in shoots under NPC and NHC treatments, respectively. Furthermore, the improved oxygen-enriched rhizosphere environment via the ONBC amendment promoted root activity and the abundance of bacterial genes involved in nutrients mineralization, further promoting shoot biomass by 1.46-fold and 2.29-fold under NPC and NHC treatments, respectively. This study proposes an environmentally friendly strategy to mitigate Cu transfer from soil to crops and improve crop productivity., This work was supported by the National Key Research and Development Program of China (021YFD1700805), Natural Science Foundation of Jiangsu Province (BK20221428), Agriculture Research System of Shanghai, China (202203), Yunnan Branch of China National Tobacco Corporation (2022530000241022), 333 High-level Talents Training Project of Jiangsu Province (2022-3-23-083). and USDA Hatch program (MAS 00549).
Published: 2023
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40. Patterns of pan‐genome occupancy and gene coexpression under water‐deficit in Brachypodium distachyon

Author: Rubén Sancho, Pilar Catalán, Bruno Contreras‐Moreira, Thomas E. Juenger, David L. Des Marais, Department of Agriculture (US), Ministerio de Ciencia e Innovación (España), Universidad de Zaragoza, Joint Genome Institute (US), Ministerio de Economía y Competitividad (España), Ibercaja, Instituto de Estudios Altoaragoneses, ARAID Foundation, and Contreras-Moreira, Bruno
Subjects: transcriptomics, Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss, genomics/proteomics, molecular evolution, Genetics, Water, Genes, Plant, Transcriptome, phenotypic plasticity, Ecology, Evolution, Behavior and Systematics, Brachypodium, Droughts
Abstract: 22 Pags.- 3 Figs.- 4 Tabls. © 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License., Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable “occupancy” in the pan-genome – genes which are either present in all studied genotypes or missing in some genotypes – show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response., This work was supported by the USDA (NIFA-2011-67012-30663) to D.L.D., NSF (IOS-0922457) to T.E.J., the Spanish Ministry of Science and Innovation CGL2016-79790-P and PID2019-108195GB-I00, University of Zaragoza UZ2016_TEC02 grant projects to P.C., and the Joint Genome Institute FP00006675 contract to P.C. and FP00006746 to D.L.D. R.S. was funded by a Spanish Ministry of Economy and Competitiveness (Mineco) FPI PhD fellowship, Mineco and Ibercaja-CAI mobility grants and Instituto de Estudios Altoaragoneses grant. B.C.M. was funded by Fundación ARAID. P.C. and R.S. were partially funded by a European Social Fund/Spanish Aragón Government Bioflora grant.
Published: 2022
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41. Evaluating different metrics from the thermal-based two-source energy balance model for monitoring grapevine water stress

Author: Héctor Nieto, María Mar Alsina, William P. Kustas, Omar García-Tejera, Fan Chen, Nicolas Bambach, Feng Gao, Joseph G. Alfieri, Lawrence E. Hipps, John H. Prueger, Lynn G. McKee, Einara Zahn, Elie Bou-Zeid, Andrew J. McElrone, Sebastian J. Castro, Nick Dokoozlian, National Aeronautics and Space Administration (US), Department of Agriculture (US), Agricultural Research Service (US), Conferencia de Rectores de las Universidades Españolas, Consejo Superior de Investigaciones Científicas (España), and Nieto, Héctor
Subjects: Soil Science, Agronomy and Crop Science, Water Science and Technology
Abstract: Precision irrigation management requires operational monitoring of crop water status. However, there is still some controversy on how to account for crop water stress. To address this question, several physiological, several physiological metrics have been proposed, such as the leaf/stem water potentials, stomatal conductance, or sap flow. On the other hand, thermal remote sensing has been shown to be a promising tool for efficiently evaluating crop stress at adequate spatial and temporal scales, via the Crop Water Stress Index (CWSI), one of the most common indices used for assessing plant stress. CWSI relates the actual crop evapotranspiration ET (related to the canopy radiometric temperature) to the potential ET (or minimum crop temperature). However, remotely sensed surface temperature from satellite sensors includes a mixture of plant canopy and soil/substrate temperatures, while what is required for accurate crop stress detection is more related to canopy metrics, such as transpiration, as the latter one avoids the influence of soil/substrate in determining crop water status or stress. The Two-Source Energy Balance (TSEB) model is one of the most widely used and robust evapotranspiration model for remote sensing. It has the capability of partitioning ET into the crop transpiration and soil evaporation components, which is required for accurate crop water stress estimates. This study aims at evaluating different TSEB metrics related to its retrievals of actual ET, transpiration and stomatal conductance, to track crop water stress in a vineyard in California, part of the GRAPEX experiment. Four eddy covariance towers were deployed in a Variable Rate Irrigation system in a Merlot vineyard that was subject to different stress periods. In addition, root-zone soil moisture, stomatal conductance and leaf/stem water potential were collected as proxy for in situ crop water stress. Results showed that the most robust variable for tracking water stress was the TSEB derived leaf stomatal conductance, with the strongest correlation with both the measured root-zone soil moisture and stomatal conductance gas exchange measurements. In addition, these metrics showed a better ability in tracking stress when the observations are taken early after noon., Funding and logistical support for the GRAPEX project were provided by E. & J. Gallo Winery and from the NASA Applied Sciences-Water Resources Program (Grant no. NNH17AE39I). This research was also supported in part by the U.S. Department of Agriculture, Agricultural Research Service. Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature.
Published: 2022
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42. Complete Genome Resources for Xylella fastidiosa Strains AlmaEM3 and BB08-1 Reveal Prophage-Associated Structural Variation Among Blueberry-Infecting Strains

Author: Blanca B. Landa, Lindsey P. Burbank, Luis F. Arias-Giraldo, Leonardo De La Fuente, Michael O'Leary, Department of Agriculture (US), and National Institutes of Health (US)
Subjects: Genetics, biology, Bioinformatics, Strain (biology), Leaf scorch, Genomics, Plant Science, Subspecies, biology.organism_classification, medicine.disease, Genome, Structural variation, Microbe-genome sequencing, medicine, Bacterial pathogens, Xylella fastidiosa, Agronomy and Crop Science, Prophage
Abstract: This work was funded by the United States Department of Agriculture–Agricultural Research Service appropriated project 2034-22000-012-00D and the Xylella fastidiosa Active Containment Through a Multidisciplinary-Oriented Research Strategy (XF-ACTORS) project. Illumina sequencing for BB08-1 was carried out at the University of California, Davis, Genome Center DNA Technologies and Expression Analysis Cores, supported by National Institute of Health Shared Instrumentation Grant 1S10OD010786-01.
Published: 2022
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43. Increasing crop rotational diversity can enhance cereal yields

Author: Monique E. Smith, Giulia Vico, Alessio Costa, Timothy Bowles, Amélie C. M. Gaudin, Sara Hallin, Christine A. Watson, Remedios Alarcòn, Antonio Berti, Andrzej Blecharczyk, Francisco J. Calderon, Steve Culman, William Deen, Craig F. Drury, Axel Garcia y. Garcia, Andrés García-Díaz, Eva Hernández Plaza, Krzysztof Jonczyk, Ortrud Jäck, R. Michael Lehman, Francesco Montemurro, Francesco Morari, Andrea Onofri, Shannon L. Osborne, José Luis Tenorio Pasamón, Boël Sandström, Inés Santín-Montanyá, Zuzanna Sawinska, Marty R. Schmer, Jaroslaw Stalenga, Jeffrey Strock, Francesco Tei, Cairistiona F. E. Topp, Domenico Ventrella, Robin L. Walker, Riccardo Bommarco, Department of Agriculture (US), Scottish Government, Swedish University of Agricultural Sciences, Biotechnology and Biological Sciences Research Council (UK), Agriculture and Agri-Food Canada, Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Vico, Giulia, Costa, Alessio, Bowles, Timothy, Gaudin, Amélie C.M., Hallin, Sara, Alarcón Víllora, M. Remedios, Berti, Antonio, Blecharczyk, Andrzej, Culman, Steve, Deen, William, Drury, Craig F., Garcia y Garcia Axel, García-Díaz, Andrés, Hernández Plaza, María Eva, Jonczyk, Krzysztof, Jäck, Ortrud, Lehman, R. Michael, Montemurro, Francesco, Morari, Francesco, Onofri, Andrea, Osborne, Shannon L., Tenorio, J. L., Sandström, Boël, Santín Montanyá, Inés, Sawinska, Zuzanna, Schmer, Marty R., Stalenga, Jaroslaw, Strock, Jeffrey, Tei, Francesco, Topp, Cairistiona F.E., Walker, Robin L., and Bommarco, Riccardo
Subjects: cereals, crop rotation, grain yield, long term experiments, General Earth and Planetary Sciences, nitrogen fertilization, Agricultural Science, crop rotation, nitrogen fertilization, cereals, long term experiments, diversity, grain yield, General Environmental Science, diversity
Abstract: 9 Pág., Diversifying agriculture by rotating a greater number of crop species in sequence is a promising practice to reduce negative impacts of crop production on the environment and maintain yields. However, it is unclear to what extent cereal yields change with crop rotation diversity and external nitrogen fertilization level over time, and which functional groups of crops provide the most yield benefit. Here, using grain yield data of small grain cereals and maize from 32 long-term (10–63 years) experiments across Europe and North America, we show that crop rotational diversity, measured as crop species diversity and functional richness, enhanced grain yields. This yield benefit increased over time. Only the yields of winter-sown small grain cereals showed a decline at the highest level of species diversity. Diversification was beneficial to all cereals with a low external nitrogen input, particularly maize, enabling a lower dependence on nitrogen fertilisers and ultimately reducing greenhouse gas emissions and nitrogen pollution. The results suggest that increasing crop functional richness rather than species diversity can be a strategy for supporting grain yields across many environments., G.V., R.B. and S.H. acknowledge FORMAS grants 2018-02872 and 2018-02321. TMB acknowledges USDA AFRI grant 2017-67013-26254. LTEs managed by SRUC were supported by the Scottish Government RESAS Strategic Research Programme under project D3-, Healthy Soils for a Green Recovery. Swedish LTEs were funded by the Swedish University of Agricultural Sciences (SLU). We thank the Lawes Agricultural Trust and Rothamsted Research for data from the e-RA database. The Rothamsted Long-term Experiments National Capability (LTE-NC) was supported by the UK BBSRC (Biotechnology and Biological Sciences Research Council, BBS/E/C/000J0300) and the Lawes Agricultural Trust. The Woodslee site was supported by the Agro-Ecosystem Resilience Program (Agriculture & Agri-Food Canada) and field management provided by field crews over 6 decades is appreciated. La Canaleja LTE (Spain) was supported by RTA2017-00006-C03-01 project (Ministry of Science and Innovation. El Encín LTEs were supported by Spanish Ministry of Economy and Competitiveness funds (projects AGL2002-04186-C03-01.03, AGL2007-65698-C03-01.03, AGL2012-39929-C03-01 of which L. Navarrete was the P.I). R.A., A.G.D. and E.H.P. are also grateful to all members of the Weed Science Group from El Encín Experimental Station for their technical assistance in managing the experiments. The Brody/Poznan University of Life Sciences long-term experiments were funded by the Polish Ministry of Education and Science. We acknowledge the E-Obs dataset from the EU-FP6 project UERRA (http://www.uerra.eu) and the Copernicus Climate Change Service, and the data providers in the ECA&D project (https://www.ecad.eu/).
Published: 2023

44. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii

Author: Julia S. Martin del Campo, Jack Rigsbee, Marcelo Bueno Batista, Florence Mus, Luis M. Rubio, Oliver Einsle, John W. Peters, Ray Dixon, Dennis R. Dean, Patricia C. Dos Santos, Biotechnology and Biological Sciences Research Council (UK), Royal Society (UK), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Department of Agriculture (US), National Science Foundation (US), Department of Energy (US), Martin Del Campo, Julia S., Bueno Batista, Marcelo, Mus, Florence, Rubio, Luis M., Einsle, O., Peters, John W., Dixon, Ray, Dean, Dennis R., and Dos Santos, Patricia C.
Subjects: Iron-only nitrogenase, Azotobacter vinelandii, Fe protein, Nitrogen fixation, MoFe protein, Nitrogenase, Respiratory protection, Molecular Biology, Biochemistry, Vanadium nitrogenase
Abstract: Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development., MBB and RD were supported by the UKRI Biotechnology and Biological Sciences Research Council, [grants BB/W009986/1 to MBB, BB/N013476/1 and BBS/E/J/000PR9797 to RD]. MBB and RD were also supported by a grant from the Royal Society, [ICA\R1\180088]. LMR was supported by FEDER/Ministerio de Ciencia, Innovación y Universidades – Agencia Estatal de Investigación [grant 2017-88475-R]. J.W.P. was supported by the US DOE, Office of Science, Office of Basic Energy Sciences under award DE-SC0018143. Partial salary support for J. W. P. was provided by the United States Department of Agriculture National Institute of Food and Agriculture, Hatch umbrella project #15621. O.E. was supported by Deutsche Forschungsgemeinschaft [RTG 1976, project no. 235777276 and PP 1927, project no. 311061829]. PDS and JR was supported by the National Science Foundation (MCB 1716535). DRD and JSMC were supported by the U.S. Department of Energy, Office of Science, Basic Energy DE-SC00106867.
Published: 2023

45. Enriched root bacterial microbiome in invaded vs native ranges of the model grass allotetraploid Brachypodium hybridum

Author: Brooke Pickett, Chelsea J. Carey, Keshav Arogyaswamy, Jon Botthoff, Mia Maltz, Pilar Catalán, Emma L. Aronson, National Institute of Food and Agriculture (US), Department of Agriculture (US), Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Gobierno de Aragón, and European Commission
Subjects: бактериальные микробиомы, Soil, нативные ареалы, Invasive species, Root, Ecology, Endophytic bacteria, Rhizosphere, food and beverages, Ecology, Evolution, Behavior and Systematics, Brachypodium, инвазивные виды
Abstract: Invasive species can shift the composition of key soil microbial groups, thus creating novel soil microbial communities. To better understand the biological drivers of invasion, we studied plant-microbial interactions in species of the Brachypodium distachyon complex, a model system for functional genomic studies of temperate grasses and bioenergy crops. While Brachypodium hybridum invasion in California is in an incipient stage, threatening natural and agricultural systems, its diploid progenitor species B. distachyon is not invasive in California. We investigated the root, soil, and rhizosphere bacterial composition of Brachypodium hybridum in both its native and invaded range, and of B. distachyon in the native range. We used high-throughput, amplicon sequencing to evaluate if the bacteria associated with these plants differ, and whether biotic controls may be driving B. hybridum invasion. Bacterial community composition of B. hybridum differed based on provenance (native or invaded range) for root, rhizosphere, and bulk soils, as did the abundance of dominant bacterial taxa. Bacteroidetes, Cyanobacteria and Bacillus spp. (species) were significantly more abundant in B. hybridum roots from the invaded range, whereas Proteobacteria, Firmicutes, Erwinia and Pseudomonas were more abundant in the native range roots. Brachypodium hybridum forms novel biotic interactions with a diverse suite of rhizosphere microbes from the invaded range, which may not exert a similar influence within its native range, ostensibly contributing to B. hybridum’s invasiveness. These associated plant microbiomes could inform future management approaches for B. hybridum in its invaded range and could be key to understanding, predicting, and preventing future plant invasions., Funding was provided from USDA NIFA in Seed Grant CA-R-PPA-5101-CG and Hatch Grant CA-R-PPA-5093-H to EA, and Spanish Ministry of Science Grants CGL2016-79790-P and PID2019-108195GB-I00 and Spanish Aragon Government and European Social Found Bioflora A01-20R Grant to PC.
Published: 2021
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46. The Role of Nanoengineered Biochar Activated with Fe for Sulfanilamide Removal from Soils and Water

Author: Pilar Velarde, LUCIA COX, Kurt Spokas, Beatriz Gamiz, Ministerio de Ciencia e Innovación (España), European Commission, Agencia Estatal de Investigación (España), Junta de Andalucía, Department of Agriculture (US), Gámiz, B., Velarde Muñoz, Pilar, Spokas, K. A., and Cox, L.
Subjects: Activated biochar, Bound residues, Organic Chemistry, Pharmaceutical Science, Water, Nanostructured materials, Soil amendments, Analytical Chemistry, Soil, activated biochar, antibiotics, biodegradation, bound residues, leaching, nanostructured materials, soil amendments, Sulfanilamide, Chemistry (miscellaneous), Antibiotics, Charcoal, Drug Discovery, Biodegradation, Leaching, Molecular Medicine, Soil Pollutants, Physical and Theoretical Chemistry
Abstract: 14 páginas.- 5 figuras.- 4 tablas.- 71 referencias.- Supplementary Materials: The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/molecules27217418/s1 .- his article belongs to the Special Issue Organic Nanomaterials: Synthesis and Applications, Biochar is a nanoengineered sorbent proposed to control the contamination derived from the presence of residual concentrations of sulfonamides in soil. In this work, we evaluated the sorption of sulfanilamide (SFA) in commercial biochar (BC) produced at 500 °C from oak hardwood (Quercus ilex) and its analog activated with 2% (w/w) Fe (BC-Fe). Subsequently, the effect on dissipation and transport of SFA in untreated soil and soil treated with BC and BC-Fe was also assessed. Laboratory batch studies revealed that BC-Fe increased the sorption of SFA as compared to the pristine BC with Kd of 278 and 98 L/kg, respectively. The dissipation of SFA in either untreated soil or soil treated with BC or BC-Fe was similar, displaying half-lives ranging between 4 and 6.4 days. Conversely, the concurrent determination of sorption during the incubation experiment showed that lower amounts of SFA in solution at the beginning of the experiments were bioavailable in BC-Fe-treated soil when compared to the rest of the treatments shortly after application. Leaching column studies confirmed the amendment’s capability to bind the SFA compound. Therefore, the decrease in bioavailability and movement of SFA in treated soils suggest that biochar soil application can reduce SFA soil and water contamination. According to our results, BC surface modification after Fe activation may be more appropriate for water decontamination than for soil since there were no significant differences between the two types of biochar when added to the soil. Therefore, these outcomes should be considered to optimize the SFA mitigation potential of biochar., This research was funded by the Spanish Ministry of Science and Innovation (MCIN/AEI/10.13039/501100011033) through grants PID2019-109456RB-I00 and by Junta de Andalucía, through grant P20-00746, with EU (FEDER) funds. The USDA is an equal-opportunity employer. Any mention of trade names or commercial products in this report is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. Institutional Review Board Statement
Published: 2022

47. Evaluation of Effective Class-Balancing Techniques for CNN-Based Assessment of Aphanomyces Root Rot Resistance in Pea (Pisum sativum L.)

Author: L. G. Divyanth, Afef Marzougui, Maria Jose González-Bernal, Rebecca J. McGee, Diego Rubiales, Sindhuja Sankaran, Department of Agriculture (US), National Institute of Food and Agriculture (US), and College of Agricultural, Human, and Natural Resource Sciences (US) CAHNRS
Subjects: Generative adversarial networks, Deep learning, Electrical and Electronic Engineering, Disease identification, plant breeding, disease identification, deep learning, generative adversarial networks, Biochemistry, Instrumentation, Atomic and Molecular Physics, and Optics, Plant breeding, Analytical Chemistry
Abstract: This article belongs to the Special Issue Machine and Deep Learning in Sensing and Imaging: Emerging Trends, Challenges and Opportunities., Aphanomyces root rot (ARR) is a devastating disease that affects the production of pea. The plants are prone to infection at any growth stage, and there are no chemical or cultural controls. Thus, the development of resistant pea cultivars is important. Phenomics technologies to support the selection of resistant cultivars through phenotyping can be valuable. One such approach is to couple imaging technologies with deep learning algorithms that are considered efficient for the assessment of disease resistance across a large number of plant genotypes. In this study, the resistance to ARR was evaluated through a CNN-based assessment of pea root images. The proposed model, DeepARRNet, was designed to classify the pea root images into three classes based on ARR severity scores, namely, resistant, intermediate, and susceptible classes. The dataset consisted of 1581 pea root images with a skewed distribution. Hence, three effective data-balancing techniques were identified to solve the prevalent problem of unbalanced datasets. Random oversampling with image transformations, generative adversarial network (GAN)-based image synthesis, and loss function with class-weighted ratio were implemented during the training process. The result indicated that the classification F1-score was 0.92 ± 0.03 when GAN-synthesized images were added, 0.91 ± 0.04 for random resampling, and 0.88 ± 0.05 when class-weighted loss function was implemented, which was higher than when an unbalanced dataset without these techniques were used (0.83 ± 0.03). The systematic approaches evaluated in this study can be applied to other image-based phenotyping datasets, which can aid the development of deep-learning models with improved performance., This activity was funded in part by US Department of Agriculture (USDA)—National Institute for Food and Agriculture (NIFA) Agriculture and Food Research Initiative Competitive Project WNP06825 (accession number 1011741), Hatch Project WNP00011 (accession numbers 1014919), and CAHNRS Emerging Research Issues project.
Published: 2022

48. Impact of advection on two-source energy balance (TSEB) canopy transpiration parameterization for vineyards in the California Central Valley

Author: William P. Kustas, Hector Nieto, Omar Garcia-Tejera, Nicolas Bambach, Andrew J. McElrone, Feng Gao, Joseph G. Alfieri, Lawrence E. Hipps, John H. Prueger, Alfonso Torres-Rua, Martha C. Anderson, Kyle Knipper, Maria Mar Alsina, Lynn G. McKee, Einara Zahn, Elie Bou-Zeid, Nick Dokoozlian, E. & J. Gallo Winery, National Aeronautics and Space Administration (US), Department of Agriculture (US), and Agricultural Research Service (US)
Subjects: Soil Science, Agronomy and Crop Science, Water Science and Technology
Abstract: Water conservation efforts for California’s agricultural industry are critical to its sustainability through severe droughts like the current one and others experienced over the last two decades. This is most critical for perennial crops, such as vineyards and orchards, which are costly to plant and maintain and constitute a significant fraction of the regional water use. It is no longer feasible to access groundwater for irrigation to replace deficit surface water resources during drought due to a significant overdraft of aquifers and new regulation limiting its use. To achieve significant water savings, the actual crop water use or evapotranspiration (ET) needs to be mapped from field to regional scales on a daily basis. This can only be achieved using remote sensing-based models, particularly thermal-based energy balance models that are sensitive to deficit irrigation conditions. The two-source energy balance (TSEB) model has been successfully applied over vineyards in California, but challenges still remain. In particular, much of the irrigated cropland in the California Central Valley is affected by advection of hot dry air masses from surrounding non-irrigated areas and the TSEB model appears to need modifications to adequately estimate ET under such conditions, as well as the partitioning between evaporation and transpiration. This study investigates the application of the TSEB model, using local observations in a vineyard having significant advection. Four versions of the transpiration algorithm in TSEB are applied and evaluated with tower eddy covariance measurements spanning 4 growing seasons. The results suggest the performance of the original transpiration algorithm based on Priestley–Taylor used in TSEB is satisfactory in all but the most extreme advective conditions, while a transpiration algorithm based on Shuttleworth–Wallace with a canopy resistance formula, which relates maximum stomata conductance to vapor pressure deficit (VPD), performs well in all cases. These modifications have potential for improving regional applications of the TSEB model in support of water management in the Central Valley., Funding and logistical support for the GRAPEX project were provided by E. & J. Gallo Winery and from the NASA Applied Sciences-Water Resources Program (Grant No. NNH17AE39I). This research was also supported in part by the U.S. Department of Agriculture, Agricultural Research Service.
Published: 2022

49. Prevention of microbes-induced spoilage in sodium chloride-free cucumber fermentations employing preservatives

Author: Ilenys M. Pérez‐Díaz, Eduardo. Medina, Clinton A. Page, Suzanne D. Johanningsmeier, Katheryne V. Daughtry, Lisa Moeller, and Department of Agriculture (US)
Subjects: Sodium, Lactic acid bacteria (LAB), Sodium Chloride, Hydrogen-Ion Concentration, Sorbic Acid, Microbial inactivation, Calcium Chloride, Sodium Benzoate, Yeasts, Vegetables, Fermentation, Food Microbiology, Cucumis sativus, Preservatives, Food Science, Acetic Acid
Abstract: 10 Figuras, This study evaluated preservatives to stabilize sodium chloride (NaCl)-free-cucumber fermentations. The brining of air-purged laboratory cucumber fermentations with 100.0 mM calcium chloride (CaCl2 ) and 25.0 mM acetic acid resulted in immediate rises in pH, the chemical reduction of the medium, and malodors. Supplementation with 3.0 mM sodium benzoate or 3.0 mM potassium sorbate enabled a decline in pH, a continuous oxidative state of the medium, and delayed rising pH spoilage. However, lactic and acetic acids eventually disappeared in fermentations supplemented with preservatives. The amount of preservatives needed to suppress growth of brined-cucumber-spoilage microbes was determined in Fermented Cucumber Juice Medium (FCJM). Supplementation of FCJM with 10.0 mM sodium benzoate was inhibitory for the spoilage yeasts, Issatchenkia occidentalis and Pichia manshurica, and the lactobacilli, Lentilactobacillus buchneri and Lentilactobacillus parafarraginis, but not of Zygosaccharomyces globiformis. Potassium sorbate inhibited the spoilage yeasts at 15.0 mM in FCJM but not the lactobacilli. Supplementation of FCJM with 20.0 mM fumaric acid had a bactericidal effect on the spoilage-associated lactobacilli. As expected, NaCl-free-commercial cucumber fermentations brined with 100 mM CaCl2 , no acetic acid, and 6 mM potassium sorbate resulted in complete fermentations, but supported rising pH, microbially induced spoilage during long-term storage. Post-fermentation supplementation with 12 mM sodium benzoate, 10 mM fumaric acid, a combination of the two, or 10 mM fumaric acid and 2 mM AITC prevented microbial activity during long-term bulk storage. PRACTICAL APPLICATION: Several preservative-based strategies for stabilizing NaCl-free cucumber fermentation in a commercial production setting were developed, enabling the implementation of a processing technology that reduces wastewater volumes and environmental impact., he authors thank Sandra Parker, Seth Fornea, and Dr. Fred Breidt with the USDA-ARS, SEA, Food Science & Market Quality and Handling Research Unit located in Raleigh, NC for administrative assistance, technical support, and manuscript proofreading, respectively. Dr. Eduardo Medina was fully funded by a postdoctoral fellowship from the Spanish Government (MECD). The study was funded by the United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southeast Area (SEA), Food Science & Market Quality and Handling Research Unit (FSMQHRU), Raleigh, NC, USA.
Published: 2022

50. Capturing Wheat Phenotypes at the Genome Level

Author: Babar Hussain, Bala A. Akpınar, Michael Alaux, Ahmed M. Algharib, Deepmala Sehgal, Zulfiqar Ali, Gudbjorg I. Aradottir, Jacqueline Batley, Arnaud Bellec, Alison R. Bentley, Halise B. Cagirici, Luigi Cattivelli, Fred Choulet, James Cockram, Francesca Desiderio, Pierre Devaux, Munevver Dogramaci, Gabriel Dorado, Susanne Dreisigacker, David Edwards, Khaoula El-Hassouni, Kellye Eversole, Tzion Fahima, Melania Figueroa, Sergio Gálvez, Kulvinder S. Gill, Liubov Govta, Alvina Gul, Goetz Hensel, Pilar Hernandez, Leonardo Abdiel Crespo-Herrera, Amir Ibrahim, Benjamin Kilian, Viktor Korzun, Tamar Krugman, Yinghui Li, Shuyu Liu, Amer F. Mahmoud, Alexey Morgounov, Tugdem Muslu, Faiza Naseer, Frank Ordon, Etienne Paux, Dragan Perovic, Gadi V. P. Reddy, Jochen Christoph Reif, Matthew Reynolds, Rajib Roychowdhury, Jackie Rudd, Taner Z. Sen, Sivakumar Sukumaran, Bahar Sogutmaz Ozdemir, Vijay Kumar Tiwari, Naimat Ullah, Turgay Unver, Selami Yazar, Rudi Appels, Hikmet Budak, Department of Agriculture (US), National Institute of Food and Agriculture (US), National Science Foundation (US), Junta de Andalucía, European Commission, Biotechnology and Biological Sciences Research Council (UK), Two Blades Foundation, Grains Research and Development Corporation (Australia), Ministry of Science and Higher Education of the Russian Federation, German Research Foundation, Czech Science Foundation, Government of Norway, Middle East Technical University [Ankara] (METU), Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan, Montana Bioagriculture Inc, Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Al-Azhar University [Cairo, Egypt], International Maize and Wheat Improvement Center (CIMMYT), Centre National de Ressources Génomiques Végétales (CNRGV), Génétique Diversité et Ecophysiologie des Céréales (GDEC), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA)
Subjects: [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, [SDV.GEN]Life Sciences [q-bio]/Genetics, Disease resistance, Genome-wide association, Abiotic-stress tolerance, Genomic selection, [SDV]Life Sciences [q-bio], Wheat, Plant Science, Quantitative trait locus mapping, QTL cloning, CRISPR/Cas9
Abstract: Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence., HB was funded by USDA-NIFA SBIRI and SBIRII. PH and SG were funded by project P18-RT-992 from Junta de Andalucía (Andalusian Regional Government), Spain (Co-funded by FEDER). JC was funded by BBSRC grant BB/P010741/1. MF is supported by the 2Blades Foundation and Grains Research and Development Corporation (project CSP1801-013RTX/9176010). VK is supported by the Ministry of Science and Higher Education of the Russian Federation (grant no. 075-15-2019-1881). GH was supported by funding of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2048/1—project ID 390686111 and grants 426557363 and 458717903, the European Regional Development Fund (Project ID ZS/2018/06/93171), and the Czech Science Foundation (CZ.02.1.01./0.0/0.0/16_019/0000827, SPP 813103381). BK thanks the Government of Norway (QZA-14/0005) for funding the initiative of “Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives” (https://www.cwrdiversity.org/project/pre-breeding/).
Published: 2022
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