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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.

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

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.

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.

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.

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/).

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., National Science Foundation Plant Genome Research Program (PGR‐1238030; ADBL, LMM, and EAA) MCA-PGR: genetic and genomic approaches to understand and improve maize responses to ozone, National Institute of General Medical Sciences R01GM128193 (LMM), National Cancer Institute R03CA222444 (AC, LMM), United States Department of Agriculture SoyFACE Global Change Research Project Number 5012-21000-030-17-S.

11 pag, 6 figs. Coordinates for the model of SrrB DHp-CA region solved by X-ray crystallography have been deposited in the Protein Data Bank, https://www.rcsb.org/ (ID code 6PAJ). This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1921307117/-/DCSupplemental., Staphylococcus aureus infections can lead to diseases that range from localized skin abscess to life-threatening toxic shock syndrome. The SrrAB two-component system (TCS) is a global regulator of S. aureus virulence and critical for survival under environmental conditions such as hypoxic, oxidative, and nitrosative stress found at sites of infection. Despite the critical role of SrrAB in S. aureus pathogenicity, the mechanism by which the SrrAB TCS senses and responds to these environmental signals remains unknown. Bioinformatics analysis showed that the SrrB histidine kinase contains several domains, including an extracellular Cache domain and a cytoplasmic HAMP-PAS-DHp-CA region. Here, we show that the PAS domain regulates both kinase and phosphatase enzyme activity of SrrB and present the structure of the DHp-CA catalytic core. Importantly, this structure shows a unique intramolecular cysteine disulfide bond in the ATP-binding domain that significantly affects autophosphorylation kinetics. In vitro data show that the redox state of the disulfide bond affects S. aureus biofilm formation and toxic shock syndrome toxin-1 production. Moreover, with the use of the rabbit infective endocarditis model, we demonstrate that the disulfide bond is a critical regulatory element of SrrB function during S. aureus infection. Our data support a model whereby the disulfide bond and PAS domain of SrrB sense and respond to the cellular redox environment to regulate S. aureus survival and pathogenesis., This work was supported by funding from the National Institutes of Health (NIH) and National Institute of Allergy and Infectious Diseases (NIAID) to E.J.F. and P.M.S. (NIAID Grant AI135305). J.M.B. was funded by the NIH (NIAID Grant AI139100-01) and US Department of Agriculture Multistate Reseach Fund (Project NE−1028). W.S.-P. was supported by NIH (NIAID Grant AI134692-03). The J.K.M. lab was supported by the Canadian Institutes of Health Research (Grant PJT-166050). A.M. was supported by grant BIO2016-78571-P from the Ministerio de Economia y Competitividad (Spain).

Funder: Howard Hughes Medical Institute, Funder: National Science Foundation; Grant(s): DBI:IIBR:CAREER #1943371, 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 towards 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.

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., Alice Casiraghi benefited from an Erasmus+ scholarship during the year 2018-2019, to do her Master thesis at the University of Valencia. The investigation in Spain was conducted in the context of Project CGL2015-68188-P, funded by “Ministerio de Economia, Industria y Competitividad” (MIMECO) of Spain. We thank Nicholas Padowski and Kelton Welch for sampling as well as funding by the University of Minnesota Rapid Agricultural Response Fund, the University of Minnesota Agricultural Experiment Station, the Minnesota Invasive Terrestrial Plant and Pest Center, the Minnesota Soybean Research and Promotion Council and the U.S. Dept. of Agriculture Sustainable Agriculture Research and Education program.

Coffee by-products contain bioactive compounds that have been shown to have the capacity to modulate human metabolism. The goal of this study was to investigate the effects of the main bioactive compounds in coffee by-products and two aqueous extracts from the coffee husk and silverskin on the activation of fibroblast growth factor 21 (FGF21) signaling and the subsequent regulation of mitochondrial bioenergetics and lipid and glucose metabolism. HepG2 cells treated with palmitic acid (PA) were used in a non-alcoholic fatty liver disease (NAFLD) cell model. The bioactive compounds from coffee by-products (50 μmol L−1) and the aqueous extracts from the coffee silverskin and coffee husk (100 μg mL−1) increased ERK1/2 phosphorylation and the secretion of FGF21 (1.3 to 1.9-fold). Coffee by-products' bioactive compounds counteracted inflammation and PA-triggered lipotoxicity. Oxidative stress markers (ROS, mitochondrial superoxide, and NADPH oxidase) and the activity of antioxidant enzymes (superoxide dismutase and catalase) were modulated through the activation of Nrf2 signaling. Mitochondrial bioenergetics were regulated by enhancing respiration and ATP production via PGC-1α, and the expression of oxidative phosphorylation complexes increased. Coffee by-products' bioactive compounds decreased lipid accumulation (23–41%) and fatty acid synthase activity (32–65%) and triggered carnitine palmitoyltransferase-1 activity (1.3 to 1.7-fold) by activating AMPK and SREBP-1c pathways. The GLUT2 expression and glucose uptake were increased (58–111%), followed by a promoted glucokinase activity (55–122%), while glucose production and phosphoenolpyruvate carboxykinase activity were reduced due to IRS-1/Akt1 regulation. The bioactive compounds from coffee by-products, primarily chlorogenic and protocatechuic acids, could regulate hepatic mitochondrial function and lipid and glucose metabolism by activating FGF21 and related signaling cascades., This research was funded by the USDA–NIFA–HATCH project (1014457), by the COCARDIOLAC project from the Spanish Ministry of Science and Innovation (RTI 2018-097504-B-I00), and the Excellence Line for University Teaching Staff within the Multiannual Agreement between the Community of Madrid and the UAM (2019–2023). MR-H. received funding from the Ministry of Universities for his predoctoral fellowship (FPU15/04238) and the support for an international research stay at the University of Illinois, Urbana-Champaign (EST18/0064).

This article belongs to the Special Issue Antioxidant Foods and Cardiometabolic Health., The cocoa shell is a by-product that may be revalorized as a source of bioactive compounds to prevent chronic cardiometabolic diseases. This study aimed to investigate the phytochemicals from the cocoa shell as targeted compounds for activating fibroblast growth factor 21 (FGF21) signaling and regulating non-alcoholic fatty liver disease (NAFLD)-related biomarkers linked to oxidative stress, mitochondrial function, and metabolism in hepatocytes. HepG2 cells treated with palmitic acid (PA, 500 µmol L−1) were used in an NAFLD cell model. Phytochemicals from the cocoa shell (50 µmol L−1) and an aqueous extract (CAE, 100 µg mL−1) enhanced ERK1/2 phosphorylation (1.7- to 3.3-fold) and FGF21 release (1.4- to 3.4-fold) via PPARα activation. Oxidative stress markers were reduced though Nrf-2 regulation. Mitochondrial function (mitochondrial respiration and ATP production) was protected by the PGC-1α pathway modulation. Cocoa shell phytochemicals reduced lipid accumulation (53–115%) and fatty acid synthase activity (59–93%) and prompted CPT-1 activity. Glucose uptake and glucokinase activity were enhanced, whereas glucose production and phosphoenolpyruvate carboxykinase activity were diminished. The increase in the phosphorylation of the insulin receptor, AKT, AMPKα, mTOR, and ERK1/2 conduced to the regulation of hepatic mitochondrial function and energy metabolism. For the first time, the cocoa shell phytochemicals are proved to modulate FGF21 signaling. Results demonstrate the in vitro preventive effect of the phytochemicals from the cocoa shell on NAFLD., This research was funded by the USDA–NIFA–HATCH project to E.G.d.M. (1014457), by the COCARDIOLAC project from the Spanish Ministry of Science and Innovation (RTI 2018-097504-B-I00), and the Excellence Line for University Teaching Staff within the Multiannual Agreement between the Community of Madrid and the UAM (2019–2023). M.R.H. received funding from the Ministry of Universities for his predoctoral fellowship (FPU15/04238) and Margarita Salas Contract (CA1/RSUE/2021-00656) and the support for an international research stay at the University of Illinois, Urbana–Champaign (EST18/0064).

This article belongs to the Special Issue Research on Tropical Food Crop Genomics., 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., This research was supported by the Dole Nutrition Institute at Dole Food Company Inc., and M.I. and J.C. were also supported by the United States Department of Agriculture National Institute of Food and Agriculture, Hatch project 1008691.

29 Pags.- 6 Figs. © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license., Dehydration proteins (dehydrins, DHNs) confer tolerance to water-stress deficit in plants. We performed a comparative genomics and evolutionary study of DHN genes in four model Brachypodium grass species. Due to limited knowledge on dehydrin expression under water deprivation stress in Brachypodium, we also performed a drought-induced gene expression analysis in 32 ecotypes of the genus’ flagship species B. distachyon showing different hydric requirements. Genomic sequence analysis detected 10 types of dehydrin genes (Bdhn) across the Brachypodium species. Domain and conserved motif contents of peptides encoded by Bdhn genes revealed eight protein architectures. Bdhn genes were spread across several chromosomes. Selection analysis indicated that all the Bdhn genes were constrained by purifying selection. Three upstream cis-regulatory motifs (BES1, MYB124, ZAT) were detected in several Bdhn genes. Gene expression analysis demonstrated that only four Bdhn1-Bdhn2, Bdhn3, and Bdhn7 genes, orthologs of wheat, barley, rice, sorghum, and maize genes, were expressed in mature leaves of B. distachyon and that all of them were more highly expressed in plants under drought conditions. Brachypodium dehydrin expression was significantly correlated with drought-response phenotypic traits (plant biomass, leaf carbon and proline contents and water use efficiency increases, and leaf water and nitrogen content decreases) being more pronounced in drought-tolerant ecotypes. Our results indicate that dehydrin type and regulation could be a key factor determining the acquisition of water-stress tolerance in grasses., This research was funded by Spanish Ministry of Science and Innovation grant number PID2019-108195GB-I00, European Social Fund/Spanish Aragón Government grant number A01-20R, Spanish Junta de Andalucía grant number P18-RT-992, USDA grant number NIFA-2011-67012- 30663. MD was funded by a Spanish Mineco FPI PhD fellowship. BCM was funded by Spanish Fundación ARAID.

Cranberries (Vaccinium macrocarpon) are full of polyphenols, which display various health benefits. Most studies have focused on extractable polyphenols (EPs) rather than non-extractable polyphenols (NEPs) but NEPs may possess important biological functions. The objective of this work was to characterize EP and NEP fractions from whole cranberries and determine their potential as anti-inflammation and anti-colon-cancer agents. Our results showed that of the identified polyphenols, anthocyanins were the major ones in the cranberry EP fraction, while phenolic acids were most abundant in the NEP fraction. The oxygen radical absorbance capacity (ORAC) of the NEPs was significantly higher than that of the EPs. Both the EPs and NEPs showed anti-inflammatory effects in inhibiting LPS-induced production of nitric oxide in macrophages. At the concentrations tested, the NEPs showed significantly higher inhibition of the production of nitric oxide in macrophages than the EPs, which was accompanied by decreased expression of inducible nitric oxide synthase (iNOS) and increased expression of HO-1. EP and NEP samples showed anti-cancer capacities in HCT116 cells. And the NEPs showed stronger inhibitory effects on the viability and colony formation capacity of human colon cancer HCT116 cells than the EPs. In a flow cytometry analysis, the NEPs caused cell cycle arrest at the G0/G1 phase and induced significant cellular apoptosis in colon cancer cells. Overall, our results suggested that both the EP and NEP fractions from cranberries were bioactive, and importantly, the NEP fraction showed promising anti-inflammation and anti-colon-cancer potential., This work was partly supported by U.S. Department of Agriculture (NIFA 2019-67017-29249), Leo and Anne Albert Charitable Trust, UMass Cranberry Health Research Center/UMass President's S&T Initiative.

15 Pags.- 9 Figs.- 2 Tabls., We analyzed the relationships between meteorological drought and hydrological drought using very dense and diverse network of gauged natural drainage basins across the conterminous U.S. Specifically, this work utilized a dataset of 289 gauging stations, covering the period 1940–2013. Drainage basins were obtained for each gauging station using a digital terrain model. In addition to meteorological data (e.g., precipitation, air temperature and the atmospheric evaporative demand), we obtained a number of topographic, soil and remote sensing variables for each defined drainage basin. A hydrological drought index (the Standardized Streamflow Index; SSI) was computed for each basin and linked to the Standardized Precipitation Evapotranspiration Index (SPEI), which was used as a metric of climatic drought severity. The relationships between different SPEI time-scales and their corresponding SSI were assessed by means of a Pearson correlation coefficient. Also, the general patterns of response of hydrological droughts to climatic droughts were identified using a principal component analysis. Overall, results demonstrate a positive response of SSI to SPEI at shorter time-scales, with strong seasonality and clear spatial differences. We also assessed the role of some climatic and environmental factors in explaining these different responses using a predictive discriminant analysis. Results indicate that elevation and vegetation coverage are the main drivers of the diverse response of SSI to SPEI time-scales. Similar analyses were made for three sub-periods (1940–1964, 1965–1989 and 1989–2013), whose results confirm considerable differences in the response of SSI to SPEI over the past eighty years., This work was supported by the research project I-Link1001 (Validation of climate drought indices for multi-sectorial applications in North America and Europe under a global warming scenario) financed by CSIC, PCIN-2015-220 and CGL2014-52135-C03-01 financed by the Spanish Commission of Science and Technology and FEDER, IMDROFLOOD financed by the Water Works 2014 co-funded call of the European Commission and INDECIS, which is part of ERA4CS, an ERA-NET initiated by JPI Climate, and funded by FORMAS (SE), DLR (DE), BMWFW (AT), IFD (DK), MINECO (ES), ANR (FR) with co-funding by the European Union (Grant 690462). Marina Peña-Gallardo was granted by the Spanish Ministry of Economy and Competitiveness. Miquel Tomas-Burguera was supported by a doctoral grant by the Spanish Ministry of Education, Culture and Sport. Jamie Hannaford was supported by the Belmont Forum project ‘DrIVER’, NERC Grant Number (grant NE/L010038/1). Marco Maneta acknowledges support from the USDA NIFA grant 2016-67026-25067.

Due to their effects on reducing recombination, chromosomal inversions may play an important role in speciation by establishing and/or maintaining linked blocks of genes causing reproductive isolation (RI) between populations. This view fits empirical data indicating that inversions typically harbor loci involved in RI. However, previous computer simulations of infinite populations with two to four loci involved in RI implied that, even with gene flux as low as 10–8 per gamete, per generation between alternative arrangements, inversions may not have large, qualitative advantages over collinear regions in maintaining population differentiation after secondary contact. Here, we report that finite population sizes can help counteract the homogenizing consequences of gene flux, especially when several fitness-related loci reside within the inversion. In these cases, the persistence time of differentiation after secondary contact can be similar to when gene flux is absent and notably longer than the persistence time without inversions. Thus, despite gene flux, population differentiation may be maintained for up to 100,000 generations, during which time new incompatibilities and/or local adaptations might accumulate and facilitate progress toward speciation. How often these conditions are met in nature remains to be determined., This study was supported by the European Regional Development Fund (FCOMP-01-0124-FEDER-014272), FCT – Foundation for Science and Technology (PTDC/BIA-EVF/113805/2009), Ministerio de Ciencia e Innovación, Spain (PGC2018-101927-B-I00, MINECO/FEDER, UE), by the Spanish National Institute of Bioinformatics (PT17/0009/0020), and by “Unidad de Excelencia María de Maeztu,” funded by the MINECO (ref: MDM-2014-0370). MR was funded by the Hasselblad Foundation (Grant for Female Scientists), European Research Council and the Swedish Research Councils VR and Formas (Linnaeus grant to the Centre for Marine Evolutionary Biology), and by an additional grant from Formas (to MR; grant number 2019-00882). JLF was funded by support from the National Science Foundation and United States Department of Agriculture NIFA program. RF was funded by FCT (SFRH/BPD/89313/2012) and by the European Union's Horizon 2020 research and innovation program, under the Marie Sklodowska-Curie grant agreement number 706376; and is currently funded by FEDER through the Operational Competitiveness Factors Program COMPETE and by National Funds through the FCT project “Hybrabbid” (PTDC/BIA-EVL/30628/2017 and POCI-01-0145-FEDER-030628). The simulations were performed on resources at Chalmers Centre for Computational Science and Engineering (C3SE), and at National Supercomputer Centre at Linköping University (NSC) provided by the Swedish National Infrastructure for Computing (SNIC), partially funded by the Swedish Research Council through grant agreement no. 2018–05973.

[Background]: Energy landscapes provide an approach to the mechanistic basis of spatial ecology and decision-making in animals. This is based on the quantification of the variation in the energy costs of movements through agiven environment, as well as how these costs vary in time and for different animal populations. Organisms asdiverse as fish, mammals, and birds will move in areas of the energy landscape that result in minimised costs andmaximised energy gain. Recently, energy landscapes have been used to link energy gain and variable energy costsof foraging to breeding success, revealing their potential use for understanding demographic changes., [Methods]: Using GPS-temperature-depth and tri-axial accelerometer loggers, stable isotope and molecular analysesof the diet, and leucocyte counts, we studied the response of gentoo (Pygoscelis papua) and chinstrap (Pygoscelisantarcticus) penguins to different energy landscapes and resources. We compared species and gentoo penguinpopulations with contrasting population trends., [Results]: Between populations, gentoo penguins from Livingston Island (Antarctica), a site with positive populationtrends, foraged in energy landscape sectors that implied lower foraging costs per energy gained compared withthose around New Island (Falkland/Malvinas Islands; sub-Antarctic), a breeding site with fluctuating energy costs offoraging, breeding success and populations. Between species, chinstrap penguins foraged in sectors of the energylandscape with lower foraging costs per bottom time, a proxy for energy gain. They also showed lowerphysiological stress, as revealed by leucocyte counts, and higher breeding success than gentoo penguins. In termsof diet, we found a flexible foraging ecology in gentoo penguins but a narrow foraging niche for chinstraps., [Conclusions]: The lower foraging costs incurred by the gentoo penguins from Livingston, may favour a higherbreeding success that would explain the species’positive population trend in the Antarctic Peninsula. The lowerforaging costs in chinstrap penguins may also explain their higher breeding success, compared to gentoos fromAntarctica but not their negative population trend. Altogether, our results suggest a link between energylandscapes and breeding success mediated by the physiological condition., JFM work was supported by the Deutsche Forschungsgemeinschaft (DFG,Germany) in the framework of the priority programme “Antarctic Research with comparative investigations in Arctic ice areas” SPP 1158 by thefollowing grant MA 2574/6–1. Martin Wikelski (Max Planck Institute of Animal Behaviour, Radolfzell, Germany) provided the earth & Ocean GPS-TD data loggers. AB was supported by the grant CTM2015–64720-R from the Spanish Agency of Research (Spain). Diet analyses from New Island were funded by a Research Grant (NBAF967) for lab work at the Biomolecular Analysis Facility -Sheffield (NBAF-S), Centre for Ecology & Hydrology, Natural Environment Research Council (NERC), U.K. (to WOCS, RM and JFM). Funding for the operation and maintenance of the local Galaxy server is provided by the German Federal Ministry of Education and Research (BMBF) project “Bielefeld-GießenCenter for Microbial Bioinformatics-BiGi” (grant 031A533) within the German Network for Bioinformatics Infrastructure (de. NBI). Thanks to the CPER (Contrat de Projet Etat-Région) and the FEDER (Fonds Européen de Développement Régional) for funding the IRMS of LIENSs laboratory. The IUF (Institut Universitaire de France) is acknowledged for its support to PB as a Senior Member. Open Access funding enabled and organized by Projekt DEAL.

[EN] The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a `SyntenyViewer¿ to view genome synteny between different cucurbit species and an `RNA-Seq¿ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system., USDA National Institute of Food and Agriculture Specialty Crop Research Initiative [2015-51181-24285]; US-Israel Binational Agricultural Research and Development Fund [IS-3333-02, IS-3877-06CR and IS-4223-09C]; USDA Agricultural Research Service, and by SNC Laboratoire ASL, de Ruiter Seeds B.V., Enza Zaden B.V., Gautier Semences S.A., Nunhems B.V., Rijk Zwaan B.V., Sakata Seed Inc, Semillas Fito S.A., Seminis Vegetable Seeds Inc, Syngenta Seeds B.V., Takii and Company Ltd, Vilmorin and Cie S.A. and Zeraim Gedera Ltd, all of them as part of the support to the International Cucurbit Genomics Initiative (ICuGI). Funding for open access charge: USDA National Institute of Food and Agriculture.

Species assemblages often have a non-random nested organization, which in vertebrate scavenger (carrion-consuming) assemblages is thought to be driven by facilitation in competitive environments. However, not all scavenger species play the same role in maintaining assemblage structure, as some species are obligate scavengers (i.e., vultures) and others are facultative, scavenging opportunistically. We used a database with 177 vertebrate scavenger species from 53 assemblages in 22 countries across five continents to identify which functional traits of scavenger species are key to maintaining the scavenging network structure. We used network analyses to relate ten traits hypothesized to affect assemblage structure with the “role” of each species in the scavenging assemblage in which it appeared. We characterized the role of a species in terms of both the proportion of monitored carcasses on which that species scavenged, or scavenging breadth (i.e., the species “normalized degree”), and the role of that species in the nested structure of the assemblage (i.e., the species “paired nested degree”), therefore identifying possible facilitative interactions among species. We found that species with high olfactory acuity, social foragers, and obligate scavengers had the widest scavenging breadth. We also found that social foragers had a large paired nested degree in scavenger assemblages, probably because their presence is easier to detect by other species to signal carcass occurrence. Our study highlights differences in the functional roles of scavenger species and can be used to identify key species for targeted conservation to maintain the ecological function of scavenger assemblages., ESG, ZMR, JMB and LNA were supported by Generalitat Valenciana (SEJI/2018/024, APOSTD/2019/016, CIDEGENT/2020/030 and ACIF/2019/056, respectively), JMB, JMPG and CGC by Juan de la Cierva contracts (MEC; IJCI-2017-32149, FJCI-2015-25632 and IJC2018-036642-I, respectively), ACA by the Govern de les Illes Balears (PD/039/2017) and ESG and MM by Ramón y Cajal contracts (MEC; RYC-2019-027216-I, RYC-2015-19231). EA was supported by La Caixa-Severo Ochoa International PhD Program 2015. NS was partly supported by the National Science Centre in Poland (2013/08/M/NZ9/00469 and 2016/22/Z/NZ8/00). MK and KJ were supported by the Slovenian Research Agency (P4-0059). Contributions of HG, KLT, EFA, OER, TLD, and JCB were partially supported through funding from U.S. Department of Agriculture and the U.S. Department of Energy under (DE-EM0004391) to the University of Georgia Research Foundation. HG was also supported by the Institute of Environmental Radioactivity at Fukushima University. ALB and JDA were partially supported by Queens College and the Graduate Center at the City University of New York. JDA is currently supported by a Ramón y Cajal contract (RYC-2017-22783). ERB and EF were supported by the USA National Science Foundation Graduate Research Fellowship (1256065). CK completed study with support from Hawk Mountain Sanctuary, The Peregrine Fund, and via Pompeo M. Maresi Memorial Fund via Princeton University. JAS and CCW were supported by the USA National Science Foundation #1255913, the American Association for University Women, and the Gordon and Betty Moore Foundation. HUW acknowledges funding from the California Department of Fish & Wildlife (P0880013). PLP was supported by the Rufford Foundation and University of Wisconsin-Madison. JB and JdT thank the Percy Sladen Memorial Fund and Mr Rodney Fuhr. Several authors were funded by funds from the MEC (CGL2012-40013-C02-01/02, CGL2015-66966-C2-1-R, CGL2015-66966-C2-1-R2, CGL2017-89905-R, RTI2018-099609-B-C21 and RTI2018-099609-B-C22) and from the Junta de Andalucía (RNM-1925). POV was supported by a research contract by the University of Lleida. EES and TMN were funded and supported by Australian Geographic, Bush Heritage Australia, Australian Academy of Sciences, Ecological Society of Australia, NSW Office of Environment and Heritage, NESP Threatened Species Recovery Hub, Emirates Wolgan Valley One and Only Resort. EP, YA, MS and UY completed study under research permit by The Republic of Turkey Ministry of Agriculture and Forestry. SAL thanks PICT (BID) 0725/2014, and IAATE. ALB and JDA would like to thank the Edmund Niles Huyck Preserve, Lyme Adirondack Forest Company, and LandVest Timberland.

Agricultural Research Service (ARS) held a joint animal health research planning workshop with the National Institute of Food and Agriculture (NIFA)., Scales are linear combinations of variables with coefficients that add up to zero and have a similar meaning to "contrast" in the analysis of variance. Scales are necessary in order to incorporate genomic information into relationship matrices for genomic selection. Statistical and biological parameterizations using scales under different assumptions have been proposed to construct alternative genomic relationship matrices. Except for the natural and orthogonal interactions approach (NOIA) method, current methods to construct relationship matrices assume Hardy-Weinberg equilibrium (HWE). The objective of this paper is to apply vector algebra to center and scale relationship matrices under non-HWE conditions, including orthogonalization by the Gram-Schmidt process., Generation of these data was supported by the USDA ARS and NIFA award 2013-68004-20362. WMR and LGR acknowledge financial support from (1) the Salvador de Madariaga program of the Ministry of Education of Spain, (2) SusAn ERA‐Net project “Sustainability of pig production through improved feed efficiency”, an ERA‐Net co-funded under the European Union’s Horizon 2020 research and innovation programme, under Grant Agreement no 696231, and (3) project AGL2016‐75942‐R, “Caracterización molecular de la eficiencia alimentaria y de los caracteres reproductivos en cerdo Ibérico.”, 18 Pág. Departamento de ​Mejora Genética Animal

Lentil is a staple in many diets around the world and growing in popularity as a quick-cooking, nutritious, plant-based source of protein in the human diet. Lentil varieties are usually grown close to where they were bred. Future climate change scenarios will result in increased temperatures and shifts in lentil crop production areas, necessitating expanded breeding efforts. We show how we can use a daylength and temperature model to identify varieties most likely to succeed in these new environments, expand genetic diversity, and give plant breeders additional knowledge and tools to help mitigate these changes for lentil producers., This research was conducted as part of the ‘Application of Genomics to Innovation in the Lentil Economy (AGILE)' project funded by Genome Canada and managed by Genome Prairie. We are grateful for the matching financial support from the Saskatchewan Pulse Growers, Western Grains Research Foundation, the Government of Saskatchewan, and the University of Saskatchewan. We acknowledge the support from our international partners: University of Basilicata (UNIBAS) in Italy; Institute for Sustainable Agriculture (IAS) in Spain; Center for Agriculture Research in the Dry Areas (ICARDA) in Morocco, India and Bangladesh; Local Initiatives for Biodiversity, Research and Development (LI-BIRD) in Nepal; and United States Department of Agriculture (USDA CRIS Project 5348-21000-017-00D) in the USA, for conducting field experiments in their respective countries.

Bacterial wilt caused by the soil-borne pathogen Ralstonia solancearum is economically devastating, with no effective methods to fight the disease. This pathogen invades plants through their roots and colonizes their xylem, clogging the vasculature and causing rapid wilting. Key to preventing colonization are the early defense responses triggered in the host’s root upon infection, which remain mostly unknown. Here, we have taken advantage of a high-throughput in vitro infection system to screen natural variability associated with the root growth inhibition phenotype caused by R. solanacearum in Arabidopsis during the first hours of infection. To analyze the genetic determinants of this trait, we have performed a genome-wide association study, identifying allelic variation at several loci related to cytokinin metabolism, including genes responsible for biosynthesis and degradation of cytokinin. Further, our data clearly demonstrate that cytokinin signaling is induced early during the infection process and cytokinin contributes to immunity against R. solanacearum. This study highlights a new role for cytokinin in root immunity, paving the way for future research that will help in understanding the mechanisms underpinning root defenses., This work was supported by the Spanish Ministry of Economy and Competitiveness grant nos RyC 2014-16158, AGL2016-78002-R, and PID2019-108595RB-I00/AEI/10.13039/501100011033 to NSC, and through the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ (SEV-2015-0533). We also acknowledge financial support from the CERCA Programme/Generalitat de Catalunya, from the Austrian Academy of Sciences through the Gregor Mendel Institute (WB and SBS) and from funding for CTA and HMB by the United States Department of Agriculture (USDA) grant no. COL00781., We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).

15 Pags.- 5 Figs.- 3 TAbls.- Supp. Mat. Copyright Owner, the Authors. Under LicenceCC BY 4.0., One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known and 10 novel QTL/genes were identified for LTT—assessed as winter survival in 10 field tests and mapped using a GWAS meta-analysis. FR-H1, FR-H2, and FR-H3 were major drivers of LTT, and candidate genes were identified for FR-H3. The principal determinants of vernalization sensitivity were VRN-H1, VRN-H2, and PPD-H1. VRN-H2 deletions conferred insensitive or intermediate sensitivity to vernalization. A subset of accessions with maximum LTT were identified as a resource for allele mining and further characterization. Facultative types comprised a small portion of the GWAS panel but may be useful for developing germplasm with this growth habit., Support was provided by the USDA-NIFA TCAP Project no. 2011-68002-30029.

Understanding the distribution of biodiversity across the Earth is one of the most challenging questions in biology. Much research has been directed at explaining the species latitudinal pattern showing that communities are richer in tropical areas; however, despite decades of research, a general consensus has not yet emerged. In addition, global biodiversity patterns are being rapidly altered by human activities. Here, we aim to describe large-scale patterns of species richness and diversity in terrestrial vertebrate scavenger (carrion-consuming) assemblages, which provide key ecosystem functions and services. We used a worldwide dataset comprising 43 sites, where vertebrate scavenger assemblages were identified using 2,485 carcasses monitored between 1991 and 2018. First, we evaluated how scavenger richness (number of species) and diversity (Shannon diversity index) varied among seasons (cold vs. warm, wet vs. dry). Then, we studied the potential effects of human impact and a set of macroecological variables related to climatic conditions on the scavenger assemblages. Vertebrate scavenger richness ranged from species-poor to species rich assemblages (4–30 species). Both scavenger richness and diversity also showed some seasonal variation. However, in general, climatic variables did not drive latitudinal patterns, as scavenger richness and diversity were not affected by temperature or rainfall. Rainfall seasonality slightly increased the number of species in the community, but its effect was weak. Instead, the human impact index included in our study was the main predictor of scavenger richness. Scavenger assemblages in highly human-impacted areas sustained the smallest number of scavenger species, suggesting human activity may be overriding other macroecological processes in shaping scavenger communities. Our results highlight the effect of human impact at a global scale. As species-rich assemblages tend to be more functional, we warn about possible reductions in ecosystem functions and the services provided by scavengers in human-dominated landscapes in the Anthropocene., SG, JMPG, and ACA were supported by Juan de la Cierva contracts (Ministerio de Economía y Competitividad, MEC; IJCI‐2015‐24947, FJCI‐2015‐25632, and IJCI‐2014‐20744, respectively). ESG was also supported by Generalitat Valenciana (SEJI/2018/024), ACA by the Govern de les Illes Balears (PD/039/2017), and MM by a Ramón y Cajal contract (MEC; RYC‐2015‐19231). EA was supported by La Caixa‐Severo Ochoa International PhD Program 2015. NS was partly supported by the National Science Centre in Poland (2013/08/M/NZ9/00469). SAL thanks PICT (BID) 0725/2014. MK and KJ were supported by the Slovenian Research Agency (P4‐0059). Contributions of KT and JCB were partially supported through funding from U.S. Department of Agriculture, the U.S. Department of Energy under (DE‐EM0004391) to the University of Georgia Research Foundation. EB and EF were supported by the USA National Science Foundation. CK completed study under research permit NCST/5/002/R/448 with support from Hawk Mountain Sanctuary, The Peregrine Fund, and via Pompeo M. Maresi Memorial Fund via Princeton University. JAS and CCW were supported by the USA National Science Foundation #1255913 and the Gordon and Betty Moore Foundation. Several authors were funded by funds from the MEC (CGL2012‐40013‐C02‐01/02, CGL2015‐66966‐C2‐1‐R and CGL2017‐89905‐R) and from the Junta de Andalucía (RNM‐1925).

Transmission is a crucial part of a viral life cycle and transmission mode can have an important impact on virus biology. It was demonstrated that transmission mode can influence the virulence and evolution of a virus; however, few empirical data are available to describe the direct underlying changes in virus population structure dynamics within the host. Potato virus Y (PVY) is an RNA virus and one of the most damaging pathogens of potato. It comprises several genetically variable strains that are transmitted between plants via different transmission modes. To investigate how transmission modes affect the within-plant viral population structure, we have used a deep sequencing approach to examine the changes in the genetic structure of populations (in leaves and tubers) of three PVY strains after successive passages by horizontal (aphid and mechanical) and vertical (via tubers) transmission modes. Nucleotide diversities of viral populations were significantly influenced by transmission modes; lineages transmitted by aphids were the least diverse, whereas lineages transmitted by tubers were the most diverse. Differences in nucleotide diversities of viral populations between leaves and tubers were transmission mode-dependent, with higher diversities in tubers than in leaves for aphid and mechanically transmitted lineages. Furthermore, aphid and tuber transmissions were shown to impose stronger genetic bottlenecks than mechanical transmission. To better understand the structure of virus populations within the host, transmission mode, movement of the virus within the host, and the number of replication cycles after transmission event need to be considered. Collectively, our results suggest a significant impact of virus transmission modes on the within-plant diversity of virus populations and provide quantitative fundamental data for understanding how transmission can shape virus diversity in the natural ecosystems, where different transmission modes are expected to affect virus population structure and consequently its evolution., This work was supported by grants to SMG and WLD from the US Department of Agriculture Specialty (USDA) Crop Research Initiative (2009-51181-05894 and 2014-51181-22373), the UK Biotechnology and Biological Sciences Research Council (BBSRC) (grant #BB/L011840/1), as part of the joint USDA-National Science Foundation-National Institutes of Health BBSRC Ecology and Evolution of Infectious Diseases program, and the USDA National Institute of Food and Agriculture (Hatch project number 1017940). WLD was partially supported by a State University of New York (SUNY) Graduate Diversity Fellowship and by a 2014/2015 National Potato Council scholarship. SFE was supported by Spain Ministerio de Ciencia e Innovacion – FEDER grant BFU2015-65037-P and Generalitat Valenciana grant PROMETEOII/2014/012. DK was financially supported by the Slovenian Research Agency (research core funding No. P4-0407 and research project No. Z1-9158).

Ralstonia solanacearum is a bacterial vascular pathogen causing devastating bacterial wilt. In the field, resistance against this pathogen is quantitative and is available for breeders only in tomato and eggplant. To understand the basis of resistance to R. solanacearum in tomato, we investigated the spatio-temporal dynamics of bacterial colonization using non-invasive live monitoring techniques coupled to grafting of susceptible and resistant varieties. We found four ‘bottlenecks’ that limit the bacterium in resistant tomato: root colonization, vertical movement from roots to shoots, circular vascular bundle invasion, and radial apoplastic spread in the cortex. Radial invasion of cortical extracellular spaces occurred mostly at late disease stages but was observed throughout plant infection. This study shows that resistance is expressed in both root and shoot tissues, and highlights the importance of structural constraints to bacterial spread as a resistance mechanism. It also shows that R. solanacearum is not only a vascular pathogen but spreads out of the xylem, occupying the plant apoplast niche. Our work will help elucidate the complex genetic determinants of resistance, setting the foundations to decipher the molecular mechanisms that limit pathogen colonization, which may provide new precision tools to fight bacterial wilt in the field., This work was funded by projects AGL2016-78002-R to NSC and MV, and RyC 2014–16158 to NSC (Spanish Ministry of Economy and Competitiveness). JPK was supported partially by the National Institute of Food and Agriculture of the United States Department of Agriculture grant nos 2011-51181-30963 and 2016-51181-25404 to FJL and DRP, and a Monsanto Graduate Fellowship award through North Carolina State University. AK was supported by a Netaji Subhas international fellowship from the Indian Council of Agricultural Research. The authors acknowledge financial support from the Severo Ochoa Program for Centers of Excellence in R&D (SEV‐2015‐0533) and the CERCA Program from the Catalan Government (Generalitat de Catalunya).

10 páginas.- 6 figuras.- 3 tablas.- 72 referencias.- The Supplemental material section includes AZ and PE molecular structures (Fig. S1) and adsorption-desorption coefficients (Tables S1 and S2). Supplementary data to this article can be found online at https://doi.org/10.1016/j.scitotenv.2019.135682, The application of biochar as a soil amendment can increase concentrations of soil organic matter, especially water-extractable organic substances. Due to their mobility and reactivity, more studies are needed to address the potential impact of biochar water-extractable substances (BWES) on the sorption of herbicides in agricultural soils that are periodically flooded. Two paddy soils (100 and 700 years of paddy soil development), unamended or amended with raw (BC) or washed biochar (BCW), were used to test the influence of BWES on the sorption behavior of the herbicides azimsulfuron (AZ) and penoxsulam (PE). The adsorption of AZ to biochar was much stronger than that to the soils, and it was adsorbed to a much larger extent to BC than to BCW. The depletion of polar groups in the BWES from the washed biochar reduced AZ adsorption but had no effect on PE adsorption. The adsorption of AZ increased when the younger soil (P100) was amended with BC and decreased when it was amended with BCW. In P700, which has lower dissolved organic carbon (DOC) content than P100, the adsorption of AZ increased regardless of whether biochar was raw or washed. The adsorption of PE slightly decreased when P100 was amended with BC or BCW and slightly increased when P700 was amended with BC or BCW. In order to evaluate compositional differences in the biochar and BWES before and after the washing treatment, we performed solid-state 13C NMR spectroscopy of BC and BCW, and high resolution mass spectrometry of BWES. Our observations stress the importance of proper consideration of soil and biochar properties before their incorporation into paddy soils, since biochar may reduce or increase the mobility of AZ and PE depending on soil properties and time of application. © 2019, This research was supported by the Ministry of Economy and Competitiveness ( AGL2016-77821-R and AGL2013-48446-C3-1-R ) and the Autonomous Government of Andalusia ( PAIDI AGR-264 ). The projects were co-financed with European funds (FEDER-FSE PO2007-13). M. García-Jaramillo thanks MEC / FECYT for a doctoral fellowship through AGL2010-21421-CO2-01 project of MICINN and for a mobility fellowship (EEBB-I-14-08137), that made possible this collaboration. This work was also in part supported by the U.S. Department of Agriculture, Agricultural Research Service ( 2072-1410-004 ).

Genomic prediction (GP) is the procedure whereby the genetic merits of untested candidates are predicted using genome wide marker information. Although numerous examples of GP exist in plants and animals, applications to polyploid organisms are still scarce, partly due to limited genome resources and the complexity of this system. Deep learning (DL) techniques comprise a heterogeneous collection of machine learning algorithms that have excelled at many prediction tasks. A potential advantage of DL for GP over standard linear model methods is that DL can potentially take into account all genetic interactions, including dominance and epistasis, which are expected to be of special relevance in most polyploids. In this study, we evaluated the predictive accuracy of linear and DL techniques in two important small fruits or berries: strawberry and blueberry. The two datasets contained a total of 1,358 allopolyploid strawberry (2n=8x=112) and 1,802 autopolyploid blueberry (2n=4x=48) individuals, genotyped for 9,908 and 73,045 single nucleotide polymorphism (SNP) markers, respectively, and phenotyped for five agronomic traits each. DL depends on numerous parameters that influence performance and optimizing hyperparameter values can be a critical step. Here we show that interactions between hyperparameter combinations should be expected and that the number of convolutional filters and regularization in the first layers can have an important effect on model performance. In terms of genomic prediction, we did not find an advantage of DL over linear model methods, except when the epistasis component was important. Linear Bayesian models were better than convolutional neural networks for the full additive architecture, whereas the opposite was observed under strong epistasis. However, by using a parameterization capable of taking into account these non-linear effects, Bayesian linear models can match or exceed the predictive accuracy of DL. A semiautomatic implementation of the DL pipeline is available at https://github.com/lauzingaretti/deepGP/., LZ was supported by a PhD grant from the Ministry of Economy and Science (MINECO, Spain), by the MINECO grant AGL2016-78709-R to MP-E and from the EU through the BFU2016-77236-P (MINECO/AEI/FEDER, EU) and the “Centro de Excelencia Severo Ochoa 2016-2019” award SEV-2015-0533. VW and LO were supported by the US Department of Agriculture/National Institute of Food and Agriculture Specialty Crop Research Initiative (SCRI) project ‘RosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars' under Award Number 2014-51181-22378.

This article belongs to the Special Issue Peptides for Health Benefits 2019., The involvement of cancer stem-like cells (CSC) in the tumor pathogenesis has profound implications for cancer therapy and chemoprevention. Lunasin is a bioactive peptide from soybean and other vegetal sources with proven protective activities against cancer and other chronic diseases. The present study focused on the cytotoxic effect of peptide lunasin in colorectal cancer HCT-116 cells, both the bulk tumor and the CSC subpopulations. Lunasin inhibited the proliferation and the tumorsphere-forming capacity of HCT-116 cells. Flow cytometry results demonstrated that the inhibitory effects were related to apoptosis induction and cell cycle-arrest at G1 phase. Moreover, lunasin caused an increase in the sub-GO/G1 phase of bulk tumor cells, linked to the apoptotic events found. Immunoblotting analysis further showed that lunasin induced apoptosis through activation of caspase-3 and cleavage of PARP, and could modulate cell cycle progress through the cyclin-dependent kinase inhibitor p21. Together, these results provide new evidence on the chemopreventive activity of peptide lunasin on colorectal cancer by modulating both the parental and the tumorsphere-derived subsets of HCT-116 cells., This work has received financial support from Ministry of Economy and Competitiveness (MINECO, Spain) through the project AGL2015-66886-R, and United States Department of Agriculture. SFT is currently funded by the Instituto de Salud Carlos III (Sara Borrell fellowship CD17/00014).

2 .pdf files: File 1. Author's article final version, Post-Print (19 Pags.- 4 Figs.- 2 Tabls.). File 2. Supplementary Materials (3 Figs.- 2 Tabls.- 1 Model Equation)., Aim Previous work demonstrated the global variability of synchrony in tree growth within populations, that is, the covariance of the year‐to‐year variability in growth of individual neighbouring trees. However, there is a lack of knowledge about the causes of this variability and its trajectories through time. Here, we examine whether climate can explain variation in within‐population synchrony (WPS) across space but also through time and we develop models capable of explaining this variation. These models can be applied to the global tree cover under current and future climate change scenarios. Location Global. Time period 1901–2012. Major taxa studied Trees. Methods We estimated WPS values from a global tree‐ring width database consisting of annual growth increment measurements from multiple trees at 3,579 sites. We used generalized linear mixed effects models to infer the drivers of WPS variability and temporal trends of global WPS. We then predicted WPS values across the global extent of tree cover. Finally, we applied our model to predict future WPS based on the RCP 8.5 (2045–2065 period) emission scenario. Results Areas with the highest WPS are characterized by a combination of environments with both high mean annual temperature (>10°C) and low precipitation (, E.T. and M.V. were partially supported by National Science Foundation ‐ Partnership in International Research and Education (OISE‐1743738) and National Science Foundation ‐ Paleo Perspectives on Climate Change (AGS‐1702439). R.S.‐N. is funded by a “Juan de la Cierva” postdoctoral grant FJCI‐2017‐31595. E.T., M.S., R.S.‐N. and M.D.L. are supported by the Government of Aragón through the “Program of research groups” (group H38, “Clima, Agua, Cambio Global y Sistemas Naturales”). A.L. was supported by grant EVA4.0, No. CZ.02.1.01/0.0/0.0/16_019/0000803, financed by OP RDE and by the U.S. Department of Agriculture Forest Service.

The presence of Mycobacterium tuberculosis complex (MTBC) in wild swine, such as in wild boar (Sus scrofa) in Eurasia, is cause for serious concern. Development of accurate, efficient, and noninvasive methods to detect MTBC in wild swine would be highly beneficial to surveillance and disease management efforts in affected populations. Here, we describe the first report of identification of volatile organic compounds (VOC) obtained from the breath and feces of wild boar to distinguish between MTBC-positive and MTBC-negative boar. We analyzed breath and fecal VOC collected from 15 MTBC-positive and 18 MTBC-negative wild boar in Dona&ntilde, a National Park in Southeast Spain. Analyses were divided into three age classes, namely, adults (&gt, 2 years), sub-adults (12&ndash, 24 months), and juveniles (&lt, 12 months). We identified significant compounds by applying the two-tailed statistical t-test for two samples assuming unequal variance, with an &alpha, value of 0.05. One statistically significant VOC was identified in breath samples from adult wild boar and 14 were identified in breath samples from juvenile wild boar. One statistically significant VOC was identified in fecal samples collected from sub-adult wild boar and three were identified in fecal samples from juvenile wild boar. In addition, discriminant function analysis (DFA) was used to build classification models for MTBC prediction in juvenile animals. Using DFA, we were able to distinguish between MTBC-positive juvenile wild boar and MTBC-negative juvenile wild boar using breath VOC or fecal VOC. Based on our results, further research is warranted and should be performed using larger sample sizes, as well as wild boar from various geographic locations, to verify these compounds as biomarkers for MTBC infection in this species. This new approach to detect MTBC infection in free-ranging wild boar potentially comprises a reliable and efficient screening tool for surveillance in animal populations.

7 Pags.- 1 Tabl.- 7 Figs.- Copyright © 2020 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND)., Large-scale continuous crop monitoring systems (CMS) are key to detect and manage agricultural production anomalies. Current CMS exploit meteorological and crop growth models, and satellite imagery, but have underutilized legacy sources of information such as operational crop expert surveys with long and uninterrupted records. We argue that crop expert assessments, despite their subjective and categorical nature, capture the complexities of assessing the “status” of a crop better than any model or remote sensing retrieval. This is because crop rating data naturally encapsulates the broad expert knowledge of many individual surveyors spread throughout the country, constituting a sophisticated network of “people as sensors” that provide consistent and accurate information on crop progress. We analyze data from the US Department of Agriculture (USDA) Crop Progress and Condition (CPC) survey between 1987 and 2019 for four major crops across the US, and show how to transform the original qualitative data into a continuous, probabilistic variable better suited to quantitative analysis. Although the CPC reflects the subjective perception of many surveyors at different locations, the underlying models that describe the reported crop status are statistically robust and maintain similar characteristics across different crops, exhibit long-term stability, and have nation-wide validity. We discuss the origin and interpretation of existing spatial and temporal biases in the survey data. Finally, we propose a quantitative Crop Condition Index based on the CPC survey and demonstrate how this index can be used to monitor crop status and provide earlier and more precise predictions of crop yields than official USDA forecasts released midseason., S.B.’s research is supported by the Spanish Ministry of Science and Innovation (Grant CGL2017-83866-C3-3-R) and Fundación Biodiversidad, Ministry of Ecological Transition (Grant CA_CC_2018). M.P.M.’s support is from the USDA-National Institute of Food and Agriculture (NIFA) (Grant 2016-67026-25067) and the NASA Established Program to Stimulate Competitive Research (EPSCoR) program (Grant 80NSSC18M0025M). This research was made possible thanks to a mobility grant of the Spanish Ministry of Education, Culture, and Sports, within the framework of the “Programa Estatal de Promoción del Talento y su Empleabilidad en I+D+i,” “Salvador de Madariaga” program.

Estuaries are subject to diverse anthropogenic stressors, such as shellfish aquaculture, which involve extensive use of estuarine tidelands. Pacific oyster Crassostrea gigas aquaculture is a century-old practice in US West Coast estuaries that contributes significantly to the regional culture and economy. Native eelgrass Zostera marina also commonly occurs in intertidal areas where oyster aquaculture is practiced. Eelgrass is federally protected in the USA as ‘essential fish habitat’, restricting aquaculture activities within or near eelgrass. To contribute scientific information useful for management decisions, we sought to compare fish habitat use of oyster aquaculture and eelgrass, as well as the edges between these 2 habitats, in Willapa Bay, Washington, USA. Furthermore, given a recent shift towards off-bottom culture methods, in part to protect seagrasses, long-line and on-bottom oyster aquaculture habitats were compared. A combination of direct (underwater video, minnow traps) and indirect (predation tethering units, eelgrass surveys) methods were employed to characterize differences in fish habitat use. Eelgrass density declined within both aquaculture habitats but less so within long-line aquaculture. Most fish species in our study used long-line oyster aquaculture and eelgrass habitats similarly with minimal edge effects, and on-bottom aquaculture was used less than either of the other 2 habitat types. These results are consistent with previously observed positive relationships between fish abundance and vertical habitat structure, but also reveal species-specific behavior; larger mesopredators like Pacific staghorn sculpins were sighted more often in aquaculture than in interior eelgrass habitats., This work was funded in part by2 NOAA NMFS Saltonstall-Kennedy grants (2014/2015NOAA-NMFS-FHQ-2015-2004246 and 2016/2017 NA16NMF4270254), a 2016−2018 Oregon State University Agricultural Research Foundation grant to F.T., and projectfunds of the USDA Agricultural Research Service (CRIS Pro-ject 2072-63000-004-00D).

Diabetes and metabolic syndrome are associated with the typical American high glycemia diet and result in accumulation of high levels of advanced glycation end products (AGEs), particularly upon aging. AGEs form when sugars or their metabolites react with proteins. Associated with a myriad of age‐related diseases, AGEs accumulate in many tissues and are cytotoxic. To date, efforts to limit glycation pharmacologically have failed in human trials. Thus, it is crucial to identify systems that remove AGEs, but such research is scanty. Here, we determined if and how AGEs might be cleared by autophagy. Our in vivo mouse and C. elegans models, in which we altered proteolysis or glycative burden, as well as experiments in five types of cells, revealed more than six criteria indicating that p62‐dependent autophagy is a conserved pathway that plays a critical role in the removal of AGEs. Activation of autophagic removal of AGEs requires p62, and blocking this pathway results in accumulation of AGEs and compromised viability. Deficiency of p62 accelerates accumulation of AGEs in soluble and insoluble fractions. p62 itself is subject to glycative inactivation and accumulates as high mass species. Accumulation of p62 in retinal pigment epithelium is reversed by switching to a lower glycemia diet. Since diminution of glycative damage is associated with reduced risk for age‐related diseases, including age‐related macular degeneration, cardiovascular disease, diabetes, Alzheimer's, and Parkinson's, discovery of methods to limit AGEs or enhance p62‐dependent autophagy offers novel potential therapeutic targets to treat AGEs‐related pathologies., AGEs are toxic compounds formed by non‐enzymatic reactions between sugars and proteins. AGEs are prone to aggregate. Insoluble AGEs are efficiently removed via p62‐selective autophagy. The autophagic removal of AGEs is a conserved pathway, and the lack of p62 leads to accumulation of toxic AGEs in mouse and worms. Enhanced autophagy is protective against glycation‐derived damage. p62‐dependent autophagy offers novel potential therapeutic targets to treat AGEs‐related pathologies.

6 páginas, 1 tabla, 3 figuras.-- Pesavento, P. A. et al., Ovine herpesvirus 2 (OvHV-2) is one of the gammaherpesviruses in the genus Macavirus that can cause malignant catarrhal fever (MCF) in ungulates. Sheep are the adapted host for OvHV-2 and it is generally assumed that infection is not associated with disease in this species. However, cases of "polyarteritis nodosa" or idiopathic systemic necrotizing vasculitis reported in sheep are similar to vascular lesions in clinically susceptible species with MCF. Using a recently developed in situ hybridization (ISH) method, we were able to identify OvHV-2 nucleic acids within lesions and correlate the viral distribution with systemic necrotizing vasculitis in 9 sheep, including both naturally and experimentally OvHV-2-infected animals. ISH, combined with polymerase chain reaction and histology, identify OvHV-2 as the likely agent responsible for sporadic, MCF-like vascular disease in sheep., The author(s) received the following financial support for the research, authorship, and/or publication of this article: Support funding to the Li laboratory for this project is from USDA-ARS CWU 2029-3200-037-00D. In the Pesavento laboratory, the study was supported by Boehringer Ingelheim Vetmedica and the Bernice Barbour Foundation for research in naturally occurring infectious disease.

13 páginas, 2 tablas, 7 figuras., Neospora caninum is one of the main causes of abortion in cattle, and recent studies have highlighted its relevance as an abortifacient in small ruminants. Vaccines or drugs for the control of neosporosis are lacking. Bumped kinase inhibitors (BKIs), which are ATP-competitive inhibitors of calcium dependent protein kinase 1 (CDPK1), were shown to be highly efficacious against several apicomplexan parasites in vitro and in laboratory animal models. We here present the pharmacokinetics, safety and efficacy of BKI-1553 in pregnant ewes and foetuses using a pregnant sheep model of N. caninum infection. BKI-1553 showed exposure in pregnant ewes with trough concentrations of approximately 4 mu M, and of 1 mu M in foetuses. Subcutaneous BKI-1553 administration increased rectal temperatures shortly after treatment, and resulted in dermal nodules triggering a slight monocytosis after repeated doses at short intervals. BKI-1553 treatment decreased fever in infected pregnant ewes already after two applications, resulted in a 37-50% reduction in foetal mortality, and modulated immune responses; IFN. levels were increased early after infection and IgG levels were reduced subsequently. N. caninum was abundantly found in placental tissues; however, parasite detection in foetal brain tissue decreased from 94% in the infected/untreated group to 69-71% in the treated groups. In summary, BKI-1553 confers partial protection against abortion in a ruminant experimental model of N. caninum infection during pregnancy. In addition, reduced parasite detection, parasite load and lesions in foetal brains were observed., We gratefully acknowledge Jacobo Sampere from the SALUVETgroup (Complutense University of Madrid, Spain), Teresa Navarro andJosé María González (University of Zaragoza, Spain), Isabel Ayala,Lucas Troya, Clara Colmenero, Dolores González, Natalia Peral,Verónica Pérez, Ignacio Gómez and Isabel Santiago from the Clinical Veterinary Hospital (Complutense University of Madrid, Spain) for their excellent technical assistance, and also Rama Subba Rao Vidadala and Dustin Maly (Department of Chemistry, University of Washington) fortheir assistance in further purification of the study drug. The AnimalExperimentation Service (SEA) at the University of Zaragoza is ac-knowledged for providing their facilities to carry out the reproduction programme. Roberto Sánchez Sánchez is supported by a fellowship from the Spanish Ministry of Education, Culture and Sports (MECD), asa part of the Program of Training of University Teaching Staff (FPU,grant number FPU13/03438). Patricia Vázquez has a Juan de la Cierva-Formación post-doctoral contract (FJCI-2014-20982) from the Spanish Ministry of Economy and Competitiveness (MINECO). Andrew Hemphill is supported by the Swiss National Science Foundation grant(No. 310030 165782). This work was supported by the Public Health Service, National Institutes of Health, Bethesda, MD (grants R01 AI111341 and R01 HD 080670), the U.S. Department of Agriculture(grant 2014-67015-22106) and the Community of Madrid, Spain(PLATESA, S2013/ABI2906).

Crop simulation models are valuable tools for quantifying crop yield response to water, and for devising strategies to improve agricultural water management. However, applicability of the majority of crop models is limited greatly by a failure to provide open-access to model source code. In this study, we present an open-source version of the FAO AquaCrop model, which simulates efficiently water-limited crop production across diverse environmental and agronomic conditions. Our model, called AquaCrop-OpenSource (AquaCrop-OS), can be run in multiple programming languages and operating systems. Support for parallel execution reduces significantly simulation times when applying the model in large geospatial frameworks, for long-run policy analysis, or for uncertainty assessment. Furthermore, AquaCrop-OS is compliant with the Open Modelling Interface standard facilitating linkage to other disciplinary models, for example to guide integrated water resources planning., This research was funded in part by USDA NIFA Award number 2012-67003-23227 and by a PhD studentship from the Grantham Institute at Imperial College London. Further support was provided by the Daugherty Water for Food Global Institute at the University of Nebraska.

As demand for freshwater increases while supply remains stagnant, the critical need for sustainable water use in agriculture has led the EPA Strategic Plan to call for new technologies that can optimize water allocation in real-time. This work assesses the use of cloud-based artificial intelligence to detect early indicators of water stress across six container-grown ornamental shrub species. Near-infrared images were previously collected with modified Canon and MAPIR Survey II cameras deployed via a small unmanned aircraft system (sUAS) at an altitude of 30 meters. Cropped images of plants in no, low-, and high-water stress conditions were split into four-fold cross-validation sets and used to train models through IBM Watson’s Visual Recognition service. Despite constraints such as small sample size (36 plants, 150 images) and low image resolution (150 pixels by 150 pixels per plant), Watson generated models were able to detect indicators of stress after 48 hours of water deprivation with a significant to marginally significant degree of separation in four out of five species tested (p < 0.10). Two models were also able to detect indicators of water stress after only 24 hours, with models trained on images of as few as eight water-stressed Buddleia plants achieving an average area under the curve (AUC) of 0.9884 across four folds. Ease of pre-processing, minimal amount of training data required, and outsourced computation make cloud-based artificial intelligence services such as IBM Watson Visual Recognition an attractive tool for agriculture analytics. Cloud-based artificial intelligence can be combined with technologies such as sUAS and spectral imaging to help crop producers identify deficient irrigation strategies and intervene before crop value is diminished. When brought to scale, frameworks such as these can drive responsive irrigation systems that monitor crop status in real-time and maximize sustainable water use., This work was partially supported by a grant from the J. Frank Schmidt Family Charitable Foundation and is based on work supported by NIFA/USDA under project numbers SC-1700540, SC-1700543 and 2014-51181-22372 (USDA-SCRI Clean WateR3). Research of Drs. Peña and de Castro was financed by the “Salvador de Madariaga” for Visiting Researchers in Foreign Centers Program (Spanish MICINN funds) and the Intramural-CSIC Project (ref. 201940E074), respectively.

International audience; The international seed trade is considered relatively safe from a phytosanitary point of view and is therefore less regulated than trade in other plants for planting. However, the pests carried by traded seeds are not well known. We assessed insects and fungi in 58 traded seed lots of 11 gymnosperm and angiosperm tree species from North America, Europe, and Asia. Insects were detected by X-raying and molecular methods. The fungal community was characterized using high-throughput sequencing (HTS) and by growing fungi on non-selective agar. About 30% of the seed lots contained insect larvae. Gymnosperms contained mostly hymenopteran (Megastigmus spp.) and dipteran (Cecidomyiidae) larvae, while angiosperms contained lepidopteran (Cydia latiferreana) and coleopteran (Curculio spp.) larvae. HTS indicated the presence of fungi in all seed lots and fungi grew on non-selective agar from 96% of the seed lots. Fungal abundance and diversity were much higher than insect diversity and abundance, especially in angiosperm seeds. Almost 50% of all fungal exact sequence variants (ESVs) found in angiosperms were potential pathogens, in comparison with around 30% of potentially pathogenic ESVs found in gymnosperms. The results of this study indicate that seeds may pose a greater risk of pest introduction than previously believed or accounted for. A rapid risk assessment suggests that only a small number of species identified in this study is of phytosanitary concern. However, more research is needed to enable better risk assessment, especially to increase knowledge about the potential for transmission of fungi to seedlings and the host range and impact of identified species.

16 páginas, 3 tablas, 6 figuras., Previous studies on drug efficacy showed low protection against abortion and vertical transmission of Toxoplasma gondii in pregnant sheep. Bumped kinase inhibitors (BKIs), which are ATP-competitive inhibitors of calcium-dependent protein kinase 1 (CDPK1), were shown to be highly efficacious against several apicomplexan parasites in vitro and in laboratory animal models. Here, we present the safety and efficacy of BKI-1294 treatment (dosed orally at 100 mg/kg of body weight 5 times every 48 h) initiated 48 h after oral infection of sheep at midpregnancy with 1,000 TgShSp1 oocysts. BKI-1294 demonstrated systemic exposure in pregnant ewes, with maximum plasma concentrations of 2 to 3 M and trough concentrations of 0.4 M at 48 h after each dose. Oral administration of BKI-1294 in uninfected sheep at midpregnancy was deemed safe, since there were no changes in behavior, fecal consistency, rectal temperatures, hematological and biochemical parameters, or fetal mortality/morbidity. In ewes infected with a T. gondii oocyst dose lethal for fetuses, BKI-1294 treatment led to a minor rectal temperature increase after infection and a decrease in fetal/lamb mortality of 71%. None of the lambs born alive in the treated group exhibited congenital encephalitis lesions, and vertical transmission was prevented in 53% of them. BKI-1294 treatment during infection led to strong interferon gamma production after cell stimulation in vitro and a low humoral immune response to soluble tachyzoite antigens but high levels of anti-SAG1 antibodies. The results demonstrate a proof of concept for the therapeutic use of BKI-1294 to protect ovine fetuses from T. gondii infection during pregnancy., We gratefully acknowledge the SALUVET group (Complutense University of Madrid, Spain), Luis Miguel Ferrer, Jose Ventura, José Calasanz Jiménez, Francisco Saura, Teresa Navarro, and José María González from the University of Zaragoza (Spain), and Victor Herrero and Javier Blanco from Clinical Veterinary Hospital (Complutense University of Madrid, Spain) for their excellent technical assistance, Dale Kempf and Kennan Marsh, from AbbVie, Inc., for their suggestion of the Phosal vehicle used in the experiments reported here, Rama S. R. Vidadala and Dustin J. Maly, Department of Chemistry, University of Washington, for characterization and further purification of BKI-1294, and advice from Robert Choy and Eugenio L. de Hostos from the PATH Drug Development Program. The Animal Experimentation Service (SEA) at the University of Zaragoza is acknowledged for providing their facilities to carry out the reproduction program. R.S.-S. is supported by a fellowship from the Spanish Ministry of Education, Culture and Sports (MECD), as a part of the Program of Training of University Teaching Staff (FPU; grant number FPU13/03438). A.H. is supported by a Swiss National Science Foundation grant (no. 310030-165782). This work was supported by the Public Health Service, National Institutes of Health, Bethesda, MD (grants R01 AI 111341 and R01 HD 080670), the U.S. Department of Agriculture (grant 2014-67015-22106), and the Community of Madrid, Spain (PLATESA2, P2018/BAA-4370). I.F., A.H., K.K.O., W.C.V.V., and L.M.O.-M. conceived the study and participated in its design. R.S.-S. wrote the manuscript, with results interpretation and discussion inputs from I.F., J.R.-C., A.H., M.A.H., L.K.B., W.C.V.V., and L.M.O.-M. J.J.R. selected the animals and executed the reproductive program. R.S.-S., I.F., and M.R. carried out oocyst infection and drug administration. R.S.-S., I.F., M.R., M.P.D., M.G.-H., E.T., and J.B. participated in clinical examination and sampling of animals and performed necropsies and hematological, biochemical, and histopathological analyses. M.H., L.K.B., R.C., G.R.W., and K.K.O. determined the pharmacokinetics of the compound. R.S.-S. performed peripheral blood stimulation assay, serological assays, PCR analyses, statistical analysis, and interpretation of the results. All authors read and approved the final manuscript. W.C.V.V. is the president and co-owner of ParaTheraTech, Inc., a company that is developing BKIs for animal health. W.C.V.V. did not perform the experiments or interpret the results of the experiments, but he did edit the paper and helped plan the experiments. The other authors have no competing interests to declare.

© The Author(s). 2019, [Background] The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant eaters among its approximately 315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing., [Results] We explore the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representative of the two most species-rich beetle suborders. We contrast the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We find gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant feeding, we identify families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There is notable support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes., [Conclusions] Our explicit modeling of the evolution of gene repertoires across 18 species identifies putative adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant feeding in general, in driving beetle diversification., This work was supported by the United States National Science Foundation (DEB 1355169) and the United States Department of Agriculture (cooperative agreement 8130-0547-CA) to DDM, the Spanish grant CGL2013-42589-P awarded by the MINECO and co-financed by FEDER to BCE, the Science Foundation DFG grant BA2152/11-1, 2, the BGI-Shenzhen, the China National Genebank, and the following Swiss National Science Foundation grants: 31003A_143936 (PI), 31003A_173048 (MRR), PP00P3_170664 (RMW), and PP00P3_172899 (NA). Funding for open access charge: Geneva Natural History Museum.

International audience

Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry., A fruitful genomic resource Detailed genomic maps from the fruit-bearing trees of the Prunus genus should greatly accelerate the breeding of superior cultivars. These plants produce a variety of popular fruits, but until relatively recently, breeders had only limited genetic information with which to work. Pere Arús of Spain’s Institute of Agrifood Research and Technology and colleagues have now reviewed the rapid advances in Prunus genomics that have taken place since 2010, when researchers completed the first genome assembly for this genus. In the ensuing decade, increasingly high-quality genomes from the peach, Japanese apricot, and cherry have allowed scientists to home in on chromosomal regions associated with key traits such as fruit quality and disease resistance. These data also offer valuable genetic markers that agronomists can use to guide the production of healthier trees and more commercially desirable fruits.

The small cabbage white butterfly, Pieris rapae, is a major agricultural pest of cruciferous crops and has been introduced to every continent except South America and Antarctica as a result of human activities. In an effort to reconstruct the near-global invasion history of P. rapae, we developed a citizen science project, the “Pieris Project,” and successfully amassed thousands of specimens from 32 countries worldwide. We then generated and analyzed nuclear (double-digest restriction site-associated DNA fragment procedure [ddRAD]) and mitochondrial DNA sequence data for these samples to reconstruct and compare different global invasion history scenarios. Our results bolster historical accounts of the global spread and timing of P. rapae introductions. We provide molecular evidence supporting the hypothesis that the ongoing divergence of the European and Asian subspecies of P. rapae (∼1,200 y B.P.) coincides with the diversification of brassicaceous crops and the development of human trade routes such as the Silk Route (Silk Road). The further spread of P. rapae over the last ∼160 y was facilitated by human movement and trade, resulting in an almost linear series of at least 4 founding events, with each introduced population going through a severe bottleneck and serving as the source for the next introduction. Management efforts of this agricultural pest may need to consider the current existence of multiple genetically distinct populations. Finally, the international success of the Pieris Project demonstrates the power of the public to aid scientists in collections-based research addressing important questions in invasion biology, and in ecology and evolutionary biology more broadly., This research was funded by US Department of Agriculture-National Institute of Food and Agriculture Postdoctoral Fellowship Grant 2017-67012-26999 (to S.F.R.). A.E. is supported by a National Science Foundation Graduate Research Fellowship under Grant NSF-1447692. R.V. was supported by project CGL2016-76322-P (Spanish Agencia Estatal de Investigación and European Union Regional Development Fund). G.T. is supported by Ministerio de Economia y Competitividad Programme IJCI-2016-29083 and by the National Geographic Society (Grant WW1-300R-18). E.A.H. was supported by Marie Curie Actions International Outgoing Fellowship 330136.

More effective methods to detect bovine tuberculosis, caused by Mycobacterium bovis, in wildlife, is of paramount importance for preventing disease spread to other wild animals, livestock, and human beings. In this study, we analyzed the volatile organic compounds emitted by fecal samples collected from free-ranging wild boar captured in Do&ntilde, ana National Park, Spain, with an electronic nose system based on organically-functionalized gold nanoparticles. The animals were separated by the age group for performing the analysis. Adult (&gt, 24 months) and sub-adult (12&ndash, 24 months) animals were anesthetized before sample collection, whereas the juvenile (&lt, 12 months) animals were manually restrained while collecting the sample. Good accuracy was obtained for the adult and sub-adult classification models: 100% during the training phase and 88.9% during the testing phase for the adult animals, and 100% during both the training and testing phase for the sub-adult animals, respectively. The results obtained could be important for the further development of a non-invasive and less expensive detection method of bovine tuberculosis in wildlife populations.

The wild pig population on Molokai, Hawaii, USA is a possible reservoir for bovine tuberculosis, caused by Mycobacterium bovis, and has been implicated in decades past as the source of disease for the island&rsquo, s domestic cattle. Heat-inactivated vaccines have been effective for reducing disease prevalence in wild boar in Spain and could prove useful for managing M. bovis in Molokai wild pigs. We designed an experiment to test this vaccine in wild pigs of Molokai genetics. Fifteen 3&ndash, 4-month-old pigs were orally administered 106&ndash, 107 colony forming units (cfu) of heat-inactivated M. bovis (Vaccinates, n = 8, 0.2 mL) or phosphate buffered saline (Controls, n = 7, 0.2 mL). Each dose was administered in a 0.5 mL tube embedded in a fruit candy/cracked corn mix. Boosters were given seven weeks post-prime in the same manner and dose. Nineteen weeks post-prime, pigs were orally challenged with 1 &times, 106 cfu of virulent M. bovis. Twelve weeks post-challenge, pigs were euthanized and necropsied, at which time 23 different tissues from the head, thorax, and abdomen were collected and examined. Each tissue was assigned a lesion score. Ordinal lesion score data were analyzed using non-parametric Wilcoxon Signed Rank test. Effect size was calculated using Cohen&rsquo, s d. Four of eight Vaccinates and four of seven Controls had gross and microscopic lesions, as well as culture-positive tissues. Vaccinates had statistically lower lesion scores than Controls in the following areas: gross thoracic lesion scores (p = 0.013 Cohen&rsquo, s d = 0.33) and microscopic thoracic lesion scores (p = 0.002, Cohen&rsquo, s d = 0.39). There were no differences in head lesion scores alone, both gross and microscopic, nor were there differences when comparing combined gross and microscopic head and thoracic lesion scores. These results are indicative that this vaccination protocol affords a modest degree of infection containment with this vaccine in Molokai wild pigs.

14 Pags.- 11 Figs., We present an analysis of the sensitivity of three key crops (alfalfa, barley and winter wheat) produced in the northwestern United States to climatic and agricultural market anomalies using widely used standardized indices. Rather than investigating sensitivity of crop yields (production per unit area), we focus on agricultural production (yield * harvested area) anomalies, which captures both variations in yield and the effect of decision-making factors such as allocation of cropping area. We used two well-known standardized precipitation and reference evapotranspiration (ETo) indices (SPI and EDDI, respectively) and a standardized crop value index in a multivariate linear regression analysis to determine the characteristic timing and time-scales of precipitation and ETo anomalies that best explain annual crop production anomalies. Since climatic and market factors are standardized, regression coefficients are interpreted as a sensitivity measure that captures the relative effect of climatic and agricultural markets on agricultural production. Results show that alfalfa production was most sensitive climatic anomalies while barley and wheat production was more responsive to crop prices. Sensitivity to precipitation anomalies followed gradients in precipitation, temperature, and soil moisture regimes across the study area where drier and warmer climates were associated with increased sensitivity to climatic anomalies. We found that irrigation decoupled alfalfa production from climatic variability, but the effect of irrigation on decoupling barley production was less clear. Winter wheat production was most sensitive to price anomalies, and alfalfa was least sensitive. Omitting agricultural market conditions and other farmer incentives may introduce biases in our understanding of how drought and climate change impact agricultural production., This work has been supported by the United States Department of Agriculture, USDA-NIFA research grant 2016-67026-25067, and by the NASA EPSCoR program research grant 80NSSC18M0025. P.W. also acknowledges partial support from the NSF EPSCoR cooperative agreement EPS-1101342.

Tree–grass ecosystems are widely distributed. However, their phenology has not yet been fully characterized. The technique of repeated digital photographs for plant phenology monitoring (hereafter referred as PhenoCam) provide opportunities for long-term monitoring of plant phenology, and extracting phenological transition dates (PTDs, e.g., start of the growing season). Here, we aim to evaluate the utility of near-infrared-enabled PhenoCam for monitoring the phenology of structure (i.e., greenness) and physiology (i.e., gross primary productivity—GPP) at four tree–grass Mediterranean sites. We computed four vegetation indexes (VIs) from PhenoCams: (1) green chromatic coordinates (GCC), (2) normalized difference vegetation index (CamNDVI), (3) near-infrared reflectance of vegetation index (CamNIRv), and (4) ratio vegetation index (CamRVI). GPP is derived from eddy covariance flux tower measurement. Then, we extracted PTDs and their uncertainty from different VIs and GPP. The consistency between structural (VIs) and physiological (GPP) phenology was then evaluated. CamNIRv is best at representing the PTDs of GPP during the Green-up period, while CamNDVI is best during the Dry-down period. Moreover, CamNIRv outperforms the other VIs in tracking growing season length of GPP. In summary, the results show it is promising to track structural and physiology phenology of seasonally dry Mediterranean ecosystem using near-infrared-enabled PhenoCam. We suggest using multiple VIs to better represent the variation of GPP., The authors acknowledge the Alexander von Humboldt Foundation for supporting this research with the Max-Planck Prize to Markus Reichstein. Y.L. and M.M. gratefully acknowledge financial support from the China Scholarship Council. We are also thankful for financial support from the Spanish Ministry of Economy and Competitiveness through the FLUXPEC project “Monitoring changes in water and carbon fluxes from remote and proximal sensing in a Mediterranean dehesa ecosystem” (CGL2012-34383). The development of PhenoCam has been supported by the Northeastern States Research Cooperative, NSF’s Macrosystems Biology program (award EF-1065029 and EF-1702697), DOE’s Regional and Global Climate Modeling program (award DE-SC0016011), and the US National Park Service Inventory and Monitoring Program and the USA National Phenology Network (grant number G10AP00129 from the United States Geological Survey). The authors thank Sujan Koirala for relevant technical assistance and comments on graphics. The authors thank two anonymous reviewers and the editor for constructive comments to improve the earlier manuscript. The authors thank Andrew Durso for final proofreading for English.

21 Pags.- 5 Tabls.- 8 Figs. © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/)., Accurate crop yield assessments using satellite remote sensing-based methods are of interest for regional monitoring and the design of policies that promote agricultural resiliency and food security. However, the application of current vegetation productivity algorithms derived from global satellite observations is generally too coarse to capture cropland heterogeneity. The fusion of data from different sensors can provide enhanced information and overcome many of the limitations of individual sensors. In thitables study, we estimate annual crop yields for seven important crop types across Montana in the continental USA from 2008–2015, including alfalfa, barley, maize, peas, durum wheat, spring wheat and winter wheat. We used a satellite data-driven light use efficiency (LUE) model to estimate gross primary productivity (GPP) over croplands at 30-m spatial resolution and eight-day time steps using a fused NDVI dataset constructed by blending Landsat (5 or 7) and Terra MODIS reflectance data. The fused 30-m NDVI record showed good consistency with the original Landsat and MODIS data, but provides better spatiotemporal delineations of cropland vegetation growth. Crop yields were estimated at 30-m resolution as the product of estimated GPP accumulated over the growing season and a crop-specific harvest index (HIGPP). The resulting GPP estimates capture characteristic cropland productivity patterns and seasonal variations, while the estimated annual crop production results correspond favorably with reported county-level crop production data (r = 0.96, relative RMSE = 37.0%, p < 0.05) from the U.S. Department of Agriculture (USDA). The performance of estimated crop yields at a finer (field) scale was generally lower, but still meaningful (r = 0.42, relative RMSE = 50.8%, p < 0.05). Our methods and results are suitable for operational applications of crop yield monitoring at regional scales, suggesting the potential of using global satellite observations to improve agricultural management, policy decisions and regional/global food security., This work was conducted at the University of Montana with funding provided by the USDA NIFA (National Institute of Food and Agriculture) contract 658 2016-67026-25067, USDA 365063, NASA EPSCoR (Established Program to Stimulate Competitive Research) contract 80NSSC18M0025 and NASA (NNX14AI50G, NNX14A169G, NNX08AG87A).