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25. Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Author

Mitros, Therese, Session, Adam M, James, Brandon T, Wu, Guohong Albert, Belaffif, Mohammad B, Clark, Lindsay V, Shu, Shengqiang, Dong, Hongxu, Barling, Adam, Holmes, Jessica R, Mattick, Jessica E, Bredeson, Jessen V, Liu, Siyao, Farrar, Kerrie, Głowacka, Katarzyna, Jeżowski, Stanisław, Barry, Kerrie, Chae, Won Byoung, Juvik, John A, Gifford, Justin, Oladeinde, Adebosola, Yamada, Toshihiko, Grimwood, Jane, Putnam, Nicholas H, De Vega, Jose, Barth, Susanne, Klaas, Manfred, Hodkinson, Trevor, Li, Laigeng, Jin, Xiaoli, Peng, Junhua, Yu, Chang Yeon, Heo, Kweon, Yoo, Ji Hye, Ghimire, Bimal Kumar, Donnison, Iain S, Schmutz, Jeremy, Hudson, Matthew E, Sacks, Erik J, Moose, Stephen P, Swaminathan, Kankshita, and Rokhsar, Daniel S

Subjects
Biotechnology, Human Genome, Genetics, Affordable and Clean Energy, Biomass, Chromosomes, Plant, DNA Transposable Elements, Diploidy, Evolution, Molecular, Gene Expression Regulation, Plant, Genetic Variation, Genome, Plant, Genomics, Models, Genetic, Phylogeny, Poaceae, Polyploidy, Saccharum, Seasons, Sorghum
Abstract

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

Published
2020

28. Real‐world effectiveness and safety of oral azvudine versus nirmatrelvir‒ritonavir (Paxlovid) in hospitalized patients with COVID-19: a multicenter, retrospective, cohort study.

Author

Wang, Haiyu, Cui, Guangying, Cheng, Ming, Aji, Tuerganaili, Li, Guotao, Hu, Xinjun, Li, Guangming, Zhang, Shixi, Zhang, Yanyang, Diao, Linqi, Li, Pan, Wang, Ling, Yuan, Yiqiang, Qian, Guowu, Zhang, Ruiqing, Jin, Xiaoli, Wang, Juan, Luo, Hong, Zhang, Donghua, and Wang, Mingming

Published
2025
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30. Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

Author

Clifton‐Brown, John, Harfouche, Antoine, Casler, Michael D, Jones, Huw Dylan, Macalpine, William J, Murphy‐Bokern, Donal, Smart, Lawrence B, Adler, Anneli, Ashman, Chris, Awty‐Carroll, Danny, Bastien, Catherine, Bopper, Sebastian, Botnari, Vasile, Brancourt‐Hulmel, Maryse, Chen, Zhiyong, Clark, Lindsay V, Cosentino, Salvatore, Dalton, Sue, Davey, Chris, Dolstra, Oene, Donnison, Iain, Flavell, Richard, Greef, Joerg, Hanley, Steve, Hastings, Astley, Hertzberg, Magnus, Hsu, Tsai‐Wen, Huang, Lin S, Iurato, Antonella, Jensen, Elaine, Jin, Xiaoli, Jørgensen, Uffe, Kiesel, Andreas, Kim, Do‐Soon, Liu, Jianxiu, McCalmont, Jon P, McMahon, Bernard G, Mos, Michal, Robson, Paul, Sacks, Erik J, Sandu, Anatolii, Scalici, Giovanni, Schwarz, Kai, Scordia, Danilo, Shafiei, Reza, Shield, Ian, Slavov, Gancho, Stanton, Brian J, Swaminathan, Kankshita, Taylor, Gail, Torres, Andres F, Trindade, Luisa M, Tschaplinski, Timothy, Tuskan, Gerald A, Yamada, Toshihiko, Yu, Chang Yeon, Zalesny, Ronald S, Zong, Junqin, and Lewandowski, Iris

Subjects
Affordable and Clean Energy, bioenergy, feedstocks, lignocellulose, M. sacchariflorus, M. sinensis, Miscanthus, Panicum virgatum, perennial biomass crop, Populus spp., Salix spp., M. sacchariflorus, M. sinensis, Agricultural Biotechnology
Abstract

Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output-input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.

Published
2019

31. Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar.

Author

Clifton-Brown, John, Harfouche, Antoine, Casler, Michael D, Dylan Jones, Huw, Macalpine, William J, Murphy-Bokern, Donal, Smart, Lawrence B, Adler, Anneli, Ashman, Chris, Awty-Carroll, Danny, Bastien, Catherine, Bopper, Sebastian, Botnari, Vasile, Brancourt-Hulmel, Maryse, Chen, Zhiyong, Clark, Lindsay V, Cosentino, Salvatore, Dalton, Sue, Davey, Chris, Dolstra, Oene, Donnison, Iain, Flavell, Richard, Greef, Joerg, Hanley, Steve, Hastings, Astley, Hertzberg, Magnus, Hsu, Tsai-Wen, Huang, Lin S, Iurato, Antonella, Jensen, Elaine, Jin, Xiaoli, Jørgensen, Uffe, Kiesel, Andreas, Kim, Do-Soon, Liu, Jianxiu, McCalmont, Jon P, McMahon, Bernard G, Mos, Michal, Robson, Paul, Sacks, Erik J, Sandu, Anatolii, Scalici, Giovanni, Schwarz, Kai, Scordia, Danilo, Shafiei, Reza, Shield, Ian, Slavov, Gancho, Stanton, Brian J, Swaminathan, Kankshita, Taylor, Gail, Torres, Andres F, Trindade, Luisa M, Tschaplinski, Timothy, Tuskan, Gerald A, Yamada, Toshihiko, Yeon Yu, Chang, Zalesny, Ronald S, Zong, Junqin, and Lewandowski, Iris

Subjects
M. sacchariflorus, M. sinensis, Miscanthus, Panicum virgatum, Populus spp., Salix spp., bioenergy, feedstocks, lignocellulose, perennial biomass crop, M. sacchariflorus, M. sinensis, Agricultural Biotechnology
Abstract

Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output-input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.

Published
2019

42. Structural Distortion of g‐C3N4 Induced by a Schiff Base Reaction for Efficient Photocatalytic H2 Evolution.

Author

Yang, Chunxia, Cao, Hailong, Su, Fengyun, Tian, Mengzhen, Xie, Haiquan, Zhang, Yezhen, Jin, Xiaoli, Li, Xin, and Li, Zhengdao

Subjects
SCHIFF bases, ELECTRON distribution, SPECTRAL sensitivity, VISIBLE spectra, CHARGE carriers
Abstract

Photocatalytic H2 evolution by water splitting is a promising approach to address the challenges of environmental pollution and energy scarcity. Graphitic carbon nitride (g‐C3N4) has emerged as a star photocatalyst because of its numerous advantages. To address the limitations of traditional g‐C3N4, namely its inadequate visible light response and rapid recombination of photogenerated carriers, we employed a schiff base reaction to synthesize −C=N− doped g‐C3N4. The introduction of −C=N− groups at the bridging nitrogen sites induced structural distortion in g‐C3N4, facilitating n‐π* electronic transitions from the lone pair electrons of nitrogen atom and extending light absorption up to 600 nm. Moreover, the presence of heterogeneous π‐conjugated electron distribution effectively traps photogenerated electrons and enhances charge carrier separation. Benefiting from its expanded spectral response range, unique electronic properties, increased specific surface area, the doped g‐C3N4 exhibited outstanding photocatalytic H2 evolution performance of 1050.13 μmol/g/h. The value was 5.9 times greater than the pristine g‐C3N4. [ABSTRACT FROM AUTHOR]

Published
2024
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44. Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides.

Author

Ren, Jing, Chen, Liang, Jin, Xiaoli, Zhang, Miaomiao, You, Frank, Wang, Jirui, Frenkel, Vladimir, Yin, Xuegui, Nevo, Eviatar, Sun, Dongfa, Luo, Ming-Cheng, and Peng, Junhua

Subjects
SNP marker, genetic differentiation, natural selection, solar radiation, wild emmer wheat
Abstract

Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ FST ≤ 0.15) or high genetic differentiation (FST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different FST -outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.

Published
2017

45. Boosting Carrier Separation on a BiOBr/Bi4O5Br2 Direct Z-Scheme Heterojunction for Superior Photocatalytic Nitrogen Fixation

Author

Wang, Huiqing, primary, Chen, Zhuohua, additional, Shang, Yaru, additional, Lv, Chade, additional, Zhang, Xuhan, additional, Li, Fei, additional, Huang, Qunzeng, additional, Liu, Xiaodi, additional, Liu, Wenmin, additional, Zhao, Liang, additional, Ye, Liqun, additional, Xie, Haiquan, additional, and Jin, Xiaoli, additional

Published
2024
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46. Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis , and diversity centred around the Yellow Sea

Author

Clark, Lindsay V., Jin, Xiaoli, Petersen, Karen Koefoed, Anzoua, Kossanou G., Bagmet, Larissa, Chebukin, Pavel, Deuter, Martin, Dzyubenko, Elena, Dzyubenko, Nicolay, Heo, Kweon, Johnson, Douglas A., Jørgensen, Uffe, Kjeldsen, Jens Bonderup, Nagano, Hironori, Peng, Junhua, Sabitov, Andrey, Yamada, Toshihiko, Yoo, Ji Hye, Yu, Chang Yeon, Long, Stephen P., and Sacks, Erik J.

Published
2019

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