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ARS Home » Southeast Area » Griffin, Georgia » Plant Genetic Resources Conservation Unit » Research » Publications at this Location » Publication #375422
Research Project: Conservation, Characterization, Evaluation, and Distribution of Grain, Oilseed, Vegetable, Subtropical and Tropical Legume, and Warm Season Grass Genetic Resources and Associated Information

Location: Plant Genetic Resources Conservation Unit

Title: Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

Author
item LOVELL, JOHN - Genome Sequencing Center
item MACQUEEN, ALICE - University Of Texas
item MAMIDI, SUJAN - Genome Sequencing Center
item BONNETTE, JASON - University Of Texas
item JENKINS, JERRY - Genome Sequencing Center
item NAPIER, JOSEPH - University Of Texas
item SREEDASYAM, AVINASH - Genome Sequencing Center
item HEALEY, ADAM - Genome Sequencing Center
item SESSION, ADAM - Energy Joint Genome Institute
item SHU, SHENGQUIANG - Energy Joint Genome Institute
item BARRY, KERRIE - Energy Joint Genome Institute
item BONOS, STACEY - Rutgers University
item BOSTON, LORIBETH - Genome Sequencing Center
item DAUM, CHRISTOPHER - Energy Joint Genome Institute
item DESHPANDE, SHWETA - Energy Joint Genome Institute
item EWING, AREN - Energy Joint Genome Institute
item GRABOWSKI, PAUL - Genome Sequencing Center
item HAQUE, TASLIMA - University Of Texas
item Harrison, Melanie
item JIANG, JIMING - Michigan State University
item KUDRNA, DAVE - University Of Arizona
item LIPZEN, ANNA - Energy Joint Genome Institute
item PENDERGAST IV, THOMAS - University Of Georgia
item PLOTT, CHRIS - Genome Sequencing Center
item QI, PENG - University Of Georgia
item SASKI, CHRISTOPHER - Clemson University
item SHAKIROV, EUGENE - University Of Texas
item SIMS, DAVID - Genome Sequencing Center
item SHARMA, MANOJ - Jawaharlal Nehru University
item SHARMA, RITA - Jawaharlal Nehru University
item STEWART, ADA - Genome Sequencing Center
item SINGAN, VASANTH - Energy Joint Genome Institute
item TANG, YUHONG - Noble Research Institute
item THIBIVILLIER, SANDRA - Non ARS Employee
item WEBBER, JENELL - Genome Sequencing Center
item WENG, XIAOYU - University Of Texas
item WILLIAMS, MELISSA - Genome Sequencing Center
item WU, ALBERT - Energy Joint Genome Institute
item YOSHINAGA, YUKO - Energy Joint Genome Institute
item ZANE, MATTHEW - Energy Joint Genome Institute
item ZHANG, LI - Genome Sequencing Center
item ZHANG, JIYI - University Of Georgia
item BEHRMAN, KATHERINE - University Of Texas At Austin
item BOE, ARVID - South Dakota State University
item Fay, Philip
item FRITSCHI, FELIX - University Of Missouri
item JASTRO, JULIE - Argonne National Laboratory
item LLOYD-REILLEY, JOHN - US Department Of Agriculture (USDA)
item MARTINEZ-REYNA, JUAN MANUEL - Argonne National Laboratory
item MATAMALA, ROSER - Argonne National Laboratory
item Mitchell, Robert - Rob
item ROUQUETTE JR., FRANCIS - Texas A&M Agrilife
item RONALD, PAM - University Of California, Davis
item SAHA, MALAY - Noble Research Institute
item Tobias, Christian
item UDVARDI, MICHAEL - Noble Research Institute
item WING, ROD - University Of Arizona
item WU, YANQI - Oklahoma State University
item BARTLEY, LAURA - University Of Oklahoma
item Casler, Michael
item DEVOS, KATRIEN - University Of Georgia
item LOWRY, DAVID - Michigan State University
item ROKHSAR, DAN - Energy Joint Genome Institute
item GRIMWOOD, JANE - Genome Sequencing Center
item JUENGER, THOMAS - University Of Texas
item SCHMUTZ, JEREMY - Genome Sequencing Center

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/16/2020
Publication Date: 1/27/2021
Citation: Lovell, J.T., MacQueen, A.H., Mamidi, S., Bonnette, J., Jenkins, J., Napier, J.D., Sreedasyam, A., Healey, A., Session, A., Shu, S., Barry, K., Bonos, S., Boston, L., Daum, C., Deshpande, S., Ewing, A., Grabowski, P., Haque, T., Harrison, M.L., Jiang, J., Kudrna, D., Lipzen, A., Pendergast IV, T.H., Plott, C., Qi, P., Saski, C.A., Shakirov, E., Sims, D., Sharma, M., Sharma, R., Stewart, A., Singan, V., Tang, Y., Thibivillier, S., Webber, J., Weng, X., Williams, M., Wu, A., Yoshinaga, Y., Zane, M., Zhang, L., Zhang, J., Behrman, K.D., Boe, A.R., Fay, P.A., Fritschi, F.B., Jastro, J.D., Lloyd-Reilley, J., Martinez-Reyna, J., Matamala, R., Mitchell, R., Rouquette Jr., F.M., Ronald, P., Saha, M., Tobias, C.M., Udvardi, M., Wing, R., Wu, Y., Bartley, L.E., Casler, M.D., Devos, K.M., Lowry, D.B., Rokhsar, D., Grimwood, J., Juenger, T.E., Schmutz, J. 2021. Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature Genetics. 590:438-444. https://doi.org/10.1038/s41586-020-03127-1.
DOI: https://doi.org/10.1038/s41586-020-03127-1

Interpretive Summary: Switchgrass is a perennial grass undergoing development as a candidate for biomass production in support of an emerging bioenergy and bioproducts industry. The genetics of switchgrass are complex, so knowledge of the organization of its genome and its evolutionary history are critical to support development of new adapted varieties to optimize biomass production across the broad geographic range of switchgrass. This paper reports a team effort to develop a comprehensive DNA sequence of the entire switchgrass genome, combined with a comprehensive analysis of its evolutionary history. This analysis revealed three distinct switchgrass populations: Gulf Coast, Atlantic, and Midwest. These populations form distinct gene pools that form a basis for breeding and selection to develop varieties suitable for use in diverse agricultural systems and environments. These results represent a huge step forward in understanding the genetic structure of this candidate bioenergy crop and the evolution of one of the most widespread and abundant native perennial grasses in North America. More broadly, the complete switchgrass genome will open new avenues through which native grasses can benefit agriculture and conservation.

Technical Abstract: Long term climate change and periodic environmental extremes threaten food and fuel security and global crop productivity in general. While molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation — knowledge that until now has been limited to the minority of plants with small, inbred or diploid genomes. Here, we present the complete genome assembly and annotation for the biofuel crop switchgrass, the first for an outbred polyploid plant. We leverage these genome resources and phenotypes from ten common gardens to build a database of climate-yield-gene associations and to dissect the impact of outcrossing and polyploidy on switchgrass adaptive evolution. Outcrossing has accelerated adaptation to and postglacial colonization of northern climates through introgression of alleles from a pre-adapted northern gene pool, while polyploidy has facilitated adaptation through fractionation of gene function and the surprising discovery of highly elevated heritable genetic diversity on the non-dominant subgenome. This interplay between molecular evolution, polyploidy, outcrossing and local adaptation would have been obscured without a complete genome sequence and annotation. Combined, the genome resources and gene-trait associations developed here provide breeders with necessary tools to expand the per-hectare yield and climate envelope of economically sustainable biofuel production.