Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

Authors

John T Lovell, Alice H MacQueen, Sujan Mamidi, Jason Bonnette, Jerry Jenkins, Joseph D Napier, Avinash Sreedasyam, Adam Healey, Adam Session, Shengqiang Shu, Kerrie Barry, Stacy Bonos, LoriBeth Boston, Christopher Daum, Shweta Deshpande, Aren Ewing,

Paul P Grabowski, Taslima Haque, Melanie Harrison, Jiming Jiang, Dave Kudrna, Anna Lipzen, Thomas H Pendergast, Chris Plott, Peng Qi, Christopher A Saski, Eugene V Shakirov, David Sims, Manoj Sharma, Rita Sharma, Ada Stewart, Vasanth R Singan,

Yuhong Tang, Sandra Thibivillier, Jenell Webber, Xiaoyu Weng, Melissa Williams, Guohong Albert Wu, Yuko Yoshinaga, Matthew Zane, Li Zhang, Jiyi Zhang, Kathrine D Behrman, Arvid R Boe, Philip A Fay, Felix B Fritschi, Julie D Jastrow, John Lloyd-Reilley,

Juan Manuel Martínez-Reyna, Roser Matamala, Robert B Mitchell, Francis M Rouquette, Pamela Ronald, Malay Saha, Christian M Tobias, Michael Udvardi, Rod A Wing, Yanqi Wu, Laura E Bartley, Michael Casler, Katrien M Devos, David B Lowry, Daniel S Rokhsar,

Jane Grimwood, Thomas E Juenger, Jeremy Schmutz

Nature (2021) https://doi.org/10.1038/s41586-020-03127-1
Received: 1 July 2020
Accepted: 16 December 2020
Published online: 27 January 2021

Abstract

Long-term climate change and periodic environmental extremes threaten food and fuel security and global crop productivity. Although 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 has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.