Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

Lovell, John T.; MacQueen, Alice H.; Mamidi, Sujan; Bonnette, Jason; Jenkins, Jerry; Napier, Joseph D.; Sreedasyam, Avinash; Healey, Adam; Session, Adam; Shu, Shengqiang; Barry, Kerrie; Bonos, Stacy; Boston, LoriBeth; Daum, Christopher; Deshpande, Shweta; Ewing, Aren; Grabowski, Paul P.; Haque, Taslima; Harrison, Melanie; Jiang, Jiming; Kudrna, Dave; Lipzen, Anna; Pendergast, Thomas H.; Plott, Chris; Qi, Peng; Saski, Christopher A.; Shakirov, Eugene V.; Sims, David; Sharma, Manoj; Sharma, Rita; Stewart, Ada; Singan, Vasanth R.; Tang, Yuhong; Thibivillier, Sandra; Webber, Jenell; Weng, Xiaoyu; Williams, Melissa; Wu, Guohong Albert; Yoshinaga, Yuko; Zane, Matthew; Zhang, Li; Zhang, Jiyi; Behrman, Kathrine D.; Boe, Arvid R.; Fay, Philip A.; Fritschi, Felix B.; Jastrow, Julie D.; Lloyd-Reilley, John; Martínez-Reyna, Juan Manuel; Matamala, Roser; Mitchell, Robert B.; Rouquette, Francis M.; Ronald, Pamela; Saha, Malay; Tobias, Christian M.; Udvardi, Michael; Wing, Rod A.; Wu, Yanqi; Bartley, Laura E.; Casler, Michael; Devos, Katrien M.; Lowry, David B.; Rokhsar, Daniel S.; Grimwood, Jane; Juenger, Thomas E.; Schmutz, Jeremy

doi:10.1038/s41586-020-03127-1

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

Journal Article · Wed Jan 27 00:00:00 EST 2021 · Nature (London)

DOI:https://doi.org/10.1038/s41586-020-03127-1· OSTI ID:1773844

^[1]; MacQueen, Alice H. ^[2]; Mamidi, Sujan ^[3]; Bonnette, Jason ^[2]; ^[3]; ^[2]; ^[3]; Healey, Adam ^[3]; Session, Adam ^[4]; ^[5]; Barry, Kerrie ^[5]; Bonos, Stacy ^[6]; Boston, LoriBeth ^[3]; Daum, Christopher ^[5]; Deshpande, Shweta ^[5]; Ewing, Aren ^[5]; Grabowski, Paul P. ^[3]; Haque, Taslima ^[2]; Harrison, Melanie ^[7]; ^[8] more »

HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States); University of Texas at Austin
Univ. of Texas, Austin, TX (United States)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Rutgers Univ., New Brunswick, NJ (United States)
US Dept. of Agriculture (USDA), Griffin, GA (United States)
Michigan State Univ., East Lansing, MI (United States)
Univ. of Arizona, Tucson, AZ (United States)
Univ. of Georgia, Athens, GA (United States)
Clemson Univ., SC (United States)
Univ. of Texas, Austin, TX (United States); Marshall Univ., Huntington, WV (United States)
Jawaharlal Nehru Univ., New Delhi (India)
Noble Research Inst. LLC, Ardmore, OK (United States)
Univ. of Nebraska, Lincoln, NE (United States)
South Dakota State Univ., Brookings, SD (United States)
US Dept. of Agriculture (USDA), Temple, TX (United States)
Univ. of Missouri, Columbia, MO (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)
US Dept. of Agriculture (USDA), Kingsville, TX (United States)
Antonio Narro Agrarian Autonomous Univ., Saltillo (Mexico)
US Dept. of Agriculture (USDA), Lincoln, NE (United States)
Texas A & M Univ., Overton, TX (United States)
Univ. of California, Davis, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States)
US Dept. of Agriculture (USDA), Albany, CA (United States)
Oklahoma State Univ., Stillwater, OK (United States)
Univ. of Oklahoma, Norman, OK (United States); Washington State Univ., Pullman, WA (United States)
US Dept. of Agriculture (USDA), Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States)
Univ. of Georgia, Athens, GA (United States); USDOE Center for Bioenergy Innovation, Oak Ridge, TN (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Berkeley, CA (United States); Chan-Zuckerberg Biohub, San Francisco, CA (United States)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States); Great Lakes Bioenergy Research Center, Madison, WI (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Michigan State Univ., East Lansing, MI (United States); Univ. of Georgia, Athens, GA (United States); Univ. of Texas, Austin, TX (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231; AC02-06CH11357; FC02-07ER64494; SC0010743; SC0014156; SC0017883; SC0018409

OSTI ID:: 1773844

Alternate ID(s):: OSTI ID: 1826700
OSTI ID: 1776871
OSTI ID: 1787614

Journal Information:: Nature (London), Journal Name: Nature (London) Journal Issue: 7846 Vol. 590; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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