QTL x environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient

Authors: LOWRY, DAVID - Michigan State University; LOVELL, JOHN - University Of Texas At Austin; ZHANG, LI - University Of Texas At Austin; BONNETTE, JASON - University Of Texas At Austin; Fay, Philip; Mitchell, Robert - Rob; LLOYD-REILLEY, JOHN - Natural Resources Conservation Service (NRCS, USDA); BOE, ARVID - South Dakota State University; WU, YANQI - Oklahoma State University; ROUQUETTE, FRANCIS - Texas A&M Agrilife; WYNIA, RICHARD - Natural Resources Conservation Service (NRCS, USDA); WENG, XIAOYU - University Of Texas; BEHRMAN, KATHRINE - Natural Resources Conservation Service (NRCS, USDA); HEALEY, ADAM - Hudsonalpha Institute For Biotechnology; BARRY, KERRIE - Energy Joint Genome Institute; LIPZEN, ANNA - Energy Joint Genome Institute; BAUER, DIANE - Energy Joint Genome Institute; SHARMA, ADITI - Energy Joint Genome Institute; JENKINS, JERRY - Hudsonalpha Institute For Biotechnology; SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology; FRITSCHI, FELIX - University Of Missouri; JUENGER, THOMAS - University Of Texas At Austin

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2019
Publication Date: 6/25/2019
Citation: Lowry, D.B., Lovell, J.T., Zhang, L., Bonnette, J., Fay, P.A., Mitchell, R., Lloyd-Reilley, J., Boe, A.R., Wu, Y., Rouquette, F.M., Wynia, R.L., Weng, X., Behrman, K.D., Healey, A., Barry, K., Lipzen, A., Bauer, D., Sharma, A., Jenkins, J., Schmutz, J., Fritschi, F.B., Juenger, T.E. 2019. QTL x environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient. Proceedings of the National Academy of Sciences. 116(26):12933-12941. https://doi.org/10.1073/pnas.1821543116.
DOI: https://doi.org/10.1073/pnas.1821543116

Interpretive Summary: Finding the specific genes that adapt plants to their environments is a central goal of plant biology, and critical to breeding improved crops for agricultural production. This study tests for specific genes (‘loci’) that underlie adaptation to the environment (‘local adaptation’) in switchgrass, an emerging biofuel crop and dominant tallgrass species. The study assessed genetic variation at 10 locations spread across a large regional gradient in the range of switchgrass from Texas to South Dakota, USA. This is one of the largest studies to date of genetic controls of plant adaptation to the environment. The study identified loci related to biomass yield and found that that most loci contributed to local adaptation at some sites but were neutral in their contribution to adaptation at others. Few loci caused negative effects. By identifying genetic loci related to biomass yield across a large portion of the range of switchgrass, these results will inform breeding of new locally adapted varieties of switchgrass.

Technical Abstract: Local adaptation is the process by which natural selection drives divergence between environmental conditions over geographic space. Theory suggests that local adaptation should result from genetic trade-offs at individual loci across habitats. However, the few studies that have examined the genetic basis of local adaptation in nature have mostly found that adaptive loci are conditionally neutral and thus, have effects in some environments without clear trade-offs in other environments. The observed prevalence of conditional neutrality may be due to the experimental designs of studies of adaptation, which have used inbred annual study species, only two common gardens, and biparental mapping populations. Here, we expand genetics of local adaptation research by studying the effects of locally adaptive loci with a four-parent outbred mapping population in the outcrossing perennial species, switchgrass. To clarify how locally adapted loci individually contribute across environmental gradients, we conducted a study at 10 common gardens across the Great Plains of the USA. As in most previous studies, we find a preponderance of conditionally neutral loci. However, in contrast to previous studies, our many site experiment allowed us to examine conditionally neutral patterns at multiple points along an environmental gradient. Further, we calculated the combined effects of these loci on biomass across each of the field sites and found great potential for the development of high-yielding regionally adapted crop varieties by combining beneficial alleles of many conditionally neutral loci. Our results provide direct evidence that loci without clear trade-offs dominate the genetic architecture across the majority of the climatic range of switchgrass.