Single-gene resolution of locally adaptive genetic variation in Mexican maize

Authors: GATES, DANIEL - University Of California, Davis; RUNCIE, DAN - University Of California, Davis; JANZEN, GARRETT - Iowa State University; ROMERO NAVARRO, ALBERTO - Cornell University; WILLCOX, MARTHA - International Maize & Wheat Improvement Center (CIMMYT); SONDER, KAI - International Maize & Wheat Improvement Center (CIMMYT); SNODGRASS, SAMANTHA - Iowa State University; RODRIQYEZ-ZAPATA, FAUSTO - North Carolina State University; J.H. SAWERS, RUAIRIDH - North Carolina State University; Buckler, Edward - Ed; HEARNE, SARAH - International Maize & Wheat Improvement Center (CIMMYT); HUFFORD, MATTHEW - Iowa State University; ROSS-IBARRA, JEFFREY - University Of California, Davis

Submitted to: bioRxiv
Publication Type: Other
Publication Acceptance Date: 7/18/2019
Publication Date: 7/18/2019
Citation: Gates, D., Runcie, D., Janzen, G., Romero Navarro, A., Willcox, M., Sonder, K., Snodgrass, S., Rodriqyez-Zapata, F., J.H. Sawers, R., Buckler IV, E.S., Hearne, S., Hufford, M., Ross-Ibarra, J. 2019. Single-gene resolution of locally adaptive genetic variation in Mexican maize. bioRxiv. https://doi.org/10.1101/706739.
DOI: https://doi.org/10.1101/706739

Interpretive Summary: Breeding diverse crops that maintain high yields in a changing global climate is one of the most significant challenges facing modern agricultural research. Traditional varieties of maize grown by farmers throughout the Americas have adapted to their specific locations and environment. By examining and comparing the genetic differences between 4500 traditional varieties at millions of places in the genome, this study was able to identify natural genetic variation responsible for some of those environmental adaptations. Many of these results were confirmed by a series of large scale field trials. Importantly, the genetic resolution of this approach was much higher than prior strategies, and we frequently identified individual genes. This provides breeders clear routes to access this important genetic diversity while preserving the gains achieved through excellent varieties developed over the last century.

Technical Abstract: Threats to crop production due to climate change are one of the greatest challenges facing plant breeders today. While considerable adaptive variation exists in traditional landraces, natural populations of crop wild relatives, and ex situ germplasm collections, separating adaptive alleles from linked deleterious variants that impact agronomic traits is challenging and has limited the utility of these diverse germplasm resources. Modern genome editing techniques such as CRISPR offer a potential solution by targeting specific alleles for transfer to new backgrounds, but such methods require a higher degree of precision than traditional mapping approaches can achieve. Here we present a high-resolution genome-wide association analysis to identify loci exhibiting adaptive patterns in a large panel of more than 4500 traditional maize landraces representing the breadth of genetic diversity of maize in Mexico. We evaluate associations between genotype and plant performance in 13 common gardens across a range of environments, identifying hundreds of candidate genes underlying genotype by environment interaction. We further identify genetic associations with environment across Mexico and show that such loci are associated with variation in yield and flowering time in our field trials and predict performance in independent drought trials. Our results indicate that the variation necessary to adapt crops to changing climate exists in traditional landraces that have been subject to ongoing environmental adaptation and can be identified by both phenotypic and environmental association.