An integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops

Authors: LI, XIANRAN - Iowa State University; GUO, TINGTING - Iowa State University; WANG, JINYU - Iowa State University; BEKELE, WUBISHET - Agriculture And Agri-Food Canada; SUKUMARAN, SIVAKUMAR - International Maize & Wheat Improvement Center (CIMMYT); Vanous, Adam; MCNELLIE, JAMES - Iowa State University; CORTES, LAURA - Iowa State University; LOPES, MARTA - International Maize & Wheat Improvement Center (CIMMYT); LAMKEY, KENDALL - Iowa State University; WESTGATE, MARK - Iowa State University; MCKAY, JOHN - Colorado State University; ARCHONTOULIS, SOTIRIOS - Iowa State University; REYNOLDS, MATTHEW - International Maize & Wheat Improvement Center (CIMMYT); TINKER, NICHOLAS - Agriculture And Agri-Food Canada; SCHNABLE, PATRICK - Iowa State University; YU, JIANMING - Iowa State University

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/9/2021
Publication Date: 3/10/2021
Citation: Li, X., Guo, T., Wang, J., Bekele, W., Sukumaran, S., Vanous, A.E., Mcnellie, J., Cortes, L., Lopes, M., Lamkey, K., Westgate, M., Mckay, J., Archontoulis, S., Reynolds, M., Tinker, N., Schnable, P., Yu, J. 2021. An integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops. Molecular Plant. 14(6):874-887. https://doi.org/10.1016/j.molp.2021.03.010.
DOI: https://doi.org/10.1016/j.molp.2021.03.010

Interpretive Summary: Identifying mechanisms and pathways involved in gene-environmental interplay is a long-standing challenge. A critical step was to identify environmental indices that are both biologically relevant and estimable for new environments. With extensive field-observed complex traits, environmental profiles, and genome-wide SNPs in three major crops, we demonstrated a framework to pinpoint the genetic and environmental factors underlying phenotypic variation of diverse genetic materials. The implementation of this framework allowed for identification of genes affecting two reaction-norm parameters (i.e., intercept and slope) from flowering-time for multiple crop species. In addition, the framework allowed for robust performance predictions across all crop species.

Technical Abstract: Identifying mechanisms and pathways involved in gene-environmental interplay is a long-standing challenge. It is highly desirable to establish an integrated framework for complex trait dissection and prediction with an environmental dimension. A critical step was to identify environmental indices that are both biologically relevant and estimable for new environments. With extensive field-observed complex traits, environmental profiles, and genome-wide SNPs in three major crops, we demonstrated a framework to pinpoint the genetic and environmental factors underlying phenotypic variation of diverse genetics materials. Genes identified for two reaction-norm parameters (i.e., intercept and slope) derived from the flowering-time were less colocalized for a diverse maize panel than those for wheat and oat breeding panels, agreeing with the different diversity levels of genetic constitution of the panels. In addition, we showcased the potential of this framework for systematic performance forecasting of diverse germplasm panels in new environments. This general framework and the companion CERIS-JGRA analytical package should facilitate biologically informed dissection of complex traits and enhanced performance prediction in breeding for future climates.