Trends of genetic changes uncovered by Env- and Eigen-GWAS in wheat and barley

Abstract

The process of crop breeding over the last century has delivered new varieties with increased genetic gains, resulting in higher crop performance and yield. However in many cases, the underlying alleles and genomic regions that have underpinned this success remain unknown. This is due, in part, to the difficulty in generating sufficient phenotypic data on large numbers of historical varieties to allow such analyses to be undertaken. Here we demonstrate the ability to circumvent such bottlenecks by identifying genomic regions selected over 100 years of crop breeding using the age of a variety as a surrogate for yield. Using environmental genome-wide association scans (EnvGWAS) on variety age in two of the worlds most important crops, wheat and barley, we found strong signals of selection across the genomes of our target crops. EnvGWAS identified 16 genomic regions in barley and 10 in wheat with contrasting patterns between spring and winter types of the two crops. To further examine changes in genome structure in wheat and barley over the past century, we used the same genotypic data to derive eigenvectors for deployment in EigenGWAS. This resulted in the detection of seven major chromosomal introgressions that contributed to adaptation in wheat. The deployment of both EigenGWAS and EnvGWAS based on variety age avoids costly phenotyping and will facilitate the identification of genomic tracts that have been under selection during plant breeding in underutilized historical cultivar collections. Our results not only demonstrate the potential of using historical cultivar collections coupled with genomic data to identify chromosomal regions that have been under selection but to also guide future plant breeding strategies to maximise the rate of genetic gain and adaptation in crop improvement programs. Significance Statement100 years of plant breeding have greatly improved crop adaptation, resilience, and productivity. Generating the trait data required for these studies is prohibitively expensive and can be impossible on large historical traits. This study reports using variety age and eigenvectors of the genomic relationship matrix as surrogate traits in GWAS to locate the genomic regions that have undergone selection during varietal development in wheat and barley. In several cases these were confirmed as associated with yield and other selected traits. The success and the simplicity of the approach means it can easily be extended to other crops with a recent recorded history of plant breeding and available genomic resources.