Broadening the genetic base of crops is crucial for developing varieties to respond
to global agricultural challenges such as climate change. Here, we analysed a diverse
panel of 371 domesticated lines of the model crop barley to explore the genetics of
crop adaptation. We first collected exome sequence data and phenotypes of key life
history traits from contrasting multi-environment common garden trials. Then we applied
refined statistical methods, including some based on exomic haplotype states, for
genotype-by-environment (GxE) modelling. Sub-populations defined from exomic profiles
were coincident with barley's biology, geography and history, and explained a high
proportion of trial phenotypic variance. Clear GxE interactions indicated adaptation
profiles that varied for landraces and cultivars. Exploration of circadian clock-related
genes, associated with the environmentally adaptive days to heading trait (crucial
for the crop's spread from the Fertile Crescent), illustrated complexities in GxE
effect directions, and the importance of latitudinally based genic context in the
expression of large-effect alleles. Our analysis supports a gene-level scientific
understanding of crop adaption and leads to practical opportunities for crop improvement,
allowing the prioritisation of genomic regions and particular sets of lines for breeding
efforts seeking to cope with climate change and other stresses.
