Abstract
SummaryBroadening 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 (G×E) 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 G×E 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 G×E 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.
Highlights
Barley (Hordeum vulgare ssp. vulgare) is globally the fourth most important cereal crop after maize, rice and wheat
Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change
We analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation
Summary
Barley (Hordeum vulgare ssp. vulgare) is globally the fourth most important cereal crop after maize, rice and wheat (http://faostat.fao.org). Flowering time, reflected in the days to heading (DTH) trait, which is the time elapsed between planting of the crop and ear emergence, is an important adaptive feature in the spread of many cereal crops from their origins, enabling the matching of reproductive seed production to appropriate environmental conditions of temperature, precipitation, evapotranspiration, light and other variables (Nakamichi, 2015). Understanding genetic variation in DTH is of academic interest for exploring the domestication and expansion of cereal crops and of practical importance for addressing the future climate change-related shifts that will be required in production. The spring and winter growth habits of different barley varieties, with their different responses to cold, heat and light, make the crop interesting for exploring environmentally adaptive responses in agriculture (Dawson et al, 2015)
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