Marginal mountain environments drive adaptive diversification in Alpine rye landraces

Cereals play a central role in the human diet and agriculture worldwide, and their productivity and quality are threatened by climate change, with impacts expected to intensify over the coming decades. Among cereal crops, rye (Secale cereale L.) plays a valuable role in wheat genetic improvement as well as in marginal economies, and offers ideal features to study plant adaptation to environmental and climatic conditions. In this study, we expanded an existing collection of rye landraces from the Western Alps to study rye adaptation to marginal mountain environments. Population structure, gene flows and the association between genomic loci and environmental variables were studied through genotype-environment association. Results showed that despite demographic history and neutral processes being the driving forces for rye diversification, a relevant number of loci involved in stress responses were associated with marginality and climate. These loci are of great interest for further exploitation in rye and wheat breeding.