Rainfall patterns during barley seed development underlie genomic variation for germination after flooding

The diversity of plant genetic resources is the result of complex evolutionary processes, including adaptation to environmental stresses. High precipitation levels during the growing season may result in soil flooding events that place major constraints on crop productivity. Barley (Hordeum vulgare) is one of the most important cereals worldwide and serves as a model for studying the molecular responses of plants to climate change, due to its wide adaptability and diffusion to different environments. We explored the genetic associations of a global collection of barley landraces and wild relatives with rainfall regimes recorded in their growing areas. We found that the rainfall patterns observed during the driest months of the year and corresponding to the seed development period correlated significantly with the subsequent capacity of barley accessions to germinate after flooding. We then conducted an environmental genome-wide association study (eGWAS) and analysed exome sequencing data, which revealed a narrow region on barley chromosome 1 with a possible influence on barley response to rainfall patterns. Using molecular approaches, we identified gene candidates involved in seed morphology and dormancy that are crucial for barley germination in soil after a flooding event in a natural environment.