Comparative genomics of seed dormancy using Brachypodium distachyon as a model for temperate cereals

Abstract Seed dormancy is a natural mechanism that delays germination until conditions are most suitable. Previous studies have shown that phylogenies and environmental conditions shape the evolutionary trajectories of seed dormancy, making it an interesting subject for comparative genomics analysis between the dicot model plant Arabidopsis thaliana (Arabidopsis), the tropical cereal crop rice ( Oryza sativa ), and Brachypodium distachyon (Brachypodium), the monocot model plant for temperate grasses, which include important cereal crops like wheat, barley, and oat. We curated genes with known functions in seed dormancy and compared their evolutionary relationships between Arabidopsis, rice, and Brachypodium (accession Bd21), highlighting conserved central hormonal pathways while also revealing gene loss and duplication events. The Brachypodium genome encodes conserved components of major pathways regulating seed dormancy induction, maintenance and release, most notably seed covering-mediated dormancy imposition, plant hormones (ABA, GA, Auxin, Ethylene, Jasmonate, Brassinosteroids) metabolism and signalling, environmental signals (temperature, light and nutrient) perception and integration. Major seed dormancy genes, including MFT , MKK3 , Sdr4 , AlaAT and DOG1, show high homology between cereal species while lacking similar roles in Arabidopsis in some cases. Overall, our results indicate a conserved mechanism governing seed dormancy via the central hormonal pathways integrating diverse environmental cues through coordinated molecular components.