Identification of novel loci regulating dormancy in barley and association with hypoxia sensitivity

Low seed dormancy is an essential trait in malting barley since malting involves rapid and uniform induction of germination. At least two major QTLs on chromosome 5H, SD1 and SD2, regulate dormancy in multiple barley populations, and additional genetic regions are thought to be involved. To identify novel genetic loci that might be associated with dormancy, a panel of genotypes from diverse agro-ecosystems were evaluated alongside two Canadian biparental populations for germination rate. Association mapping revealed QTLs within the SD1 and SD2 loci in the Canadian populations, while neither of these loci were linked to dormancy in the diversity panel. The diversity panel identified 14 additional marker-trait associations, including novel genetic loci. An alanine aminotransferase (AlaAT1) underlies dormancy regulation at the SD1 allele and is thought to help mitigate the suppressive effects of hypoxia on respiration during grain fill. Additional testing with four genotypes carrying either dormant or non-dormant AlaAT1 alleles revealed that dormant alleles had increased hypoxia sensitivity and hypoxia-responsive gene expression during grain fill. Together, this work indicates that multiple genetic regions influence dormancy and suggests that hypoxia influences dormancy establishment in barley. HighlightDormancy is regulated by distinct genetic regions in North American barley compared to African barley. The SD1 locus influences dormancy in North American lines and genotypes with the dormant SD1 allele are more sensitive to hypoxia.