Barley genetics elucidate the genetic architecture of cold-induced late maturity α-amylase for wheat improvement

Late maturity α-amylase (LMA) poses severe quality and economic threats to cereal crops by degrading grain quality through cold-induced alpha-amylase synthesis. Despite its economic impact, the genetic mechanism of cold-induced LMA remains poorly understood, particularly in hexaploid wheat due to its large, redundant genome. To overcome these limitations, we used barley as a diploid model to dissect the genetic architecture of cold-induced LMA. A genome-wide association study (GWAS) was conducted on 352 accessions from the mini-world barley core collection grown under controlled normal and cold-stressed conditions. This analysis identified eight significant and 20 suggestive SNPs. Multi-model GWAS (BLINK, FarmCPU, MLMM), haplotype, and allele-specific analyses revealed cold-responsive hotspots on chromosomes 3H and 5H, the latter colocalizing with the frost tolerance locus Fr-H2. SNP-to-gene mapping prioritized candidates involved in hormonal crosstalk (ABA/GA/JA, TIFY3, SnRK kinases), redox regulation (APX4, GST), and sugar transport (SWEET4), implicating pathways known to influence α-amylase induction and stress responses. In addition, orthology analysis linked barley loci to known wheat LMA QTL (QLMA.agt-5B) and stress-responsive genes (TaCBFIVd, TaTIFY3B). These findings demonstrate the value of barley as a cross-species model and provide a framework for improving grain quality in cereals.