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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\u2013world 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\n                    <jats:italic>Fr-H2<\/jats:italic>\n                    . 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 \u03b1-amylase induction and stress responses. In addition, orthology analysis linked barley loci to known wheat LMA QTL (\n                    <jats:italic>QLMA.agt-5B<\/jats:italic>\n                    ) and stress-responsive genes (\n                    <jats:italic>TaCBFIVd<\/jats:italic>\n                    ,\n                    <jats:italic>TaTIFY3B<\/jats:italic>\n                    ). These findings demonstrate the value of barley as a cross-species model and provide a framework for improving grain quality in cereals.\n                  <\/jats:p>","DOI":"10.1038\/s41598-026-58186-7","type":"journal-article","created":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T11:54:53Z","timestamp":1782561293000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Barley genetics elucidate the genetic architecture of cold-induced late maturity \u03b1-amylase for wheat improvement"],"prefix":"10.1038","volume":"16","author":[{"given":"Bipin","family":"Neupane","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elliott J.","family":"Marston","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert S.","family":"Brueggeman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deven R.","family":"See","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,27]]},"reference":[{"key":"58186_CR1","doi-asserted-by":"publisher","first-page":"352","DOI":"10.3390\/agronomy9070352","volume":"9","author":"P Giraldo","year":"2019","unstructured":"Giraldo, P., Benavente, E., Manzano-Agugliaro, F. & Gimenez, E. 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