QTL-seq identifies genomic regions and candidate genes for tiller angle and thermo-inducible leaf colour in barley mutant-derived doubled haploid populations

Tiller angle and thermo-inducible leaf colour are agronomically important traits in barley, yet their genetic basis remains poorly understood. In this study, QTL-seq was applied to two doubled haploid (DH) populations derived from crosses between gamma-ray-induced mutants of the elite barley cultivar Vlamingh (V-V-HD and V-V-Y) and the Australian malting barley cultivar Buloke. The V-V-HD mutant exhibited a prostrate growth habit during vegetative development followed by erect growth after booting, whereas V-V-Y displayed thermo-inducible chlorophyll deficiency. Whole-genome resequencing of contrasting phenotypic bulks combined with ΔSNP index analysis identified tiller angle-associated genomic regions on chromosomes 4H, 3H and 7H. Several candidate genes within the chromosome 4H region were associated with chromatin regulation, cellular homeostasis and developmental signalling, while the chromosome 3H region contained an F-box family protein and other candidates involved in regulatory processes. For thermo-inducible leaf colour, a major genomic region was identified on chromosome 4H, along with a secondary genomic region on chromosome 5H. Leaf colour candidates within the chromosome 4H region included ubiquitin-proteasome components carrying predicted high-impact variants, chaperone-related candidates encoding DnaJ, DnaK/Hsp70, BAG family chaperone regulator 6, a heat shock transcription factor, and an SR splicing factor, several of which showed heat-responsive expression. The chromosome 5H region contained cross-validated missense or regulatory variants in genes including a GAMETE EXPRESSED 2 protein, a serine/threonine protein phosphatase 7 and a 5-nucleotidase. Eight KASP markers were developed for the leaf colour-associated 4H region, of which seven showed concordance with the contrasting phenotypes in selected DH lines. Overall, this study identifies genomic regions and prioritised genes associated with tiller angle and thermo-inducible leaf colour and provides trait-linked markers for further validation and barley improvement.