Genetic dissection of root traits in barley identifies major QTLs and domestication signature

KEY MESSAGE: Using genome-wide association analysis in a barley germplasm panel, we identified root trait QTLs, domestication-driven morphological shifts, and candidate genes to guide breeding for improved root ideotypes in modern cultivars. Root system architecture (RSA) determines the plant's ability to anchor to soil and absorb water and nutrients, thereby affecting productivity and stress tolerance. In this study, we investigated phenotypic variation for seven root traits at the seedling stage, performed a genome-wide association study (GWAS), and identified novel quantitative trait loci (QTLs) and candidate genes using a germplasm collection representing global barley diversity. Traits heritability ranged from 0.70 to 0.88. Domestication and breeding syndromes were detected for seminal root number (SRN), which increased from 4.2 roots in wild accessions to 5.9 in landraces to 6.3 in modern cultivars. Similarly, root growth angle (RGA) widened from 42.9° in wild accessions to 60.3° in modern cultivars. Lateral root density and length increased from wild barley to cultivars, while average seminal root length (ARL) shortened. GWAS identified 106 QTLs explaining 25-61% of the phenotypic variation per trait. Candidate genes at GWAS peaks for SRN encoded ARABIDILLO- and WD-40-related proteins, an exocyst complex component, and a serine protease; UDP-glycosyltransferase for RGA; and jasmonate receptor and F-box encoding genes for ARL. Our findings provide valuable insights for molecular biologists and breeders to design and implement root architecture ideotypes in new cultivars, enhancing their adaptability to challenging environments.