Mapping Quantitative Trait Loci for Pre-Harvest Sprouting Resistance in Wheat Using Berkut × Worrakatta Recombinant Inbred Lines

Abstract Background Pre-harvest sprouting (PHS) in wheat is a significant global challenge influenced by climate. This study aimed to decipher the genetic underpinnings of PHS and identify resistance genes using 309 recombinant inbred lines (RILs) derived from the "Berkut × Worrakatta" cross. Methods:Phenotypic assessment of PHS traits was performed using the whole-spike sprouting method across various environments, complemented by quantitative trait loci (QTL) analysis employing a wheat 50K SNP chip. Results Results showed high PHS rates in both parental lines across multiple environments. Progeny exhibited substantial variation in PHS rates, with coefficients of variation ranging from 0.16 to 0.19 and a phenotypic variation ranging from 23.92% to 100%, suggesting pronounced transgressive segregation. Nine QTLs associated with PHS were identified on chromosomes 1AL, 1DL, 2AL, 2AS, 2BS, 3DS, 4BL, and 7BL. These loci accounted for 2.67% to 6.39% of the phenotypic variation. Notably, the enhancer alleles at four loci—1DL, 2BS, 4BL, and 7BL—originated from 'Worrakatta', and 'Berkut' contributed the enhancer alleles at the remaining five loci. Two QTLs, QPHS.xjau-1AL.1 and QPHS.xjau-1AL.2 , were stable across multiple environments. Specifically, QPHS.xjau-1AL.1 was present in three environments and explained 3.86% to 6.39% of the phenotypic variation, while QPHS.xjau-1AL.2 appeared in one environment under average conditions, explaining 2.67% to 4.87% of the variation. Conclusions Our study also identified eight candidate genes associated with wheat PHS, including those encoding MYB transcription factors that influence flavonoid biosynthesis and grain color, as well as genes involved in stress response and gibberellin biosynthesis, which are crucial for plant growth and development. These genes represent vital targets for enhancing wheat PHS resistance.