QTL detection, validation, candidate genes and KASP markers for pre-harvest sprouting tolerance in white grained common wheat.

BACKGROUND: Pre-harvest sprouting (PHS) in common wheat refers to the premature germination of grains on the spike under high humid conditions. This phenomenon increase alpha-amylase activity and degrade starch, resulting in reduced falling number (FN) and compromised milling and baking quality. The genetic control of PHS is complex and polygenic, presenting a significant challenge but also offering opportunities for trait improvement through targeted breeding. RESULTS: A doubled haploid (DH) population comprising 386 lines, derived from a cross between two white-grained spring wheat genotypes SC8021-V2 (PHS-tolerant) and AC Karma (moderately susceptible to PHS), were evaluated for sprouting score (SS) and FN traits across two locations over two crop seasons in India. The population was genotyped using the Infinium iSelect 90K SNP array. Using composite interval mapping (CIM) and R/qtl, 29 main-effect QTL (MQTL) for SS and FN explaining 2.10-8.63% (SS) and 2.10-10.93% (FN) of the phenotypic variation were identified on 13 chromosomes. CIM exclusively revealed 9 MQTL (SS, 7; FN, 1; SS + FN, 1), R/qtl exclusively revealed 8 MQTL (SS, 6; FN, 2), and 12 MQTL (SS, 6; FN, 5; SS + FN, 1) were revealed by both; 16 MQTL were not previously reported. Nineteen first-order epistatic interactions involving 18 SNPs were also detected. We validated six stable MQTL for SS by confirming their favourable alleles in five highly PHS-tolerant DH lines. A set of 368 candidate genes encoding 42 distinct domains were identified; twenty-two were associated with ABA signaling. Candidate genes have multifaceted role regulating seed dormancy, hormone signaling, seed coat formation, starch metabolism, and stress adaptation contributing to PHS resilience. Three breeder-friendly KASP markers for three QTL for sprouting score (two on 2B, one on 4B) were developed and validated. CONCLUSIONS: This study provides novel insights and discovered 16 previously unreported QTL, epistatic interactions, and key candidate genes, highlighting the complex regulation of PHS-related traits. The availability of three diagnostic KASP markers offer practical tools for marker-assisted selection, facilitating the genetic improvement of PHS in common wheat.