Fine Mapping of a Major Locus for Leaf Sheath Hairiness in Wheat Identifies TaSAIN1-4D as a Candidate Gene

Background/Objectives: Leaf sheath hairiness (LSH) is an adaptive trait in wheat that improves tolerance to biotic and abiotic stresses. Although trichome development has been extensively studied in model plants, the genetic basis of LSH in Triticeae crops remains poorly defined. Methods: In this study, the inheritance and genetic architecture of LSH were investigated. Two F2 populations were used, derived from crosses between the glabrous lines ‘Shumai 830’ and ‘Shumai 2262’ and the hairy line ‘Zhongkelanmai 1’. BSA-seq was combined with KASP marker genotyping to map and refine the trait locus. Candidate genes were evaluated through comparative genomics; sequence variation; and subcellular localization prediction. Results: Phenotypic evaluation revealed that LSH is a dominant trait, segregating at a 3:1 ratio in F2 populations. BSA-seq identified a major locus, QLsh.cwnu-4D, on chromosome 4DL. Fine mapping with KASP markers refined this region to a 1.67 Mb interval overlapping a 530 kb trichome-associated linkage disequilibrium block in Aegilops tauschii. Within this interval, TaSAIN1-4D, a salt-inducible protein unique to Triticeae, was identified as the strongest candidate gene. Extensive sequence variation among alleles (TaSAIN1-4Da; TaSAIN1-4Db; TaSAIN1-4Dc), including large insertions and multiple SNPs, indicated potential functional diversification. Predicted nuclear localization of TaSAIN1-4D supports a role in trichome regulation and stress adaptation. The co-dominant KASP marker K-cwnu-4D-502238348 was tightly linked to LSH and cosegregated perfectly, making it a reliable tool for marker-assisted selection. Conclusions: This study clarifies the genetic architecture of leaf sheath hairiness in wheat and identifies TaSAIN1-4D as a likely regulator. These findings provide a practical marker-assisted selection tool that can accelerate the development of improved wheat varieties with desirable leaf surface traits.