Dissecting the genetic architecture of pre-harvest sprouting tolerance in Indian dwarf wheat (Triticum sphaerococcum) by multi-locus association analysis.

Wheat, a major staple crop, contributes significantly to global protein and calorie intake. However, the increasing challenges posed by climate change and a growing population threaten its stable production. Pre-harvest sprouting (PHS), triggered by prolonged rainfall and humidity before harvest, significantly reduces wheat grain yield and quality. This study is the first to assess PHS tolerance (PHST) in a global collection of 116 T. sphaerococcum accessions, which were characterized at three different locations. A 35 K Axiom single nucleotide polymorphism (SNP) array was used to genotype these accessions and finally 15, 308 high quality SNPs were used to perform Genome-wide association studies (GWAS) employing two single-locus GWAS (SL-GWAS) and four multi-locus GWAS (ML-GWAS) models. Consequently, twelve marker-trait associations (MTAs) controlling PHST were identified using SL-GWAS and ML- GWAS models (p < 0.001). Among these, five MTAs (AX-94415302, AX-94919611, AX-94403953, AX-95220897, and AX-94756068), were consistently found across all the tested environments. In silico analysis revealed that these SNPs were located within the candidate genes (CGs) containing domains such as LRR, NAC, serine/threonine kinase, F-box, WRKY, SANT/Myb, cytochrome P450, homeobox-like, and WD40, which are involved in regulating seed germination, dormancy, and abiotic stress tolerance. Furthermore, haplotype analysis led to the identification of a variable number of haplotypes across 10 MTAs. Notably, three haplotypes, namely H005, H006, and H007 were present in PHS tolerant accessions, TS28, TS64 and TS81 respectively, representing favourable allelic combinations for PHST. These findings provide valuable genetic resources and potential targets for breeding strategies to enhance PHST in wheat.