Integrative multi-locus GWAS and SNP effect analysis reveal the genetic basis of heading, maturity, and grain-filling duration in a bread wheat

Phenological traits, heading date (HD), grain filling duration (GFD), and maturity date (MD) are critical determinants of wheat adaptation, productivity, and climate resilience. Here, we dissected the genetic architecture of these traits using a core collection of 562 bread wheat (Triticum aestivum L.) accessions genotyped with the 35 K Axiom® array. Population structure indicated discrete subgroups with moderate relatedness, and linkage disequilibrium decayed fastest in the A subgenome (∼1.5 Mb) relative to B and D subgenomes (∼2.1 Mb). A multi-locus GWAS (FarmCPU and BLINK) across 24 phenotypic datasets (five individual years, across-year means, BLUPs, and BLUEs) detected 261 non-redundant trait-associated SNPs. Post-GWAS, structure-adjusted one-way tests revealed significant phenotypic differences among genotype classes at 238 loci. Mining flowering/senescence-related genes within LD windows of significant SNPs identified key homologs: Ppd1, TFL1b, JMJ30, PIN1AT, VRN5, and STAY-GREEN, linking photoperiod/circadian, chromatin, and hormonal pathways. Furthermore, the magnitude of allelic effects, measured using ΔMean (trait mean difference between alleles), identified eight, four, and four novel SNPs significantly affecting HD (7–11 days), MD (6–8 days), and GFD (∼3 days), respectively. Haplotype-based refinement of these regions identified putative causal variants from six genes, including a stop-gain SNP AX-95222044 in TraesCS4B02G307900; missense variants in TraesCS3D02G203900 (RAVE complex proteinRav1 C-terminal; AX-95156660) and TraesCS3B02G218500 (pyruvate kinase; AX-94455109); and three impactful 3′-UTR SNPs, AX-94678469 (TraesCS1B02G196200, ARM-repeat protein), AX-94842780 (TraesCS3D02G020400, F-box protein) and AX-95131834 (TraesCS6D02G184100, chloroplast Fe-S cluster assembly protein). These findings uncover novel candidate genes underlying wheat phenology and provide valuable genomic targets for marker-assisted selection and climate-resilient breeding programs.