Genome-Wide Association Study on Spike Architecture Traits and Elite Haplotype Mining in Winter Wheat

Spike-related traits constitute a key factor influencing wheat yield. This study conducted a genome-wide association study (GWAS) on wheat spike-related traits to identify significant loci controlling these traits, thereby providing theoretical references for research on genetic improvement of wheat spike-related traits.

Using a panel of 261 winter wheat varieties (lines), we measured spike-related phenotypic traits and performed genome-wide association studies (GWAS) with the wheat 90K SNP array, employing the Fixed and Random Model Circulating Probability Unification (Farm CPU) model. Stable and significant loci identified through this analysis were further subjected to haplotype analysis.

Under three environmental conditions, all 11 panicle-related traits exhibited extensive phenotypic variation, with coefficients of variation (CV) ranging from 3.63 to 64.29. The heritability estimates for these traits varied between 0.42 and 0.84. Highly significant differences (P<0.001) were observed among genotype, environment, and genotype × environment interactions. Genome-wide association study (GWAS) identified 171 loci significantly associated with the 11 traits (P<0.001), including 20 pleiotropic loci detected in two or more environments. These loci were associated with eight panicle traits: panicle length (3 loci), peduncle length (7 loci), sterile spikelet number (1 locus), fertile spikelet number (2 loci), total spikelet number (2 loci), grains per panicle (1 locus), grain weight per panicle (2 loci), and thousand-grain weight (2 loci). The phenotypic contribution rates of these loci ranged from 0.95% to 18.54%. A pleiotropic locus (Ra_c10072_677) significantly associated with both grain weight per panicle and grains per panicle was identified on chromosome 7B, demonstrating phenotypic contribution rates ranging from 2.62% to 6.16%. The marker wsnp_Ex_rep_c69639_68590556, which showed consistent association with peduncle length across two or more environmental conditions (explaining 5.94% of the genetic variation), was selected for haplotype analysis. Three haplotypes (Hap1, Hap2, and Hap3) were characterized, with distribution frequencies of 77.40%, 13.70%, and 8.80%, respectively. Phenotypic analysis revealed that 261 winter wheat cultivars (lines) carrying haplotype Hap3 (30.58 cm) exhibited significantly greater peduncle length (P<0.001) compared to those with Hap1 (28.67 cm) and Hap2 (27.49 cm). The haplotype distribution frequencies showed significant geographic divergence: Hap1 predominated in the Northern Winter Wheat Region, Hap2 was more prevalent in the Huang-Huai Winter Wheat Region, while Hap3 displayed no substantial frequency (>5%) across all winter wheat regions. For stably detected loci across three environments, candidate gene mining identified four genes associated with panicle development. These genes, functionally annotated as encoding MYB transcription factors and F-box domain-containing proteins, represent key candidates influencing panicle architecture.

The spike traits of wheat exhibited significant variation across different genotypes. A total of twenty stably associated loci were identified across two or more environments. Three distinct haplotypes significantly associated with the peduncle length were detected on chromosome 7B, and four candidate genes potentially related to spike traits were screened out.