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.

The quality of wheat grain was an important factor affecting the processing quality and nutritional. Mining loci and candidate genes significantly associated with wheat grain quality traits provided a basis for broadening the understanding of the genetic mechanism of quality traits and molecular marker-assisted quality.

By measuring five quality traits, including protein content (GPC), wet gluten content (WGC), starch content (GSC), settling value (SV) and grain hardness (GH), in 259 winter wheat varieties (lines) from domestic and abroad, and conducting genome-wide association analysis in combination with 90K SNP chip, the significant association loci located were subjected to haplotype analysis.

All five traits conformed to normal distribution and showed rich variation among different environments, and the coefficient of variation of sedimentation value was the largest (20.11%-24.42%). All traits have shown highly significant differences (P<0.001) among genotype, environment, and genotype×environment, with a broad-sense heritability of 0.77-0.84. A total of 44 loci significantly associated (P<0.001) with five traits were detected by genome-wide association analysis, distributed in 19 linkage groups other than chromosomes 1D and 3D. Eighteen loci were stable in two or more environments, involving all five traits including protein content (12), wet gluten content (9), starch content (11), sedimentation value (12) and grain hardness (7), explaining 4.27%-10.98% of the genetic variation. Thirteen of them were multi-effect loci, with the largest number of multi-effect loci (7) associated with traits such as protein content, wet gluten content, settling value and starch content. The GENE-0762_631, IAAV7742 and RAC875_c66845_466 loci located on 2B, 2D and 3A chromosomes were detected simultaneously at two environmental and BLUP values with a range of 4.32%-7.07% phenotypic contribution. Through haplotype analysis of multi-effect loci present in multiple environments with high phenotypic contribution, four different haplotypes, Hap1, Hap2, Hap3 and Hap4, which were significantly associated with traits such as protein content, sedimentation value and starch content, were uncovered at the D_GDS7LZN02F4FP5_176 locus of chromosome 5D, among them Hap1 was a high starch content haplotype (P<0.001), while Hap2 and Hap3 were both haplotypes with high protein content and sedimentation value (P<0.05), and the four haplotypes accounted for 74.22%, 16.21%, 6.92% and 2.65%, respectively. The distribution frequencies of haplotypes from different sources of winter wheat were analyzed, in which the distribution frequencies of haplotype Hap2 with high protein content and sedimentation value were from high to low in the Huanghuai winter wheat regions>northern winter wheat region>abroad varieties>middle and lower reaches of the Yangtze River winter wheat region>southwest winter wheat region. Candidate genes were mined for stable genetic loci, and 10 candidate genes that might be related to wheat grain quality were screened.

In the study, 18 stable loci significantly associated with grain quality traits were detected, 4 different haplotypes were identified, and 10 candidate genes related to grain quality were screened.

Starch is the main component of wheat kernel and plays an important role in processing. The gelatinization characteristic of starch is an important index to evaluate its quality. The genetic variation of starch gelatinization was studied to provide basis for improving wheat quality.

Seven starch gelatinization traits, including gelatinization temperature, peak time, peak viscosity, trough viscosity, final viscosity, decay value and recovery value, were phenotypically determined in 205 winter wheat varieties. Genome-wide association analysis was performed using 90K chip, and haplotype analysis was performed on the stable and significant sites found.

The seven characteristics, such as pasting temperature, showed abundant variation in different environments, and the coefficient of variation of attenuation value was the largest (29.31%-31.14%). There were significant differences among genotype, environment and genotype × environment, and the generalized heritability was 0.69-0.86. Through genome-wide association analysis, we found 198 loci that showed significant associations with seven traits. It was distributed in 20 other linked groups except 6D chromosome. There were 58 sites that were stable in 2 or more environments, involving all 7 traits, such as pasting temperature (10), peak time (5), peak viscosity (12), trough viscosity (10), final viscosity (7), break down (4) and set back (10), which could explain 5.54%-22.21% of genetic variation, twenty-one new sites were identified. By haplotype analysis of multiple effector sites that exist in multiple environments and have high phenotypic contribution, Four haplotypes, Hap1 (66.84%), Hap2 (16.84%), Hap3 (9.70%) and Hap4 (6.63%), were found at Kukri_c17417_407 on chromosome 4A, which were significantly related to peak viscosity and break down. Where Hap2 is the peak viscosity and high break down. (P<0.0001). The distribution frequency of varieties (lines) containing haplotype Hap2 in different ecological regions was from high to low as Huanghuai winter wheat region>foreign varieties>Southwest winter wheat region>Middle and lower reaches of Yangtze River winter wheat region>Northern winter wheat region. There were 11 single cause multieffect sites, among which there were 3 multiple effect sites associated with final viscosity, set back, peak time and trough viscosity. Jagger_c4026_328 and other 11 stable genetic loci located on 1B, 2A, 3A, 3B, 4A, 4B, 5B and 6B were mined, and 11 candidate genes that might be related to wheat starch gelatinization traits were screened.

In this study, RVA parameters had high heritability, and the RVA parameters of wheat starch were different in different environments. In this study, RVA parameters had high heritability, and the RVA parameters of wheat starch were different in different environments. 58 stable loci were detected that were significantly associated with starch gelatinization traits, and 4 different haplotypes were identified on chromosome 4A that were significantly associated with peak viscosity and break down, and 11 candidate genes related to starch gelatinization were screened, which could provide help for marker-assisted high-quality wheat breeding.