Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (3): 499-514.doi: 10.3864/j.issn.0578-1752.2026.03.003

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-Wide Association Study and Candidate Gene Identification for Thousand Grain Weight in Winter Wheat

WANG YongSheng1,2(), NIU Li1,2, WANG ChangJie1,2, MA LiHua1,2, LIAN XiaoXiao1, MENG YaXiong1,2, MA XiaoLe1,2, YAO LiRong1,2, ZHANG Hong1,2, YANG Ke1,2, LI BaoChun2,3, WANG HuaJun1,2, SI ErJing1,2(), WANG JunCheng1,2()   

  1. 1 College of Agronomy, Gansu Agricultural University, Lanzhou 730070
    2 State Key Laboratory of Aridland Crop Science, Lanzhou 730070
    3 College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070
  • Received:2025-07-31 Accepted:2025-09-15 Online:2026-02-01 Published:2026-01-31
  • Contact: SI ErJing, WANG JunCheng

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Abstract:

【Objective】Thousand-grain weight (TGW), a key determinant of final wheat yield, is of great importance for genetic dissection. Precise identification of stable loci and key candidate genes controlling TGW provides theoretical foundations and genetic resources for marker-assisted breeding of high-TGW and high-yield wheat varieties. 【Method】A total of 291 wheat accessions from diverse origins were genotyped using a 100K SNP array. TGW phenotypic data collected over two consecutive years and their best linear unbiased predictions (BLUPs) were analyzed using a genome-wide association study (GWAS) based on a mixed linear model (MLM) incorporating both population structure (P) and kinship (K). Significant loci were further subjected to haplotype analysis. 【Result】TGW showed broad variation across years and BLUP values (mean: 38.24-38.82 g; coefficient of variation: 17.62%-19.93%). The correlation between years was 0.88 (P<0.01), and correlations with BLUP values reached 0.97 (P<0.01). Phenotypic data displayed normal distributions under different environments, meeting the basic requirements for GWAS. A total of 19 SNPs significantly associated with TGW were detected on chromosomes 3B, 5A, and 7A, explaining 6.85%-9.68% of the phenotypic variation; 16 of them were repeatedly detected across multiple environments, indicating stability. Haplotype analysis at locus 7A_145980808 revealed four haplotypes (Hap1-Hap4), of which Hap4 was associated with high TGW (P<0.01) and Hap2 with low TGW (P<0.01). The frequencies of Hap1-Hap4 were 72.36%, 14.55%, 8.73%, and 4.36%, respectively. Domestic accessions were enriched for Hap3 (95.83%) and Hap4 (83.33%), with Hap4 predominantly distributed in the Northwestern winter wheat region, especially in germplasm from Gansu. Candidate gene mining within 3.6 Mb regions flanking significant loci on chromosomes 3B, 5A, and 7A identified 95 genes, among which four were highlighted based on gene annotation and expression profiles. 【Conclusion】GWAS identified 16 stable SNP loci significantly associated with TGW, four distinct haplotypes, and four key candidate genes. These genes are mainly involved in carbohydrate synthesis and transport, cell wall polysaccharide assembly, protein homeostasis, and transcriptional regulation of starch biosynthesis, providing valuable targets for molecular breeding of high-yield wheat.

Key words: wheat, thousand-grain weight, SNP markers, GWAS, haplotype, candidate genes

Table 1

Statistical analysis of thousand-grain weight of 291 winter wheat varieties"

环境
Environment		 最大值
Max (g)		 最小值
Min (g)		 平均值
Average (g)		 标准差
SD (%)		 峰度
Kurtosis		 偏度
Skewness		 变异系数
Coefficient of variation (%)		 相关系数 Correlation coefficient
E1 E2
E1 57.44 20.26 38.39 7.25 -0.48 0.13 18.87
E2 57.10 19.12 38.82 7.70 -0.62 0.01 19.83 0.88**
E3 56.07 21.90 38.61 6.80 -0.55 0.09 17.62 0.97** 0.97**

Fig. 1

Distribution map of thousand-grain weight of wheat A: 2022-2023 environment; B: 2023-2024 environment; C: BLUP value in a joint environment"

Fig. 2

Heat map of the spatial distribution of molecular marker density in the whole chromosome set of wheat"

Table 2

Distribution of 100K SNP microarray markers on each chromosome in the wheat genome"

染色体 Chromosome 染色体长度 Chromosome length (Mb) 标记数目 Number 标记密度 Density (markers/Mb)
1A 597.39 12892 21.58
1B 699.10 10645 15.23
1D 498.58 5626 11.28
2A 787.40 14438 18.34
2B 812.47 15453 19.02
2D 655.52 6628 10.11
3A 753.13 8471 11.25
3B 851.47 14238 16.72
3D 618.91 3861 6.24
4A 753.69 10308 13.68
4B 673.37 7616 11.31
4D 517.87 2190 4.23
5A 713.16 10341 14.50
5B 714.75 13228 18.51
5D 569.44 4150 7.29
6A 622.46 9200 14.78
6B 730.93 12594 17.23
6D 495.25 3986 8.05
7A 744.23 11698 15.72
7B 763.26 12149 15.92
7D 642.35 5546 8.63
A基因组A genome 4971.46 77348 15.56
B基因组B genome 5245.35 85923 16.38
D基因组D genome 3997.92 31987 8.00
总计Total 14214.73 195285 13.74

Fig. 3

Kinship analysis of 291 winter wheat germplasms A: Frequency distribution map of kinship coefficient; B: Kinship coefficient heat map"

Fig. 4

Population structure analysis of 291 winter wheat materials A: NJ evolutionary tree of the population; B: Principal component analysis; C: ΔK value of the population; D: Population structure diagram"

Fig. 5

Linkage disequilibrium analysis of 291 winter wheat materials"

Fig. 6

Manhattan diagram and Q-Q diagram of thousand-grain weight of wheat A: Environment 2022-2023; B: Environment 2023-2024; C: BLUP value in a joint environment"

Table 3

Significant loci of thousand-grain weight under mixed linear model"

环境Environment 标记 Marker 染色体 Chr. 位置 Position (bp) 显著性阈值 -log10(P) 贡献率 R2 (%)
E1/E3 3B_143949526 3B 143949526 4.58-4.62 8.25-8.36
E2/E3 5A_579847898 5A 579847898 4.83-4.92 7.91-8.06
E2/E3 5A_579848522 5A 579848522 4.60-4.74 7.50-7.76
E2/E3 5A_579921639 5A 579921639 4.48-4.76 7.30-7.80
E2/E3 5A_579921681 5A 579921681 4.20-4.44 6.85-7.27
E2/E3 5A_579921718 5A 579921718 4.35-4.55 7.22-7.64
E2/E3 5A_579955478 5A 579955478 4.24-4.76 6.91-7.79
E2/E3 7A_148378633 7A 148378633 4.55-5.59 7.69-9.68

Fig. 7

Haplotype analysis on chromosome 7A A: LD block corresponding to the 7A_145980808 locus; B: Four haplotypes formed by different allelic combinations within the block; C: Thousand-grain weight differences among materials carrying different haplotypes"

Fig. 8

Distribution frequency of four haplotypes and source regions of Hap4 A: Distribution frequency of four haplotypes; B: Source regions of Hap4"

Table 4

Prediction and annotation of important candidate genes for thousand-grain weight in wheat"

候选基因
Candidate genes		 染色体位置
Chromosome location
(bp)		 基因注释或编码蛋白
Gene annotation or coding proteins		 拟南芥同源基因
Homologs in Arabidopsis thaliana
TraesCS3B03G0336700 3B: 128948207-128950128 赤霉素3-β-羟化酶2 Gibberellin 3-beta-hydroxylase 2 AT1G15550
TraesCS3B03G0338300 3B: 130257382-130258484 β-淀粉酶 Beta-amylase AT4G36780
TraesCS3B03G0339200 3B: 130646139-130648627 F-box家族蛋白 F-box family protein AT2G03560
TraesCS3B03G0343000 3B: 132089715-132091559 糖基转移酶 Glycosyltransferase AT3G53150
TraesCS3B03G0343900 3B: 132904195-132906317 糖基转移酶 Glycosyltransferase AT3G53150
TraesCS3B03G0344400 3B: 132999447-133000637 糖基转移酶 Glycosyltransferase AT2G36750
TraesCS3B03G0345400 3B: 133381587-133383648 F-box家族蛋白 F-box family protein AT4G00755
TraesCS3B03G0345500 3B: 133384475-133386349 糖基转移酶 Glycosyltransferase AT2G36800
TraesCS3B03G0346600 3B: 133818631-133823762 硼转运蛋白 Boron transporter AT1G15460
TraesCS5A03G0902700 5A: 574194918-574199874 bHLH转录因子 Basic helix-loop-helix transcription factor AT2G20180
TraesCS5A03G0903300 5A: 574399521-574400834 F-box家族蛋白 F-box family protein AT3G48880
TraesCS5A03G0903400 5A: 574482068-574485628 转运蛋白相关家族蛋白 Transporter-related family protein AT3G13050
TraesCS5A03G0903600 5A: 574488360-574493061 转运蛋白相关家族蛋白 Transporter-related family protein AT3G13050
TraesCS5A03G0904700 5A: 575322960-575329017 生长素管化蛋白 Auxin canalization protein AT3G22810
TraesCS5A03G0912000 5A: 578061853-578067290 bHLH转录因子 Basic helix-loop-helix transcription factor AT5G43650
TraesCS5A03G0912200 5A: 578446505-578449774 WRKY转录因子 WRKY transcription factor AT2G30590
TraesCS7A03G0440800 7A: 146025353-146026920 NAC结构域蛋白 NAC domain protein AT5G18270

Fig. 9

Expression heat map of important candidate genes for thousand-grain weight in wheat"

Fig. 10

Expression analysis of key candidate genes at 20 days after flowering in wheat varieties with different thousand grain weights"

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