Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (11): 2047-2063.doi: 10.3864/j.issn.0578-1752.2023.11.002


Genome-Wide Association Study of Grain Main Quality Related Traits in Winter Wheat

DONG YiFan1(), REN Yi1, CHENG YuKun1, WANG Rui1, ZHANG ZhiHui1, SHI XiaoLei2, GENG HongWei1()   

  1. 1 College of Agronomy, Xinjiang Agricultural University/Special High Quality Triticeae Crops Engineering and Technology Research Center, Xinjiang Agricultural University/Xinjiang Wheat Industry System Innovation Team, Urumqi 830052
    2 Institute of Crop Germplasm Resources, Xinjiang Academy of Agricultural Sciences, Urumqi 830091
  • Received:2022-12-25 Accepted:2023-02-17 Online:2023-06-01 Published:2023-06-19


【Objective】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. 【Method】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. 【Result】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. 【Conclusion】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.

Key words: winter wheat, quality, SNP marker, GWAS, haplotype, candidate genes

Table 1

Statistical analysis of wheat grain quality traits in 259 natural population"

CV (%)
FF value 遗传力
GPC (%)
E1 13.52—19.22 16.38±1.15 7.01 -0.10 -0.70 16.96*** 3101.12*** 4.29*** 0.79
E2 12.77—18.67 15.55±1.21 7.77 0.40 -0.26
WGC (%)
E1 24.78—37.93 31.75±2.88 9.07 -0.03 -0.76 17.50*** 2995.32*** 4.38*** 0.79
E2 22.58—38.28 28.98±2.87 9.91 0.60 0.29
SV (mL)
E1 24.05—68.55 48.18±9.69 20.11 -0.11 -0.80 13.10*** 4212.30*** 3.67*** 0.77
E2 16.95—67.50 40.27±9.83 24.42 0.50 0.01
GSC (%)
E1 57.89—62.94 60.88±0.79 1.29 -0.64 1.10 17.84*** 2858.98*** 4.39*** 0.79
E2 59.94—64.14 62.40±0.75 1.20 -0.42 0.13
GH (%)
E1 41.22—77.87 65.21±7.28 11.17 -0.62 -0.18 17.10*** 7352.58*** 3.03*** 0.84
E2 36.07—76.42 59.20±8.12 13.71 -0.16 -0.31

Table 2

Statistical analysis of domestic and abroad winter wheat varieties (lines) for grain quality traits based on BLUP values"

Statistical parameters
国内品种Domestic varieties 国外品种
Abroad varieties
Huanghuai winter wheat region
Northern winter wheat region
Middle and lower reaches of the Yangtze River winter wheat region
Southwest winter wheat region
GPC (%)
平均值±标准差 Mean±SD 16.17±0.78 16.06±0.95 15.87±0.77 15.54±0.65 15.69±0.93
范围Range 13.94—18.15 14.46—17.98 14.32—17.10 14.62—16.89 13.61—17.6
变异系数CV (%) 4.85 5.93 4.86 4.16 5.91
WGC (%)
平均值±标准差 Mean±SD 31.58±3.66 30.91±4.35 29.56±3.75 28.03±2.63 28.73±4.04
范围Range 19.66—41.18 23.93—39.74 19.02—35.89 24.26—34.83 21.01—38.15
变异系数CV (%) 11.60 14.09 12.69 9.37 14.05
SV (mL)
平均值±标准差 Mean±SD 46.18±6.98 44.38±7.50 43.98±6.27 40.84±4.63 41.55±8.21
范围Range 29.26—61.74 29.81—62.44 30.68—53.98 34.6—51.71 24.07—61.02
变异系数CV (%) 15.11 16.91 14.26 11.33 19.76
GSC (%)
平均值±标准差 Mean±SD 61.55±0.59 61.68±0.64 61.77±0.42 62.12±0.43 61.56±0.51
范围Range 60.17—62.80 60.07—62.8 60.89—62.76 61.20—62.89 60.01—62.78
变异系数CV (%) 0.95 1.04 0.67 0.69 0.83
GH (%)
平均值±标准差 Mean±SD 63.67±4.41 62.38±5.33 60.21±4.64 58.41±4.77 61.47±5.37
范围Range 50.49—73.57 52.04—74.33 51.44—70.51 50.91—69.03 44.95—73.44
变异系数CV (%) 6.92 8.55 7.71 8.17 8.74

Fig. 1

Population structure analysis of 259 wheat varieties (lines) A: Estimation of ∆K value in population; B: Group structure diagram; C: Principal component analysis"

Fig. 2

Manhattan and Q-Q plots of wheat grain quality traits based on BLUP values A: Grain protein content; B: Wet gluten content; C: Sedimentation value; D: Grain starch content; E: Grain hardness"

Table 3

Stable loci significantly associated with wheat grain quality traits"

Position (Mb)
GPC (%)
BobWhite_c1027_1127 1A 586.91—590.20 1.26E-04-7.47E-04 4.89—7.32 E2/E3
wsnp_Ex_c5740_10081171 2B 733.71—742.81 4.60E-04-8.98E-04 4.63—5.14 E1/E3
GENE-0762_631 2B 790.44—790.76 5.76E-05-8.35E-04 4.57—6.55 E1/E2/E3
IAAV7742 2D 645.61 4.41E-05-9.28E-04 4.63—7.07 E2/E3
RAC875_c66845_466 3A 54.46—61.31 1.47E-04-9.65E-04 4.32—5.78 E1/E2/E3
wsnp_Ex_c8360_14085858 3B 5.67—5.95 6.13E-04-8.42E-04 4.55—7.67 E2/E3
Excalibur_rep_c102020_253 4A 631.90—631.92 4.96E-05-9.82E-04 4.42—7.18 E1/E3
Tdurum_contig33737_157 4B 37.69 3.04E-04-7.19E-04 4.59—5.02 E1/E3
BS00077733_51 5B 693.87 3.25E-04-9.88E-04 4.27—5.82 E2/E3
D_GDS7LZN02F4FP5_176 5D 559.92—562.12 2.12E-04-8.58E-04 4.53—6.26 E2/E3
Kukri_c74599_85 7A 14.19—19.97 6.81E-05-9.21E-04 4.64—6.40 E1/E3
RAC875_c80504_487 7A 30.09—35.60 8.05E-04-9.89E-04 5.61—8.55 E2/E3
WGC (%)
BobWhite_c1027_1127 1A 586.91 4.09E-05-7.87E-04 5.23—6.79 E2/E3
wsnp_Ex_c5740_10081171 2B 742.81 5.86E-04-9.77E-04 4.46—5.02 E1/E3
GENE-0762_631 2B 790.44—790.76 5.76E-05-7.62E-04 4.89—5.45 E1E3
RAC875_c66845_466 3A 54.46 3.75E-04-6.06E-04 4.32—4.79 E1/E2/E3
wsnp_Ex_c8360_14085858 3B 5.67—5.95 7.23E-04-8.04E-04 5.62—8.91 E2/E3
Excalibur_rep_c102020_253 4A 631.90—631.92 3.35E-04-7.28E-04 4.69—6.36 E1/E3
Tdurum_contig33737_157 4B 37.69 3.04E-04-6.37E-04 4.78—5.21 E1/E3
BS00077733_51 5B 693.87 4.66E-04-6.03E-04 4.70—5.17 E2/E3
Kukri_c74599_85 7A 14.19—19.97 4.02E-04-6.23E-04 4.74—5.08 E1/E3
SV (mL)
BobWhite_c1027_1127 1A 586.91—593.30 5.25E-04-5.79E-04 4.66—7.36 E2/E3
wsnp_Ex_c5740_10081171 2B 733.71—742.81 4.60E-04-8.23E-04 4.78—5.14 E1/E3
GENE-0762_631 2B 790.44—790.76 6.26E-04-7.09E-04 5.02—6.19 E1/E2
IAAV7742 2D 645.61 8.84E-05-6.72E-04 5.81—7.04 E1/E3
RAC875_c66845_466 3A 54.46—61.31 4.03E-04-9.58E-04 4.25—5.02 E1/E3
wsnp_Ex_c8360_14085858 3B 5.67—5.95 6.66E-04-8.40E-04 5.69—7.21 E2/E3
Excalibur_rep_c102020_253 4A 631.90—631.92 5.30E-04-6.78E-04 4.66—5.19 E1/E3
Tdurum_contig33737_157 4B 37.69 6.22E-04-7.00E-04 4.59—5.10 E1/E3
BS00077733_51 5B 693.87 5.22E-04-7.28E-04 4.63—5.24 E2/E3
D_GDS7LZN02F4FP5_176 5D 559.92—562.12 2.55E-04-7.63E-04 4.53—5.32 E2/E3
Kukri_c67_1504 6A 73.72—75.02 2.86E-04-9.14E-04 4.44—5.44 E1/E3
RAC875_c80504_487 7A 30.09—35.60 8.05E-04-8.69E-04 5.82—8.06 E2/E3
GSC (%)
BobWhite_c1027_1127 1A 593.3 5.62E-05-2.71E-04 5.06—7.59 E2/E3
wsnp_Ex_c5740_10081171 2B 733.71—742.81 4.60E-04-7.67E-04 4.46—5.11 E1/E3
GENE-0762_631 2B 790.44—790.76 9.23E-05-6.26E-04 4.57—6.02 E2/E3
IAAV7742 2D 645.61 7.78E-05-4.36E-04 5.03—6.58 E1/E2/E3
RAC875_c66845_466 3A 54.46—61.31 2.06E-04-7.26E-04 4.65—5.28 E2/E3
Excalibur_rep_c102020_253 4A 631.90—631.92 6.15E-04-8.62E-04 4.89—6.69 E1/E3
Tdurum_contig33737_157 4B 37.69 5.32E-04-5.98E-04 4.63—5.63 E1/E3
BS00077733_51 5B 693.87 4.24E-04-6.06E-04 4.27—5.82 E2/E3
D_GDS7LZN02F4FP5_176 5D 559.92—562.12 4.62E-04-7.31E-04 5.26—7.08 E2/E3
Kukri_c67_1504 6A 73.72—75.02 4.26E-04-6.26E-04 4.87—5.02 E1/E3
RAC875_c80504_487 7A 35.6 8.05E-04-9.08E-04 6.23—7.03 E2/E3
GH (%)
GENE-1019_96 2A 2.48 1.51E-04-4.90E-04 4.96—5.83 E1/E2/E3
BobWhite_c2002_100 2A 535.72 5.67E-04-7.71E-04 4.66—4.99 E1/E3
BS00081871_51 2B 12.08—17.39 6.81E-05-9.21E-04 5.08—6.40 E1/E3
wsnp_Ex_c8360_14085858 3B 5.67—5.95 6.18E-04-6.41E-04 5.60—7.99 E2/E3
BS00000020_51 5D 3.61 4.06E-07-1.82E-05 7.75—10.98 E1/E2/E3
Kukri_c74599_85 7A 14.19—19.97 5.22E-05-7.26E-04 5.02—6.21 E1/E3
Kukri_c34147_152 7A 689.95—690.05 2.81E-04-5.26E-04 6.08—6.78 E2/E3

Table 4

Stable loci significantly associated with two or more grain quality traits"

Position (Mb)
BobWhite_c1027_1127 1A 586.91—593.30 4.09E-05-7.87E-04 4.66—7.59 E2/E3
wsnp_Ex_c5740_10081171 2B 733.71—742.81 4.60E-04-9.77E-04 4.46—5.14 E1/E3
GENE-0762_631 2B 790.44—790.76 5.76E-05-8.35E-04 4.57—6.55 E1/E2/E3
蛋白质含量、沉降值、淀粉含量 GPC, SV, GSC IAAV7742 2D 645.61 4.41E-05-9.28E-04 4.63—7.07 E1/E2/E3
RAC875_c66845_466 3A 54.46—61.31 1.47E-04-9.65E-04 4.32—5.78 E1/E2/E3
wsnp_Ex_c8360_14085858 3B 5.67—5.95 6.13E-04-8.42E-04 4.55—8.91 E2/E3
Excalibur_rep_c102020_253 4A 631.90—631.92 4.96E-05-9.82E-04 4.42—7.18 E1/E3
Tdurum_contig33737_157 4B 37.69 3.04E-04-7.19E-04 4.60—5.21 E1/E3
BS00077733_51 5B 693.87 3.25E-04-9.88E-04 4.27—5.82 E2/E3
蛋白质含量、沉降值、淀粉含量 GPC, SV, GSC D_GDS7LZN02F4FP5_176 5D 559.92—562.12 2.12E-04-8.58E-04 4.53—7.08 E2/E3
沉降值、淀粉含量SV, GSC Kukri_c67_1504 6A 73.72—75.02 2.86E-04-9.14E-04 4.44—5.44 E1/E3
Kukri_c74599_85 7A 14.19—19.97 6.81E-05-9.21E-04 4.64—6.40 E1/E3
蛋白质含量、沉降值、淀粉含量 GPC, SV, GSC RAC875_c80504_487 7A 30.09—35.60 8.05E-04-9.89E-04 5.61—8.55 E2/E3

Fig. 3

Haplotype analysis of the D_GDS7LZN02F4FP5_176 locus A: LD Block analysis of the D_GDS7LZN02F4FP5_176 locus; B: Four haplotypes with different alleles; C: Quality phenotypic differences of different haplotype varieties (lines)"

Fig. 4

Distribution frequencies of haplotypes at the D_GDS7LZN02F4FP5_176 locus in winter wheat from different sources"

Table 5

Screening for candidate gene information"

Position (Mb)
Gene annotation or coding protein
籽粒硬度GH BobWhite_c2002_100 2A 535.72 TraesCS2A02G312200 锌指蛋白 Zinc finger protein
GENE-0762_631 2B 790.44—790.76 TraesCS2B02G630000 激酶家族蛋白
Kinase family protein
籽粒硬度GH BS00081871_51 2B 12.08—17.39 TraesCS2B02G027900 糖基转移酶 Glycosyltransferase
IAAV7742 2D 645.61 TraesCS2D02G587400 LRR受体样激酶家族蛋白
LRR receptor-like kinase family protein
RAC875_c66845_466 3A 54.46—61.31 TraesCS3A02G084800 细胞色素P450家族蛋白
Cytochrome P450 family protein
Excalibur_rep_c102020_253 4A 631.90—631.92 TraesCS4A02G360000 磷酸转运蛋白
Phosphate transporter protein
D_GDS7LZN02F4FP5_176 5D 559.92—562.12 TraesCS5D02G558100 糖转运蛋白,推定
Sugar transporter, putative
籽粒硬度GH BS00000020_51 5D 3.61 TraesCS5D02G004900 细胞色素P450家族蛋白
Cytochrome P450 family protein
RAC875_c80504_487 7A 30.09—35.60 TraesCS7A02G061400 F-box家族蛋白
F-box protein
Kukri_c74599_85 7A 14.19—19.97 TraesCSU02G168200 天冬氨酸蛋白酶
Aspartic proteinase
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