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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (8): 1948-1960.doi: 10.3724/SP.J.1006.2024.31052

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

Genome-wide association study of major grain quality traits in wheat based on 55K SNP arrays

PENG Xiao-Ai1(), LU Mao-Ang1, ZHANG Ling1, LIU Tong1, CAO Lei1, SONG You-Hong1, ZHENG Wen-Yin1, HE Xian-Fang2,*(), ZHU Yu-Lei1,*()   

  1. 1College of Agronomy, Anhui Agricultural University, Hefei 230036, Anhui, China
    2Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, Anhui, China
  • Received:2023-09-12 Accepted:2024-04-01 Online:2024-08-12 Published:2024-04-20
  • Contact: * E-mail: zhuyulei2011@126.com;E-mail: xianfanghe@126.com
  • Supported by:
    National Natural Science Foundation of China(31901540);Youth Backbone Teachers Overseas Academic Training Program(202008775003);Key Research and Development Plan of Anhui Province(202104f06020023)

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Abstract:

To meet people's demand for wheat quality, exploring relevant candidate genes can provide a theoretical basis for genetic improvement and molecular marker-assisted selection of high-quality wheat cultivars. In this study, phenotypic values of eight wheat grain quality traits, including water absorption, grain protein content, volume weight, wet gluten content, dough stability time, dough development time, sedimentation value, and flour yield, were detected in 118 wheat genotypes in three environments. The genotypes were analyzed using 55K SNP arrays, and a genome-wide association study was conducted using the Q+K mixed model. In three different environments, the eight grain quality traits had extensive variation, the maximum variation coefficient of sedimentation value was 16.47%-17.03%, and the heritability of each quality trait was 0.71-0.85. The 118 wheat genotypes were divided into three subgroups: subgroup I, consisting of 41 (34.75%) genotypes, mainly from Anhui; subgroup II, consisting of 32 (27.12%) genotypes, predominantly from Anhui, Jiangsu, and Sichuan provinces; and subgroup III, consisting of 45 (38.13%) genotypes, mainly from Anhui and Jiangsu provinces. 22 stable loci significantly associated with wheat grain quality traits (P < 0.001) were repeatedly detected in two or three environments, distributed on chromosomes 1B (4), 1D (1), 2B (1), 2D (1), 3B (2), 3D (1), 4D (1), 5A (1), 5B (1), 5D (3), 6B (2), 7B (3), and 7D (1), explaining 8.53% to 16.32% of the phenotypic variation. Among the stable loci, three exhibited significant pleiotropic effects, 14 were identified as novel loci for controlling wheat quality traits, and 11 candidate genes possibly associated with wheat grain quality traits were screened. The higher the number of favorable alleles, the higher the phenotypic values of quality traits. Furthermore, it was discovered that several genotypes carried favorable alleles for all eight major quality traits. Among them, the wheat cultivars Huacheng 859 and Jimai 44 contained the highest number of favorable alleles, making them valuable breeding parents for improving wheat quality. The results of this study provide a theoretical basis, parental materials, and molecular markers for the breeding of high-quality wheat.

Key words: Triticum aestivum L., quality traits, genome-wide association study, 55K array, favorable alleles

Table 1

Statistical analysis of quality indexes in 118 wheat genotypes"

性状
Trait		 环境
Environment		 最小值
Min.		 最大值
Max.		 平均值
Mean		 标准差
SD		 变异系数
CV (%)
吸水率WA (%) E1 60.60 69.27 65.38 1.74 2.66
E2 61.03 68.57 65.43 1.63 2.49
E3 57.77 67.70 64.03 1.66 2.59
平均值Mean 61.17 68.04 64.95 1.47 2.26
BLUP 61.77 67.56 64.95 1.23 1.90
蛋白质含量GPC (%) E1 11.34 18.62 13.97 1.29 9.20
E2 11.52 18.74 14.02 1.40 9.96
E3 11.38 18.76 14.36 1.34 9.31
平均值Mean 11.88 17.37 14.12 1.08 7.65
BLUP 12.53 16.44 14.13 0.77 5.44
容重VW (g L-1) E1 771.67 821.67 802.94 10.26 1.28
E2 775.33 824.00 802.23 9.79 1.22
E3 755.67 818.33 790.61 12.61 1.60
平均值Mean 776.44 816.11 798.60 8.89 1.11
BLUP 782.89 810.84 798.50 6.27 0.78
湿面筋含量WGC (%) E1 25.59 39.98 30.78 2.55 8.28
E2 25.43 37.09 30.83 2.65 8.59
E3 26.09 40.33 31.67 2.62 8.27
平均值Mean 26.69 35.64 31.09 2.07 6.67
BLUP 28.06 34.27 31.12 1.44 4.63
面团稳定时间DST (min) E1 6.30 11.93 8.81 1.06 11.99
E2 5.40 11.20 8.86 1.10 12.42
E3 6.13 12.20 9.09 1.13 12.47
平均值Mean 6.43 11.42 8.92 0.95 10.62
BLUP 6.90 10.96 8.93 0.77 8.63
面团形成时间DDT (min) E1 2.87 5.40 3.98 0.49 12.40
E2 2.97 5.30 4.05 0.54 13.36
E3 2.87 5.13 3.95 0.45 11.40
平均值Mean 3.23 4.92 3.99 0.41 10.16
BLUP 3.43 4.69 4.00 0.30 7.59
沉降值SV (mL) E1 18.20 39.97 27.60 4.70 17.03
E2 17.57 42.67 29.13 5.15 17.69
E3 21.57 46.77 31.24 5.15 16.47
平均值Mean 21.10 40.14 29.32 4.13 14.10
BLUP 23.17 37.52 29.36 3.12 10.61
出粉率FY (%) E1 60.73 68.23 64.47 1.56 2.42
E2 61.10 68.73 64.52 1.39 2.15
E3 59.27 67.23 63.08 1.73 2.74
平均值Mean 61.12 67.16 64.02 1.27 1.99
BLUP 61.90 66.26 63.99 0.92 1.44

Table 2

Analysis of variance for eight quality traits in 118 wheat genotypes"

性状Trait 基因型Genotype (G) 环境Environment (E) 基因×环境G×E 遗传力h2
吸水率WA 755.15*** 148.94*** 230.34*** 0.85
蛋白质含量GPC 409.43*** 10.30*** 221.66*** 0.73
容重VW 27,756.82*** 11,309.32*** 14,384.27*** 0.74
湿面筋含量WGC 1509.86*** 59.44*** 874.64*** 0.71
面团稳定时间DST 315.00*** 5.37*** 108.16*** 0.83
面团形成时间DDT 57.76*** 0.72*** 28.66*** 0.75
沉降值SV 5998.01*** 787.16*** 2792.60*** 0.77
出粉率FY 568.39*** 156.04*** 290.40*** 0.74

Fig. 1

Correlation analysis and distribution histogram of eight quality traits in 118 wheat genotypes ***: P < 0.001. WA: water absorption; GPC: grain protein content; VW: volume weight; WGC: wet gluten content; DST: dough stability time; DDT: dough development time; SV: sedimentation value; FY: flour yield."

Fig. 2

Population structure analysis and LD attenuation plot in 118 wheat genotypes"

Fig. 3

Manhattan plot of BLUP for the main quality traits of 118 wheat genotypes The dashed line indicates the threshold -log10(P) is 3.00; The site above the dashed line represents the significant site."

Table 3

Significantly associated SNP loci for eight quality traits in 118 wheat genotypes"

性状
Trait		 位点
Marker		 染色体
Chr.		 物理位置
Position (Mb)		 P值
P-value		 表型贡献率
R2 (%)		 环境
Environment		 先前已报道位点
Previously reported QTL
WA AX-111041836 1B 476.88 9.02E-04-9.37E-04 13.28-14.10 E1/E3/Mean QLGSC.cau-1B[11]
AX-110620539 3B 488.53-491.73 3.41E-04-8.85E-04 9.02-11.97 E1/E3/Mean
GPC AX-111049977 4D 486.54-489.74 1.48E-04-8.08E-04 8.87-11.79 E1/E3/Mean/BLUP
AX-110476332 5D 6.39 7.59E-04-9.61E-04 9.06-11.21 E1/E3/Mean QNWA.cau-5D[11]
AX-110071501 6B 172.73 9.04E-04-9.48E-04 12.45-13.10 E1/E3
AX-108729524 6B 615.98 8.81E-04-9.28E-04 12.36-12.70 E1/E3 qSV6B.1[25]
AX-95253477 7B 609.78-611.62 2.32E-04-7.52E-04 9.36-15.83 E2/E3/Mean/BLUP qHA7B.2[25]
VW AX-109484985 1B 535.59-536.59 1.79E-04-9.96E-04 8.53-12.86 E1/E3/Mean/BLUP
AX-108887454 3D 590.04 4.71E-04-6.35E-04 11.46-13.93 E1/E3/Mean
AX-111573142 5A 663.29 4.54E-04-9.49E-04 8.65-10.81 E1/E3/Mean AX-95112961[26]
WGC AX-111049977 4D 486.54-489.74 1.85E-04-9.84E-04 9.00-14.33 E1/E3/Mean/BLUP
AX-110132720 5D 227.32 4.68E-04-9.95E-04 11.64-14.72 E1/E3
DST AX-111007062 2B 201.24-209.08 2.67E-04-9.47E-04 9.17-15.37 E1/E3/Mean/BLUP
AX-110940091 2D 143.48-145.67 1.87E-04-9.92E-04 11.31-16.32 E1/E3/Mean/BLUP
AX-111505579 5D 53.19-59.29 1.61E-04-9.49E-04 12.15-13.99 E1/E2/E3/Mean/BLUP
AX-111760043 7B 628.83-634.86 8.17E-05-9.88E-04 8.88-14.90 E1/E3/Mean/BLUP qHA7B.2[25]
DDT AX-111472988 5B 544.40 9.27E-04-9.88E-04 9.80-10.65 E1/E3/Mean
AX-111760043 7B 628.83-634.86 2.70E-04-9.30E-04 9.02-15.91 E1/E3/Mean/BLUP qHA7B.2[25]
AX-110040847 7B 741.32-741.40 9.67E-04-9.87E-04 11.45-13.22 E1/E2/E3/Mean
SV AX-110101967 1B 622.47 1.27E-04-7.49E-04 13.42-16.76 E1/E3/Mean/BLUP AX-110369038[18]
AX-95253477 7B 609.78-611.62 1.51E-04-9.35E-04 9.83-15.14 E2/E3/BLUP qHA7B.2[25]
SV AX-94657532 7D 562.12 1.51E-04-9.35E-04 9.83-13.93 E2/E3/BLUP AX-108974357[18]
FY AX-109414218 1B 676.09-676.46 1.80E-04-8.17E-04 9.32-12.46 E1/E3
AX-109346236 1D 485.11-485.55 3.24E-04-8.61E-04 9.18-10.72 E1/E3/BLUP AX-94935157[18]
AX-110524075 3B 68.87 3.07E-04-4.28E-04 10.79-11.30 E1/E3/BLUP

Table 4

Selection of stable sites and information of candidate genes"

性状
Trait		 位点
Marker		 染色体
Chr.		 物理位置
Position (Mb)		 基因
Gene		 基因注释或编码蛋白
Gene annotation or coding protein
WA AX-111041836 1B 476.88 TraesCS1B01G269100 谷胱甘肽S-转移酶
Glutathione S-transferase
GPC AX-110476332 5D 6.39 TraesCS5D01G009100 细胞色素b6
Cytochrome b6
AX-110071501 6B 172.73 TraesCS6B01G162500 F-box家族蛋白
F-box family protein
AX-108729524 6B 615.98 TraesCS6B01G347600 脂转移蛋白
Lipid transfer protein
VW AX-111573142 5A 663.29 TraesCS5A01G492000 非特异性丝氨酸/苏氨酸蛋白激酶
Non-specific serine/threonine protein kinase
DST AX-111007062 2B 201.24-209.08 TraesCS2B01G215800 富含甘氨酸蛋白
Glycine-rich protein
DDT AX-110040847 7B 741.32-741.40 TraesCS7B01G484400 赤霉素调节蛋白2, 推定
Gibberellin-regulated protein 2, putative
FY AX-109414218 1B 676.09-676.46 TraesCS1B01G459700 氨基酸转运蛋白家族蛋白
Amino acid transporter family protein
DST, DDT AX-111760043 7B 628.83-634.86 TraesCS7B01G365300 NAC结构域蛋白
NAC domain protein
GPC, WGC AX-111049977 4D 486.54-489.74 TraesCS4D01G325200 蛋白激酶家族蛋白, 推定, 表达
Protein kinase family protein, putative, expressed
GPC, SV AX-95253477 7B 609.78-611.62 TraesCS7B01G353100 过氧化物酶
Peroxidase

Fig. 4

Relationship between the number of favorable alleles based on significantly associated loci and phenotypic values in 118 wheat genotypes ***: P < 0.001. WA: water absorption; GPC: grain protein content; VW: volume weight; WGC: wet gluten content; DST: dough stability time; DDT: dough development time; SV: sedimentation value; FY: flour yield."

Table 5

Favorable allelic variation, phenotypic effect, and representative carrier genotypes of significantly associated loci"

性状
Trait		 等位变异
Allele		 优异带型
Excellent
belt type		 表型效应Phenotypic effect 材料数
No. of
genotypes		 典型载体
Typical carrier
E1 E2 E3
WA AX-111041836 C 0.85 0.76 0.32 78 济麦44, 郑7698
Jimai 44, Zheng 7698
AX-110620539 T 0.88 0.74 0.67 70
GPC AX-111049977 C 0.47 -0.02 0.10 90 扬辐麦6号, 皖麦606
Yangfumai 6, Wanmai 606
AX-110476332 T 0.74 0.8 0.39 29
AX-110071501 A 0.36 0.42 0.31 105
AX-108729524 A 0.01 0.07 -0.04 101
AX-95253477 T 0.28 -0.04 0.24 55
VW AX-109484985 C 9.65 7.67 5.69 21 乐麦207 Lemai 207, 18B187, 18B248
AX-108887454 G 7.78 6.93 4.29 88
AX-111573142 T 4.05 4.90 5.19 63
WGC AX-111049977 G 1.51 1.55 1.51 103 皖麦606, 华成859, 扬辐麦6号
Wanmai 606, Huacheng 859, Yangfumai 6
AX-110132720 G 1.32 1.85 0.71 59
DST AX-111007062 G 0.42 0.40 0.52 44 烟农19, 华成859, 济麦44
Yannong 19, Huacheng 859, Jimai 44
AX-110940091 A 0.52 0.53 0.57 49
AX-111505579 G 0.47 0.70 0.58 54
AX-111760043 T 0.31 0.36 0.46 52
DDT AX-111472988 C 0.33 0.42 0.14 32 华成859 Huacheng 859,
F06-4198
AX-111760043 G 0.19 0.22 0.17 54
AX-110040847 T 0.27 0.32 0.34 30
SV AX-110101967 G 3.57 2.63 1.90 37 亿麦9号 Yimai 9, 2011
AX-95253477 T 1.85 1.72 2.12 70
AX-94657532 T 1.85 1.72 2.12 70
FY AX-109414218 G 1.24 1.16 0.99 17 2011, 浩麦1号 Haomai 1
AX-109346236 A 0.82 0.82 0.64 20
AX-110524075 T 0.85 0.74 0.34 58
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