Scientia Agricultura Sinica ›› 2021, Vol. 54 ›› Issue (10): 2053-2063.doi: 10.3864/j.issn.0578-1752.2021.10.002

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

Genome-wide Association Analysis of Wheat Grain Size Related Traits Based on SNP Markers

ZHANG Fang1(),REN Yi1,CAO JunMei2,LI FaJi3,XIA XianChun4,GENG HongWei1()   

  1. 1College of Agriculture, Xinjiang Agricultural University/Key Laboratory of Agricultural Biological Technology, Urumqi 830052
    2Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091
    3Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Huang-Huai River Valley, Ministry of Agriculture, Jinan 250100
    4Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Wheat Improvement Center, Beijing 100081
  • Received:2020-10-28 Accepted:2020-12-02 Online:2021-05-16 Published:2021-05-24
  • Contact: HongWei GENG E-mail:1807681776@qq.com;hw-geng@163.com

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Abstract:

【Objective】Grain traits are important factors affecting wheat yield. the significant locus of controlling wheat grain traits was explored by genome-wide association analysis of wheat grain traits, which provided a theoretical reference for the study of genetic improvement of wheat grain traits. 【Method】The genome-wide association analysis (GWAS) based on mixed linear model MLM (Q+K) was performed on 121 wheat grown in Xinjiang using wheat 50 K SNP chips for 6 traits which including grain length, grain width, grain length-width ratio, grain area, grain perimeter and 1000-grain weight.【Result】Six grain traits showed wide phenotypic variation in different environments, in which the maximum coefficient of variation of 1000-grain weight was 13.91-17.79 and the heritability of each grain trait was between 0.85-0.90. The polymorphism information content PIC value was 0.09-0.38, and the minimum allele frequency MAF value was 0.05-0.50. Group structure analysis shows that the natural groups used in the experiment can be divided into 4 subgroups. GWAS results showed that a total of 592 significant association sites (P<0.001) were detected in 6 traits, of which 29 SNPs were repeatedly detected in 2 or more environments, distributed in 1A(5), 1B(2), 1D, 2A(5), 3B, 5A, 5D, 6B(4), 6D, 7B and 7D(7) chromosomes, can explain 9.3% to 22.7% of the phenotypic variation. Six markers associated with stable grain length were detected, which distributed on 1A, 2A, and 7D chromosomes to explain the phenotypic variation of 9.9%-22.7%. Two markers associated with stable grain width were detected, which distributed on 3 B and 5 D chromosomes to explain the phenotypic variation of 9.6%-12.2%. Six markers associated with stable grain length-width ratio were detected, which distributed on 2A(2), 5A, 7B, and 7D(2) chromosomes to explain the phenotypic variation of 10.1%-19.4%. Three markers associated with stable grain area were detected, which distributed on 1A, 1B and 1D chromosome to explain the phenotypic variation of 9.9%-18.2%. Six markers with stable correlation with grain perimeter were detected, which distributed on 1A(2), 2A, 6D and 7D(2) chromosomes to explain the phenotypic variation of 9.3%-22.6%. Six markers associated with stable 1000-grain weight were detected, which distributed on 1B, 2A and 6B chromosomes to explain the phenotypic variation 9.7%-12.9%. Five dominant loci of pleiotropism with were found to control wheat grain traits, which distributed 1A, 2A(2) and 7D(2) chromosomes, explaining the phenotypic variation of 9.9%-22.7%.【Conclusion】In this study, the genetic diversity of the materials was abundant, a total of 29 multi-environment stability loci were found in natural population with 2 or more environmental associated with 6 grain traits.

Key words: wheat, SNP marker, GWAS, grain size-related traits

Table 1

Phenotypic data analysis of grain size related traits in the wheat nature population"

性状
Trait		 环境
Environment		 平均值
Mean		 范围
Range		 标准差
SD		 变异系数
CV (%)		 偏度
Ske.		 峰度
Kur.
千粒重
TKW		 2017 22.92 14.86—32.28 4.08 17.79 -0.18 -0.43
2018 35.55 23.13—49.03 4.95 13.91 0.05 -0.02
2019 37.84 19.15—54.15 5.62 14.85 -0.02 0.41
粒长
GL		 2017 6.44 5.66—7.59 0.34 5.24 0.54 0.88
2018 6.63 5.67—7.48 0.31 4.66 0.20 0.54
2019 6.61 5.78—7.51 0.31 4.69 0.16 0.06
粒宽
GW		 2017 3.14 2.61—3.61 0.24 7.52 -0.39 -0.28
2018 3.15 2.61—3.65 0.22 6.95 -0.19 -0.65
2019 3.27 2.69—3.64 0.18 5.50 -0.43 0.03
长宽比
LWR		 2017 2.09 1.75—2.67 0.19 9.12 0.74 0.20
2018 2.13 1.81—2.58 0.16 7.39 0.59 -0.06
2019 2.03 1.75—2.41 0.13 6.40 0.68 0.43
籽粒面积 GA 2017 15.82 11.88—19.59 1.54 9.74 -0.11 0.16
2018 16.24 12.55—21.34 1.59 9.76 0.23 0.02
2019 16.67 12.65—20.84 1.38 8.28 -0.01 0.63
籽粒周长 GC 2017 16.61 14.52—18.62 0.76 4.56 0.07 0.67
2018 16.78 14.61—19.11 0.72 4.30 0.22 0.58
2019 17.27 15.73—19.80 0.72 4.17 0.25 0.44

Table 2

Analysis of variance of grain size related traits in the wheat"

性状
Trait		 均方MS F值F value 遗传力
h2
基因型
Genotype		 环境
Environment		 基因型×环境
G×E		 误差
Error		 基因型
Genotype		 环境
Environment		 基因型×环境
G×E
千粒重TKW 157.46 17050.92 27.47 4.43 35.54*** 3848.31*** 6.20*** 0.85
粒长GL 0.60 2.74 0.10 0.02 37.54*** 170.47*** 6.18*** 0.86
粒宽GW 0.29 1.63 0.04 0.01 22.98*** 131.03*** 2.84*** 0.89
长宽比LWR 0.16 0.96 0.02 0.00 40.15*** 236.77*** 4.53*** 0.90
籽粒面积GA 14.19 52.10 1.96 0.53 26.59*** 97.66*** 3.68*** 0.87
籽粒周长GC 3.28 36.25 0.52 0.14 23.40*** 258.40*** 3.71*** 0.86

Table 3

Correlation analysis of grain size related traits in the wheat"

性状Trait 千粒重TKW 粒长GL 粒宽GW 长宽比LWR 籽粒面积GA
粒长GL 0.36***
粒宽GW 0.93*** 0.22*
长宽比LWR -0.64*** 0.42*** -0.78***
籽粒面积GA 0.90*** 0.64*** 0.88*** -0.41***
籽粒周长GC 0.58*** 0.94*** 0.49*** 0.15ns 0.83***

Supplemental table 1

Genome coverage and marker polymorphism"

染色体 Chromosome 标记数量

No. of markers		 物理长度
Physical distance (Mb)		 标记密度Density of marker 遗传多样性Genetic diversity 最小等位基因频率MAF 多态信含量 PIC
平均
Mean		 范围
Range		 平均
Mean		 范围
Range
1A 2544 602.45 0.24 0.35 0.25 0.05—0.50 0.28 0.09—0.38
1B 1469 746.65 0.29 0.34 0.25 0.05—0.50 0.27 0.09—0.38
1D 1486 498.09 0.20 0.36 0.26 0.05—0.50 0.29 0.09—0.38
2A 2682 787.57 0.31 0.38 0.29 0.05—0.50 0.3 0.09—0.38
2B 2177 802.80 0.32 0.37 0.27 0.05—0.50 0.29 0.09—0.38
2D 1308 655.89 0.26 0.37 0.27 0.05—0.50 0.29 0.09—0.38
3A 2252 750.52 0.29 0.46 0.37 0.25—0.50 0.35 0.30—0.38
3B 2275 868.70 0.34 0.42 0.33 0.17—0.50 0.33 0.24—0.38
3D 1201 626.21 0.25 0.36 0.27 0.05—0.50 0.29 0.09—0.38
4A 2063 750.43 0.29 0.46 0.39 0.26—0.50 0.36 0.30—0.38
4B 1327 672.85 0.26 0.39 0.29 0.11—0.50 0.31 0.18—0.38
4D 817 521.81 0.20 0.39 0.29 0.05—0.50 0.31 0.09—0.38
5A 2251 709.53 0.28 0.49 0.43 0.35—0.50 0.37 0.35—0.38
5B 1605 713.57 0.28 0.46 0.38 0.26—0.50 0.35 0.29—0.38
5D 1373 573.30 0.22 0.41 0.31 0.16—0.50 0.32 0.23—0.38
6A 2315 625.50 0.24 0.49 0.43 0.34—0.50 0.37 0.35—0.38
6B 1305 725.17 0.28 0.45 0.37 0.21—0.50 0.35 0.28—0.38
6D 1330 498.56 0.19 0.45 0.36 0.20—0.50 0.34 0.27—0.38
7A 2407 745.91 0.29 0.48 0.41 0.31—0.50 0.36 0.34—0.38
7B 1332 750.19 0.29 0.45 0.37 0.22—0.50 0.35 0.28—0.38
7D 1354 643.15 0.25 0.44 0.32 0.19—0.50 0.33 0.26—0.38
A基因组A genome 16514 4971.91 0.30 0.44 0.37 0.05—0.50 0.34 0.09—0.38
B基因组 B genome 11490 5279.93 0.46 0.41 0.32 0.05—0.50 0.32 0.09—0.38
D基因组 D genome 8869 4017.01 0.45 0.40 0.30 0.05—0.50 0.31 0.09—0.38
总计Total 36873 14268.85 0.39 0.42 0.33 0.05—0.50 0.32 0.09—0.38

Fig. 1

Population structure of 121 wheat accessions"

Fig. 2

Manhattan plots for grain size related traits of the diverse panel at average environment A: Grain length; b: Grain width; c: Length width ratio; d: Grain area; e: Grain circle; f: Thousand kernel weight"

Table 4

Loci for grain size related traits in the diversity panel identified by SNP-GWAS"

性状
Trait		 标记
Marker		 染色体 Chr. 位置
Position (Mb)		 混合线性模型MLM 环境
Environment		 前人报道
Previously reported
P值P value 贡献率R2 (%)
千粒重
TKW		 AX-111669426 1B 375.4 5.94E-04-7.67E-04 10.4—10.5 E1/E4 Xwmc269-Xwmc33[27]
AX-111531320 2A 204.5 5.88E-04-8.98E-04 10.3—11.3 E2/E4
AX-109874065 6B 34.0 7.73E-04-9.84E-04 9.7—10.4 E1/E2 TKW-xgwm533[28]
AX-110446017 6B 486.1 3.98E-04-7.98E-04 10.3—12.9 E1/E2 QKWpur-6B[24] AX_110368497 [25]
AX-110936500 6B 569.4 4.97E-04-6.86E-04 10.5—10.6 E1/E2
AX-109493716 6B 573.6 4.92E-04-6.58E-04 11.0—11.8 E1/E2
粒长
GL		 AX-94757616 1A 64.6 3.56E-04-7.55E-04 10.7—11.9 E2/E4
AX-111082947 1A 473.7 1.41E-06-9.42E-04 9.9—22.7 E1/E2/E3/E4
AX-94497666 2A 748.4 3.30E-04-7.90E-04 10.3—11.8 E1/E2/E3/E4 TaFlo2[25-26]
AX-111614568 7D 13.7—13.9 1.96E-05-2.03E-04 12.9—17.3 E3/E4 TaGS-D1[29]
AX-95633409 7D 33.6 4.46E-04-8.05E-04 10.7—11.9 E3/E4 QKLpur-7D.1[24]
AX-111197303 7D 47.4—49.2 2.70E-04-8.32E-04 10.9—12.6 E1/E4 QKL.caas-7DS [30] QGw.ccsu-7D.1 [31]
粒宽
GW		 AX-108948870 3B 24.6 5.20E-04-9.21E-04 10.6—12.2 E1/E4 Kukri_c14642_917[23]
AX-179477405 5D 210.6 6.78E-04-8.33E-04 9.6—10.6 E2/E4
粒长宽比
LWR		 AX-111722425 2A 131.7 1.38E-05-9.53E-04 10.1—18.3 E1/E2/E3/E4
AX-111531320 2A 204.5 3.57E-05-3.28E-04 13.0—17.1 E2/E3
AX-179560109 5A 141.9 1.02E-04-1.08E-04 14.7—15.2 E2/E3
AX-112286258 7B 709.1 1.48E-05-4.09E-04 11.1—19.4 E1/E3 QGlwr.ccsu-7B.1[32]
AX-111614568 7D 13.7—13.9 4.98E-05-5.51E-05 10.9—15.9 E1/E4 TaGS-D1[29]
AX-158554015 7D 403.7 6.09E-05-6.42E-04 10.8—15.4 E1/E2
籽粒面积
GA		 AX-95176275 1A 146.6 5.92E-04-9.82E-04 9.9—11.2 E1/E4
AX-179476290 1B 377.4 1.21E-05-8.31E-04 10.0—18.2 E3/E4 qKA1B-1[33]
AX-179477117 1D 220.5 1.21E-05-8.31E-04 10.0—18.2 E3/E4
籽粒周长
GC		 AX-111082947 1A 473.7 1.34E-06-5.56E-04 10.1—22.6 E1/E3/E4
AX-109382284 1A 546.8 2.27E-06-3.55E-04 11.8—21.3 E3/E4
AX-94497666 2A 748.4 7.62E-04-8.68E-04 9.3—10.3 E1/E4 TaFlo2[25,26]
AX-111583179 6D 242.7 2.11E-04-5.00E-04 12.0—13.2 E2/E3
AX-111614568 7D 13.7—13.9 1.04E-04-3.72E-04 11.7—14.2 E3/E4 TaGS-D1[29]
AX-111197303 7D 47.4—49.2 7.15E-04-8.05E-04 10.0—10.4 E1/E4 QKL.caas-7DS [30] QGw.ccsu-7D.1 [31]
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