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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (10): 1488-1502.doi: 10.3724/SP.J.1006.2019.91002


Genome-wide association study for main agronomic traits in common wheat

ZHAI Jun-Peng,LI Hai-Xia,BI Hui-Hui,ZHOU Si-Yuan,LUO Xiao-Yan,CHEN Shu-Lin,CHENG Xi-Yong(),XU Hai-Xia()   

  1. Henan Agricultural University / National Key Laboratory of Wheat and Maize Crop Science / Collaborative Innovation Center of Henan Grain Crops, Zhengzhou 450046, Henan, China
  • Received:2019-01-06 Accepted:2019-04-15 Online:2019-10-12 Published:2019-09-10
  • Contact: Xi-Yong CHENG,Hai-Xia XU E-mail:xyc634@163.com;hauxhx@henau.edu.cn
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2017YFD0100706);the National Major Project for Developing New GM Crops(2016ZX08002003-004);the National Key Basic Research Program (973 Program)(2014CB138105)


To illustrate the genetic mechanism of complex agronomic traits in wheat, we investigated nine agronomic traits using 150 wheat cultivars (lines) from China across four environments. Genome-wide association analysis was performed using wheat 35K genotyping assay with five association models (Q, PCA, K, PCA+K, Q+K). The results revealed that the polymorphic information content (PIC) of values was between 0.0950 and 0.5000, and the minimum allele frequency (MAF) was between 0.0500 and 0.5000. Both the population structure analysis and the PCA analysis showed that the tested materials could be divided into two sub-populations. Linkage disequilibrium analysis found that the LD decay distances of the A, B, D, and the whole genome were approximately 4.7, 8, 11, and 6 Mb, respectively. A total of 652 significant (P ≤ 0.001) marker-trait associations (MTAs) were detected, thereinto, 21 SNPs could be detected on chromosomes 1A(1), 1B(4), 2A(3), 2D(2), 3A(1), 5A(1), 5B(5), 6A(1), 6B(2), and 7D(3) in two or more environments. Three SNPs were significantly associated with two traits and the physical position of one SNP was unknown. Single SNPs could explain 7.67 % to 18.79 % phenotypic variation. It was found that eight favorable allelic variations accounted for a low proportion in the tested population. Fourteen candidate genes that may be related to agronomic traits of wheat were identified. Among them, TraesCS5B02G237200, TraesCS7D02G129700, and TraesCS1B02G426300 may play important roles in plants resistance to biotic and abiotic stress. TraesCS5B02G010800 and TraesCS7D02G436800 may be related to the hormones synthesis and response in plants. TraesCS2A02G092200 may enhance the cell wall formation of plants. TraesCS5A02G438800 may be involved in chloroplast development. The function of the other seven candidate genes is unknown.

Key words: wheat, agronomic trait, linkage disequilibrium, genome-wide association study, candidate gene

Table 1

Wheat varieties used in this study"

类别Type 品种(系) Variety (line)
Regional trail of wheat varieties in the south of Yellow and Huai Valley
中麦170 Zhongmai 170, 周麦32 Zhoumai 32, 新麦32 Xinmai 32, 锦绣21 Jinxiu 21, 商麦167 Shangmai167, 许科168 Xuke168, 中新16 Zhongxin 16, 洛麦26 Luomai 26, 豫丰11 Yufeng 11, 中金13 Zhongjin 13, 郑育麦16 Zhengyumai 16, 郑麦618 Zhengmai 618, 龙科1221 Longke 1221, 淮核12013 Huaihe 12013, 涡麦66 Womai 66, 郑麦369 Zhengmai 369, 俊达109 Junda109, 众麦7号 Zhongmai 7, 新科麦169 Xinkemai 169, 周麦36 Zhoumai 36, 中育1211 Zhongyu 1211, 先麦12 Xianmai 12, 濮麦6311 Pumai 6311, 瑞华1426 Ruihua 1426, 高麦6号 Gaomai 6, 皖科06725 Wanke 06725, 光泰68 Guangtai 68, 轮选66 Lunxuan 66, 西农511 Xinong 511, 濉1216 Sui 1216, 豫农186 Yunong 186, 华成863 Huacheng 863, 鑫农518 Xinnong 518, 藁优5766 Gaoyou 5766, 瑞华055 Ruihua 055
Regional trial of wheat varieties in Henan
藁麦5218 Gaomai 5218, 辉麦5号 Huimai 5, 西农364 Xinong 364, 中麦255 Zhongmai 255, 漯麦163 Luomai 163, 怀川11 Huaichuan 11, 创星8号 Chuangxing 8, 郑麦158 Zhengmai 158, 中麦578 Zhongmai 578, 丰德存21 Fengdecun 21, 周麦18 Zhoumai 18, 豫农804 Yunong 804
Comparative trail of wheat varieties in Henan
华冠001 Huaguan 001, 河科大163 Hekeda 163, 华冠002 Huaguan 002, 平麦19 Pingmai 19, 华冠003 Huaguan 003, 平麦20 Pingmai 20, 华冠004 Huaguan 004, 豫农216 Yunong 216, 华冠005 Huaguan 005, 许优958 Xuyou 958, 滑昌麦68 Huachangmai 68, 滑昌麦66 Huachangmai 66, 滑昌麦26 Huachangmai 26, 豫农605 Yunong 605, 岭育麦216 Lingyumai 216, 豫农606 Yunong 606, 尚农4号 Shangnong 4, 豫农607 Yunong 607, 许麦8号 Xumai 8, 豫农805 Yunong 805, 许麦9号Xumai 9, 豫农806 Yunong 806, 许麦168 Xumai 168, 许麦169 Xumai 169, 农科668 Nongke 668, 豫农519 Yunong 519, 尚农3号 Shangnong 3, 河科大LYZB Hekeda LYZB, 河科大522 Hekeda 522, 豫农517 Yunong 517
Breeding lines
豫农225 Yunong 225, 豫农243 Yunong 243, 豫农7847 Yunong 7847, 豫农8981 Yunong 8981, 豫农227 Yunong 227, 豫农246 Yunong 246, 豫农955 Yunong 955, 豫农9005 Yunong 9005, 豫农231, Yunong 231, 豫农248 Yunong 248, 豫农7961 Yunong 7961, 豫农9053 Yunong 9053, 豫农233 Yunong 233, 豫农256 Yunong 256, 豫农8819 Yunong 8819, 豫农9068 Yunong 9068, 豫农235 Yunong 235, 豫农268 Yunong 268, 豫农8858 Yunong 8858, 豫农9071 Yunong 9071, 豫农236 Yunong 236, 豫农282 Yunong 282, 豫农8861 Yunong 8861, 豫农9092 Yunong 9092, 豫农238 Yunong 238, 豫农285 Yunong 285, 豫农8909 Yunong 8909, 豫农9107 Yunong 9107, 豫农240 Yunong 240, 豫农7838 Yunong 7838, 豫农8954 Yunong 8954, 豫农9110 Yunong 9110, 豫农9305 Yunong 9305, 豫农8051 Yunong 8051, 豫农8138 Yunong 8138, 豫农8636 Yunong 8636, 豫农9308 Yunong 9308, 豫农8054 Yunong 8054, 豫农8141 Yunong 8141, 豫农8639 Yunong 8639, 豫农9311 Yunong 9311, 豫农8057 Yunong 8057, 豫农8339 Yunong 8339, 豫农8681 Yunong 8681, 豫农9334 Yunong 9334, 豫农8069 Yunong 8069, 豫农8552 Yunong 8552, 豫农8684 Yunong 8684, 豫农9338 Yunong 9338, 豫农8072 Yunong 8072, 豫农8570 Yunong 8570, 豫农8774 Yunong 8774, 豫农8042 Yunong 8042, 豫农8075 Yunong 8075, 豫农8588 Yunong 8588, 豫农8792 Yunong 8792, 豫农8045 Yunong 8045, 豫农8129 Yunong 8129, 豫农8600 Yunong 8600, 豫农8804 Yunong 8804, 豫农8048 Yunong 8048, 豫农8135 Yunong 8135, 豫农8621 Yunong 8621, 豫农8813 Yunong 8813, 豫农9113 Yunong 9113, 豫农9119 Yunong 9119, 豫农9125 Yunong 9125, 豫农9116, Yunong 9116, 豫农9122 Yunong 9112, 豫农9132 Yunong 9132, 豫农223 Yunong 223, 豫农9266 Yunong 9266, 豫农9269 Yunong 9269

Table 2

Phenotypic variation and normalization test of agronomic traits in wheat"

Table 3

Information of SNP markers"

No. of markers
distance (Mb)
最小等位基因频率 MAF 多态性信息量 PIC 标记密度
Density of marker
(Mb marker-1)
Mean Range Mean Range
1A 450 593.3 0.2583 0.0500-0.5000 0.3404 0.0950-0.5000 1.32
1B 717 689.0 0.1852 0.0526-0.4932 0.2843 0.0997-0.4999 0.96
1D 635 495.2 0.1999 0.0504-0.5000 0.2955 0.0956-0.5000 0.78
2A 517 780.7 0.2429 0.0500-0.5000 0.3275 0.0950-0.5000 1.51
2B 635 801.2 0.2597 0.0500-0.5000 0.3450 0.0950-0.5000 1.26
2D 557 651.4 0.226 0.0507-0.5000 0.3120 0.0963-0.5000 1.17
3A 318 749.5 0.2472 0.0504-0.4966 0.3377 0.0958-0.5000 2.36
3B 565 829.3 0.2870 0.0504-0.5000 0.3729 0.0956-0.5000 1.47
3D 339 614.0 0.2583 0.0504-0.5000 0.3448 0.0956-0.5000 1.81
4A 283 744.5 0.2114 0.0537-0.4966 0.3024 0.1016-0.5000 2.63
4B 316 673.2 0.1716 0.0500-0.4966 0.2663 0.0950-0.5000 2.13
4D 132 509.3 0.1676 0.0537-0.4823 0.2590 0.1016-0.4994 3.86
5A 451 708.2 0.2338 0.0500-0.5000 0.3239 0.0950-0.5000 1.57
5B 545 712.9 0.2384 0.0500-0.5000 0.3206 0.0950-0.5000 1.31
5D 393 565.9 0.2269 0.0500-0.4966 0.3083 0.0950-0.5000 1.44
6A 310 617.7 0.2449 0.0509-0.5000 0.3340 0.0965-0.5000 1.99
6B 523 720.5 0.2265 0.0507-0.5000 0.3172 0.0963-0.5000 1.38
6D 286 473.4 0.2041 0.0504-0.4932 0.2950 0.0956-0.4999 1.66
7A 418 736.5 0.2696 0.0522-0.5000 0.3561 0.0989-0.5000 1.76
7B 407 750.1 0.2737 0.0504-0.4966 0.3616 0.0958-0.5000 1.84
7D 314 636.8 0.2649 0.0500-0.5000 0.3556 0.0950-0.5000 2.03
Unmap 441 488.8 0.2262 0.0507-0.5000 0.3133 0.0963-0.5000 1.11
A 2747 4930.4 0.2440 0.0500-0.5000 0.3317 0.0950-0.5000 1.79
B 3708 5176.2 0.2346 0.0500-0.5000 0.3240 0.0950-0.5000 1.40
D 2656 3946.0 0.2211 0.0500-0.5000 0.3100 0.0950-0.5000 1.49
Whole 9552 14541.4 0.2329 0.0500-0.5000 0.3215 0.0950-0.5000 1.70

Fig. 1

Structure, PCA, and Sub-population phenotype 1-A: line chart of ΔK; 1-B: structure plot; 1-C: analysis of PCA; 1-D: sub-population phenotype. Name of each trait is given in Table 2."

Fig. 2

Linkage disequilibrium plot"

Fig. 3

Manhattan plot and Q-Q plot of each trait (part of the plots) Name of each trait is given in Table 2; A SNP that detected in two or more environments with green highlighted."

Table 4

Loci associated with agronomic traits in wheat"

P-value R2 (%)
E1 E2 E3 E4 E1 E2 E3 E4
LFI AX-95108722 2D 441569084 7.84E-04 9.49E-04 7.94 7.68
AX-94532508 6A 99932394 8.44E-04 1.35E-04 3.40E-04 7.92 10.51 9.24
P-value R2 (%)
E1 E2 E3 E4 E1 E2 E3 E4
AX-94976370 6B 157777682 4.85E-04 8.44E-04 7.02E-04 8.60 7.86 8.09
AX-94918690 6B 157777813 4.85E-04 8.44E-04 7.02E-04 8.60 7.86 8.09
KNPS AX-94385515 5B 10444933 2.53E-04 3.75E-04 9.58 9.18
AX-94459753 5B 10449146 2.55E-04 3.59E-04 9.55 9.08
AX-94799632 5B 418015877 2.39E-04 9.94E-04 9.64 7.67
AX-94547362 7D 81887538 1.78E-04 9.38E-05 10.06 10.97
TKW AX-95152265 7D 556123927 3.73E-04 1.08E-04 3.39E-04 9.17 10.84 9.16
PH AX-95094324 1A 519471561 8.88E-05 5.87E-05 8.53E-04 11.92 12.41 8.18
SL AX-95108722 2D 441569084 7.79E-06 2.18E-05 14.27 12.94
AX-94542697 3A 11350680 1.54E-04 6.10E-04 11.55 9.89
NFS AX-94385515 5B 10444933 5.60E-05 9.30E-04 7.39E-05 11.50 7.70 11.13
AX-94459753 5B 10449146 5.38E-05 9.13E-04 7.46E-05 11.35 7.69 11.11
HD AX-95197628 1B 652298582 3.34E-05 3.43E-04 12.40 9.13
AX-95073002 1B 652457758 4.36E-05 5.32E-04 12.13 8.62
AX-94748775 1B 652468844 7.50E-04 3.77E-04 3.06E-04 8.40 9.19 9.50
AX-94629503 1B 652575175 7.24E-04 3.65E-04 3.01E-04 8.07 9.01 9.31
AX-94446915 2A 44094660 5.03E-05 1.15E-04 5.01E-07 11.82 10.63 18.79
AX-94430515 2A 45085276 3.41E-04 3.00E-05 9.10 12.61
AX-94639471 2A 52130032 5.61E-04 1.92E-04 5.13E-04 8.65 10.03 8.69
AX-94690816 5A 620175970 9.08E-04 2.02E-05 9.33 17.06
AX-94402434 7D 415430669 6.40E-04 1.38E-04 9.38 10.82
AX-95629896 Unknown Unknown 9.19E-04 5.79E-04 8.35 8.74

Table 5

Stable SNP and phenotypic effect of allele variation"

表型差值Difference 材料数
No. of varieties
LFI AX-95108722 2D 441569084 T 1.94 36
G 0 113
AX-94532508 6A 99932394 C 2.79 133
T 0 13
AX-94976370 6B 157777682 C 2.58 133
T 0 16
AX-94918690 6B 157777813 G 2.58 133
A 0 16
KNPS AX-94385515 5B 10444933 C 4.78 138
T 0 10
AX-94459753 5B 10449146 C 4.78 139
T 0 10
AX-94799632 5B 418015877 C 3.22 17
T 0 132
AX-94547362 7D 81887538 A 5 139
G 0 10
TKW AX-95152265 7D 556123927 C 4.91 12
A 0 135
PH AX-95094324 1A 519471561 A 3.42 96
C 0 46
SL AX-95108722 2D 441569084 T 0.63 36
G 0 113
AX-94542697 3A 11350680 C 0.69 17
G 0 104
NFS AX-94385515 5B 10444933 C 1.25 138
T 0 10
AX-94459753 5B 10449146 C 1.25 139
T 0 10
HD AX-95197628 1B 652298582 T 3.69 139
C 0 10
AX-95073002 1B 652457758 A 3.71 136
G 0 9
AX-94748775 1B 652468844 G 2.64 131
A 0 17
AX-94629503 1B 652575175 C 2.65 131
A 0 18
AX-94446915 2A 44094660 A 3.34 139
G 0 10
AX-94430515 2A 45085276 A 1.88 37
C 0 111
AX-94639471 2A 52130032 G 3.19 136
A 0 9
AX-94690816 5A 620175970 A 3.95 7
G 0 110
表型差值Difference 材料数
No. of varieties
AX-94402434 7D 415430669 G 2.22 129
A 0 15
AX-95629896 Unknown Unknown G 2.88 135
A 0 9

Table 6

Candidate genes for agronomic traits of wheat and their annotations"

Candidate locus
Chr. | Position
Gene annotation or coding protein
KNPS 5B|4444933..16449146 AX-94385515 5B|10444933 TraesCS5B02G010800 Calcium-dependent channel, 7TM region, putative phosphate
AX-94459753 5B|10449146 TraesCS5B02G010800 Calcium-dependent channel, 7TM region, putative phosphate
5B|412015877..424015877 AX-94799632 5B|418015877 TraesCS5B02G237200 NB-ARC domain
7D|75887538..87887538 AX-94547362 7D|81887538 TraesCS7D02G129700 MATE_eukaryotic
TKW 7D|550123927..562123927 AX-95152265 7D|556123927 TraesCS7D02G436800 Auxin response factor
SL 3A|5350680..17350680 AX-94542697 3A|11350680 TraesCS3A02G017800 Unknown
KNPS/NFS 5B|4444933..16449146 AX-94385515 5B|10444933 TraesCS5B02G010800 Calcium-dependent channel, 7TM region, putative phosphate
AX-94459753 5B|10449146 TraesCS5B02G010800 Calcium-dependent channel, 7TM region, putative phosphate
HD 1B|646298582..658575175 AX-95197628 1B|652298582 TraesCS1B02G426000 Unknown
AX-95073002 1B|652457758 TraesCS1B02G426300 Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25
AX-94748775 1B|652468844 TraesCS1B02G426600 Unknown
AX-94629503 1B|652575175 TraesCS1B02G427100 Unknown
2A|38094660..51085276 AX-94446915 2A|44094660 TraesCS2A02G091700 Unknown
AX-94430515 2A|45085276 TraesCS2A02G092200 Wound-induced protein WI12
2A|46130032..58130032 AX-94639471 2A|52130032 TraesCS2A02G099200 Unknown
5A|614175970..626175970 AX-94690816 5A|620175970 TraesCS5A02G438800 Glutamine amidotransferases class-II (GATase).
7D|409430669..421430669 AX-94402434 7D|415430669 TraesCS7D02G325100 Unknown
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