普通小麦主要农艺性状的全基因组关联分析

doi:10.3724/SP.J.1006.2019.91002

Abstract

Abstract:

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

ZHAI Jun-Peng,LI Hai-Xia,BI Hui-Hui,ZHOU Si-Yuan,LUO Xiao-Yan,CHEN Shu-Lin,CHENG Xi-Yong,XU Hai-Xia. Genome-wide association study for main agronomic traits in common wheat[J].Acta Agronomica Sinica, 2019, 45(10): 1488-1502.

Figures/Tables 9

Table 1

Wheat varieties used in this study"

类别Type	品种(系) Variety (line)
国家黄淮南片区域试验 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
河南省区域试验 Regional trial of wheat varieties in Henan Province	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
小麦联合体品种比较试验 Comparative trail of wheat varieties in Henan Province	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
高代品系 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 1

Table 2

Table 3

Fig. 1

Fig. 2

Fig. 3

Table 4

Table 5

Table 6

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染色体 Chr.	标记数目 No. of markers	物理长度Physical 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)
染色体 Chr.	标记数目 No. of markers	物理长度Physical distance (Mb)	Mean	Range	Mean	Range	标记密度 Density of marker (Mb marker^-1)
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

性状 Trait		标记 SNP		染色体 Chr.		物理位置 Position		P-value							R² (%)
性状 Trait		标记 SNP		染色体 Chr.		物理位置 Position		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
性状 Trait	标记 SNP		染色体 Chr.		物理位置 Position		P-value									R² (%)
性状 Trait	标记 SNP		染色体 Chr.		物理位置 Position		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

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

性状 Trait	候选位点 Candidate locus	标记 SNP	物理位置 Chr. \| Position	基因 Gene	基因注释或编码蛋白 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

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

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