Genome-Wide Association Analysis and Allelic Mining of Grain Shape-Related Traits in Rice

doi:10.1016/j.rsci.2018.09.002

Abstract

Abstract:

Excavating single nucleotide polymorphisms (SNPs) significantly associated with rice grain shape and predicting candidate genes through genome-wide association study (GWAS) can provide a theoretical basis for discovery and utilization of excellent genetic resources in rice. Based on 16 352 SNPs, 161 natural indica rice varieties with various grain sizes in southern China were used for GWAS of grain shape-related traits, referring to grain length (GL), grain width (GW), 1000-grain weight (TGW), and grain length/width (GLW). Phenotypic statistics showed that coefficient of variation values for these four traits GL, GW, TGW and GLW were 9.92%, 9.09%, 20.20% and 16.38%, respectively. Each trait showed a normal distribution, and there was a certain correlation between these traits. Through general linear model correlation analysis, a total of 38 significant loci were identified, and a range of 100 kb upstream and downstream of the significant loci was identified as the candidate interval. On chromosome 3, GS3 and qGL3 were found to regulate GL. On chromosome 6, TGW6 and GW6a were found to regulate TGW. Also, some QTLs related to grain shape were found on chromosomes 5 and 9. Besides that, using sequenced 3K-germplasm resources, we found that there are 22 overlapped varieties between these two natural populations. Twenty-six SNPs and fourteen haplotypes were identified in five regions of GS3 genes. The detection of multiple candidate genes/QTLs within the candidate interval is beneficial for further excavation of superior rice genetic resources.

Key words: candidate gene, grain shape, genome-wide association study, haplotype, rice, single nucleotide polymorphism

Yang Lv, Yueying Wang, Jahan Noushin, Haitao Hu, Ping Chen, Lianguang Shang, Haiyan Lin, Guojun Dong, Jiang Hu, Zhenyu Gao, Qian Qian, Yu Zhang, Longbiao Guo. Genome-Wide Association Analysis and Allelic Mining of Grain Shape-Related Traits in Rice[J]. Rice Science, 2019, 26(6): 384-392.

Figures/Tables 8

References 46

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No.	Variety	Origin	No.	Variety	Origin	No.	Variety	Origin
1	Hucchao1hao	Sichuan	55	Zhubao384	Guangdong	109	Xianfeng1hao	Zhejiang
2	Hucheng17	Sichuan	56	Baoxuan2hao	Guangxi	110	Zaolian31	Zhejiang
3	Huhongzao1hao	Sichuan	57	Guangnan1hao	Guangxi	111	Zaoxian141	Zhejiang
4	Hunanzao1hao	Sichuan	58	Hongnan	Guangxi	112	Zhechang3hao	Zhejiang
5	Hushuang1011	Sichuan	59	Jiefang1hao	Guangxi	113	Zhengui9hao	Zhejiang
6	Aimakang	Sichuan	60	Jinguang202	Guangxi	114	Zhenlong13	Zhejiang
7	Aituogu151	Sichuan	61	Tuanjie1hao	Guangxi	115	Zhenxian97B	Zhejiang
8	CDR22	Sichuan	62	Nanjing1hao	Jiangsu	116	Zhongganzao	Zhejiang
9	Chengduai8hao	Sichuan	63	Qinglian16	Jiangsu	117	Zhufei10hao	Zhejiang
10	Chenghui448	Sichuan	64	Zhuxi26	Jiangsu	118	Zhuke2hao	Zhejiang
11	Chuanxiang29B	Sichuan	65	508	Jiangxi	119	Zhulianai	Zhejiang
12	Fuhui838	Sichuan	66	5450	Jiangxi	120	1296	Hubei
13	Gang46B	Sichuan	67	6001	Jiangxi	121	Ezao1hao	Hubei
14	K17B	Sichuan	68	6004	Jiangxi	122	Ezao6hao	Hubei
15	Shuhui527	Sichuan	69	6188	Jiangxi	123	Ezhong2hao	Hubei
16	Yixiang1B	Sichuan	70	7004	Jiangxi	124	Huaai15	Hubei
17	Annandao	Anhui	71	7005	Jiangxi	125	Jingainuo	Hubei
18	Dengdengqi	Anhui	72	Aihong11	Jiangxi	126	Chun389B	Sichuan
19	Mafangxian	Anhui	73	Bayiwan	Jiangxi	127	Aizizhan	Hunan
20	Wuhu71zao	Anhui	74	Gannanzao20	Jiangxi	128	Chenwan3hao	Hunan
21	XieqingzaoB	Anhui	75	Gannanzao23	Jiangxi	129	Fanzi	Hunan
22	Zhuguang23	Anhui	76	Jiangxisimiao	Jiangxi	130	Hongmidongzhan	Hunan
23	Aijiaonante	Guangdong	77	Jingnong3hao	Jiangxi	131	Hunanzao	Hunan
24	Conglu51	Guangdong	78	Jingnong69	Jiangxi	132	Laohuanggu	Hunan
25	Fengaizhan1	Guangdong	79	Jiunongzao1hao	Jiangxi	133	Liguzao	Hunan
26	Guangchang13	Guangdong	80	Liantangzao	Jiangxi	134	Luguiai	Hunan
27	Guangchangai	Guangdong	81	Nantehao	Jiangxi	135	Xiangaizao10hao	Hunan
28	Guangjie9hao	Guangdong	82	Wanxian22	Jiangxi	136	Xiangaizao2hao	Hunan
29	Guangluai4hao	Guangdong	83	Xingheng1hao	Jiangxi	137	Xiangaizao4hao	Hunan
30	Guangnongai1hao	Guangdong	84	Xiujiangwan3hao	Jiangxi	138	Xiangaizao7hao	Hunan
31	Guangwen10hao	Guangdong	85	Xiujiangzao4hao	Jiangxi	139	Xiangaizao8hao	Hunan
32	Guangxuan3hao	Guangdong	86	Xiujiangzao9hao	Jiangxi	140	Xiangaizao9hao	Hunan
33	Guichao13	Guangdong	87	Youzhanzi	Jiangxi	141	Xiangwanxian2hao	Hunan
34	Guichao2hao	Guangdong	88	5006	Henan	142	Xiangzaoxian1hao	Hunan
35	Guinongzhan	Guangdong	89	73-1	Henan	143	Xiangzhongxian1hao	Hunan
36	Hongmeizao	Guangdong	90	77xuan7	Henan	144	Yuchi231-8	Hunan
37	Huanghuazhan	Guangdong	91	Dongxuan2hao	Henan	145	Aibaiqiu	Fujian
38	Qiguizao25	Guangdong	92	Xinai1hao	Henan	146	Aijiaobaimizai	Fujian
39	Qinghuaai6hao	Guangdong	93	Aikezao	Zhejiang	147	Fushe31	Fujian
40	Qingliuai	Guangdong	94	Aiqing3hao	Zhejiang	148	Guangdabai	Fujian
41	Qishanzhan	Guangdong	95	Aiwu	Zhejiang	149	Hong410	Fujian
42	Qiuguiai11	Guangdong	96	Butuoai	Zhejiang	150	Hongwan52	Fujian
43	Sanerai	Guangdong	97	Erjiuduo	Zhejiang	151	Hongyun33	Fujian
44	Shengai7hao	Guangdong	98	Erjiuqing	Zhejiang	152	Jinghong1hao	Fujian
45	Shuanggui36	Guangdong	99	Guiluai8hao	Zhejiang	153	Longge113	Fujian
46	Shuangqizhan	Guangdong	100	Hongtu31	Zhejiang	154	Lucaihao	Fujian
47	Shuangzhuzhan	Guangdong	101	Junxie	Zhejiang	155	Minghui63	Fujian
48	Teqingxuanhui	Guangdong	102	Qingganhuang	Zhejiang	156	Qiuzhan470	Fujian
49	Tesanai	Guangdong	103	Qingmazao	Zhejiang	157	Yuanshannuo	Fujian
50	Texianzhan13	Guangdong	104	Sanjiufeng	Zhejiang	158	ZhenD-1	Fujian
51	Tonghongai	Guangdong	105	Shaonuo2hao	Zhejiang	159	Zhenhong17	Fujian
52	Yuexiangzhan	Guangdong	106	Shenglong	Zhejiang	160	Zhenmu85	Fujian
53	Zhaiyeqing8hao	Guangdong	107	Taizao5hao	Zhejiang	161	Zhuliuai	Fujian
54	Zhenguiai1hao	Guangdong	108	Wenxuanqing	Zhejiang

No.	Variety	Origin	No.	Variety	Origin	No.	Variety	Origin
1	Hucchao1hao	Sichuan	55	Zhubao384	Guangdong	109	Xianfeng1hao	Zhejiang
2	Hucheng17	Sichuan	56	Baoxuan2hao	Guangxi	110	Zaolian31	Zhejiang
3	Huhongzao1hao	Sichuan	57	Guangnan1hao	Guangxi	111	Zaoxian141	Zhejiang
4	Hunanzao1hao	Sichuan	58	Hongnan	Guangxi	112	Zhechang3hao	Zhejiang
5	Hushuang1011	Sichuan	59	Jiefang1hao	Guangxi	113	Zhengui9hao	Zhejiang
6	Aimakang	Sichuan	60	Jinguang202	Guangxi	114	Zhenlong13	Zhejiang
7	Aituogu151	Sichuan	61	Tuanjie1hao	Guangxi	115	Zhenxian97B	Zhejiang
8	CDR22	Sichuan	62	Nanjing1hao	Jiangsu	116	Zhongganzao	Zhejiang
9	Chengduai8hao	Sichuan	63	Qinglian16	Jiangsu	117	Zhufei10hao	Zhejiang
10	Chenghui448	Sichuan	64	Zhuxi26	Jiangsu	118	Zhuke2hao	Zhejiang
11	Chuanxiang29B	Sichuan	65	508	Jiangxi	119	Zhulianai	Zhejiang
12	Fuhui838	Sichuan	66	5450	Jiangxi	120	1296	Hubei
13	Gang46B	Sichuan	67	6001	Jiangxi	121	Ezao1hao	Hubei
14	K17B	Sichuan	68	6004	Jiangxi	122	Ezao6hao	Hubei
15	Shuhui527	Sichuan	69	6188	Jiangxi	123	Ezhong2hao	Hubei
16	Yixiang1B	Sichuan	70	7004	Jiangxi	124	Huaai15	Hubei
17	Annandao	Anhui	71	7005	Jiangxi	125	Jingainuo	Hubei
18	Dengdengqi	Anhui	72	Aihong11	Jiangxi	126	Chun389B	Sichuan
19	Mafangxian	Anhui	73	Bayiwan	Jiangxi	127	Aizizhan	Hunan
20	Wuhu71zao	Anhui	74	Gannanzao20	Jiangxi	128	Chenwan3hao	Hunan
21	XieqingzaoB	Anhui	75	Gannanzao23	Jiangxi	129	Fanzi	Hunan
22	Zhuguang23	Anhui	76	Jiangxisimiao	Jiangxi	130	Hongmidongzhan	Hunan
23	Aijiaonante	Guangdong	77	Jingnong3hao	Jiangxi	131	Hunanzao	Hunan
24	Conglu51	Guangdong	78	Jingnong69	Jiangxi	132	Laohuanggu	Hunan
25	Fengaizhan1	Guangdong	79	Jiunongzao1hao	Jiangxi	133	Liguzao	Hunan
26	Guangchang13	Guangdong	80	Liantangzao	Jiangxi	134	Luguiai	Hunan
27	Guangchangai	Guangdong	81	Nantehao	Jiangxi	135	Xiangaizao10hao	Hunan
28	Guangjie9hao	Guangdong	82	Wanxian22	Jiangxi	136	Xiangaizao2hao	Hunan
29	Guangluai4hao	Guangdong	83	Xingheng1hao	Jiangxi	137	Xiangaizao4hao	Hunan
30	Guangnongai1hao	Guangdong	84	Xiujiangwan3hao	Jiangxi	138	Xiangaizao7hao	Hunan
31	Guangwen10hao	Guangdong	85	Xiujiangzao4hao	Jiangxi	139	Xiangaizao8hao	Hunan
32	Guangxuan3hao	Guangdong	86	Xiujiangzao9hao	Jiangxi	140	Xiangaizao9hao	Hunan
33	Guichao13	Guangdong	87	Youzhanzi	Jiangxi	141	Xiangwanxian2hao	Hunan
34	Guichao2hao	Guangdong	88	5006	Henan	142	Xiangzaoxian1hao	Hunan
35	Guinongzhan	Guangdong	89	73-1	Henan	143	Xiangzhongxian1hao	Hunan
36	Hongmeizao	Guangdong	90	77xuan7	Henan	144	Yuchi231-8	Hunan
37	Huanghuazhan	Guangdong	91	Dongxuan2hao	Henan	145	Aibaiqiu	Fujian
38	Qiguizao25	Guangdong	92	Xinai1hao	Henan	146	Aijiaobaimizai	Fujian
39	Qinghuaai6hao	Guangdong	93	Aikezao	Zhejiang	147	Fushe31	Fujian
40	Qingliuai	Guangdong	94	Aiqing3hao	Zhejiang	148	Guangdabai	Fujian
41	Qishanzhan	Guangdong	95	Aiwu	Zhejiang	149	Hong410	Fujian
42	Qiuguiai11	Guangdong	96	Butuoai	Zhejiang	150	Hongwan52	Fujian
43	Sanerai	Guangdong	97	Erjiuduo	Zhejiang	151	Hongyun33	Fujian
44	Shengai7hao	Guangdong	98	Erjiuqing	Zhejiang	152	Jinghong1hao	Fujian
45	Shuanggui36	Guangdong	99	Guiluai8hao	Zhejiang	153	Longge113	Fujian
46	Shuangqizhan	Guangdong	100	Hongtu31	Zhejiang	154	Lucaihao	Fujian
47	Shuangzhuzhan	Guangdong	101	Junxie	Zhejiang	155	Minghui63	Fujian
48	Teqingxuanhui	Guangdong	102	Qingganhuang	Zhejiang	156	Qiuzhan470	Fujian
49	Tesanai	Guangdong	103	Qingmazao	Zhejiang	157	Yuanshannuo	Fujian
50	Texianzhan13	Guangdong	104	Sanjiufeng	Zhejiang	158	ZhenD-1	Fujian
51	Tonghongai	Guangdong	105	Shaonuo2hao	Zhejiang	159	Zhenhong17	Fujian
52	Yuexiangzhan	Guangdong	106	Shenglong	Zhejiang	160	Zhenmu85	Fujian
53	Zhaiyeqing8hao	Guangdong	107	Taizao5hao	Zhejiang	161	Zhuliuai	Fujian
54	Zhenguiai1hao	Guangdong	108	Wenxuanqing	Zhejiang

Trait	Mean	SD	Max	Min	CV (%)
GL (mm)	8.37	0.83	11.19	7.09	9.92
GW (mm)	2.97	0.27	3.56	2.27	9.09
TGW (g)	26.05	5.26	39.34	16.93	20.20
GLW	2.87	0.47	4.33	2.20	16.38

Trait	Mean	SD	Max	Min	CV (%)
GL (mm)	8.37	0.83	11.19	7.09	9.92
GW (mm)	2.97	0.27	3.56	2.27	9.09
TGW (g)	26.05	5.26	39.34	16.93	20.20
GLW	2.87	0.47	4.33	2.20	16.38

Trait	Chr	SNP site ^a (bp)	Major allele	Minor allele	MAF	-log(P)	Candidate gene/QTL
GL	3	17 302 647	A	G	0.42	13.38	Os03g0407400
	3	19 320 570	A	G	0.32	4.21	Os03g0646900
	3	21 821 785	A	G	0.33	4.60	Os03g0646900
	5	15 731 341	A	G	0.45	4.46
	6	1 764 762	C	A	0.10	7.38
	6	1 867 223	A	G	0.28	4.86
	6	2 009 738	C	A	0.30	4.36
	7	9 004 374	A	G	0.43	4.11
GW	4	6 470 963	A	G	0.31	4.72
	5	15 731 341	A	G	0.45	4.23
	6	24 170 016	C	A	0.49	6.03	Os06g0623700
	6	26 025 122	A	G	0.47	4.45	Os06g0650300
	8	3 681 009	A	G	0.27	8.80
	9	20 143 516	A	G	0.37	4.01
	11	11 962 160	G	A	0.24	5.61
	11	12 028 646	G	A	0.19	7.08
	11	14 891 499	A	T	0.20	5.93
GLW	1	12 869 918	A	T	0.19	6.49
	1	15 765 545	A	G	0.26	6.40
	2	31 232 596	A	C	0.49	4.86
	3	17 302 647	A	G	0.42	8.61	Os03g0407400
	3	19 320 570	A	G	0.32	4.05
	3	20 622 588	A	C	0.15	4.95	Os03g0646900
	3	21 821 785	A	G	0.33	4.19
	3	30 021 901	A	G	0.42	5.33
	5	15 731 341	A	G	0.45	7.24	qKw5
	6	1 764 762	C	A	0.10	7.58
	6	24 170 016	C	A	0.49	5.26
	7	9 004 374	A	G	0.43	4.05
	8	3 681 009	A	G	0.27	4.19
	9	19 020 266	A	C	0.41	5.93	qGL9
	9	20 143 516	A	G	0.37	6.83	qGL9
	10	11 961 180	T	A	0.43	4.74
	11	11 962 160	G	A	0.24	5.30
	11	12 028 646	G	A	0.19	6.27
	11	14 891 499	A	T	0.20	6.31
	12	2 963 765	G	A	0.34	4.06
TGW	3	17 302 647	A	G	0.42	5.72	Os03g0407400