锌胁迫下甘蓝型油菜发芽期下胚轴长的全基因组关联分析

doi:10.3724/SP.J.1006.2021.04037

Abstract

Abstract:

Zinc (Zn) is one of the important mircroelements, but the excessive amount application would affect plant growth and development. Genome-wide association analysis (GWAS) was performed on the relative hypocotyl length (RHL) using the 140 B. napus genotyped under zinc stress treatment (30 mg L^-1) at germination stage by Illumina 60K SNP array, and then significant SNP locus and candidate genes were detected. In the study, the population structure analysis revealed that the 140 B. napus were classified into two subgroups, and the kinship coefficients of the 89% materials were less than 0.1, indicating the tested population had a distant relationship. GWAS analysis indicated that there were significantly 8 SNP locus correlated to RHL, and single SNP loci could give an explanation on the 22.0%-33.2% phenotype variation. The differential expressed gene (DEGs) were detected by RNA-Seq. GO enrichment analysis indicated that the up-regulated genes mainly participated in redox reaction, ion transport, stress response, defense response and sulfur compound transport. Nineteen candidate genes response to zinc stress were identified by GWAS analysis and RNA-seq, including the genes encoding zinc finger protein (B-box type and ZFP1), glutathione transferase GSTU21, peroxidase family protein, ABC and MFS transporters, cell wall-related kinase protein, and genes encoding transcription factors (TF), such as BnaA07g27330D (MYB), BnaA02g30270D (bHLH), BnaA07g27840D (WRKY57), BnaA07g31860D (ORA47), and BnaA07g28000 (NAC). This study laid the foundation for understanding the molecular mechanism of zinc stress in B. napus.

Key words: Brassica napus, heavy metal, zinc stress, GWAS, germination stage

WEI Li-Juan, SHEN Shu-Lin, HUANG Xiao-Hu, MA Guo-Qiang, WANG Xi-Tong, YANG Yi-Ling, LI Huan-Dong, WANG Shu-Xian, ZHU Mei-Chen, TANG Zhang-Lin, LU Kun, LI Jia-Na, QU Cun-Min. Genome-wide association analysis reveals zinc-tolerant loci of rapeseed at germination stage[J].Acta Agronomica Sinica, 2021, 47(2): 262-274.

Figures/Tables 11

Table S1

Detailed information of the 140 B. napus accessions"

编号 Number	材料名称 Accessions	生态型 Ecotype	来源 Source
1	中双3号Zhongshuang 3	半冬性Semi-winter	中国浙江Zhejiang, China
2	镇油5号Zhenyou 5	半冬性Semi-winter	中国江苏Jiangsu, China
3	SWU46	半冬性Semi-winter	中国重庆Chongqing, China
4	WH-127	半冬性Semi-winter	中国湖北Hubei, China
5	WH-41	半冬性Semi-winter	中国湖北Hubei, China
6	WX10329	半冬性Semi-winter	中国湖南Hunan, China
7	JY-16	半冬性Semi-winter	中国湖北Hubei, China
8	黔油331 Qianyou 331	半冬性Semi-winter	中国贵州Guizhou, China
编号 Number	材料名称 Accessions	生态型 Ecotype	来源 Source
9	SWU47	半冬性Semi-winter	中国重庆Chongqing, China
10	浙双72 Zheshuang 72	半冬性Semi-winter	中国浙江Zhejiang, China
11	沪油17 Huyou 17	半冬性Semi-winter	中国上海Shanghai, China
12	中双7号Zhongshuang 7	半冬性Semi-winter	中国武汉Wuhan, China
13	WH-26	半冬性Semi-winter	中国湖北Hubei, China
14	Taisetsu	冬性Winter	日本Japan
15	M114	半冬性 Semi-winter	中国China
16	中油589 Zhongyou 589	半冬性Semi-winter	中国武汉Wuhan, China
17	农林43 Nonglin 43	冬性Winter	日本Japan
18	广德8104 Guangde 8104	半冬性Semi-winter	中国江苏Jiangsu, China
19	至尊Zhizun	半冬性Semi-winter	中国湖北Hubei, China
20	中双2号Zhongshuang 2	半冬性Semi-winter	中国湖北Hubei, China
21	中双4号Zhongshuang 4	半冬性Semi-winter	中国湖北Hubei, China
22	华油3号Huayou 3	半冬性Semi-winter	中国湖北Hubei, China
23	宁油14 Ningyou 14	半冬性Semi-winter	中国江苏Jiangsu, China
24	华油12 Huayou 12	半冬性Semi-winter	中国湖北Hubei, China
25	湖北白花油菜Hubei white flower rape	半冬性Semi-winter	中国湖北Hubei, China
26	WH-58	半冬性Semi-winter	中国湖北Hubei, China
27	699	半冬性Semi-winter	中国湖北Hubei, China
28	SWU63	半冬性Semi-winter	中国重庆Chongqing, China
29	WH-57	半冬性Semi-winter	中国湖北Hubei, China
30	苏油1号Shuyou 1	半冬性Semi-winter	中国江苏Jiangsu, China
31	WH-19	半冬性Semi-winter	中国湖北Hubei, China
32	中双4号Zhongshuang 4	半冬性Semi-winter	中国湖北Hubei, China
33	Nakate Chousen	春性Spring	朝鲜DPRK
34	广德761 Gaungde 761	半冬性Semi-winter	中国江苏Jiangsu, China
35	SWU110	半冬性Semi-winter	中国重庆Chongqing, China
36	7094	半冬性Semi-winter	中国湖北Hubei, China
37	SWU71	半冬性Semi-winter	中国重庆Chongqing, China
38	1111	半冬性Semi-winter	中国湖北Hubei, China
39	Erake	半冬性Semi-winter	波兰Poland
40	Campino	春性Spring	德国Germany
41	宁油10号 Ningyou 10	半冬性Semi-winter	中国江苏Jiangsu, China
42	中双11DH Zhongshuang 11DH	半冬性Semi-winter	中国湖北Hubei, China
43	浙双8号 Zheshuang 8	半冬性Semi-winter	中国浙江Zhejiang, China
44	cresor	春性Spring	法国France
45	浙油17 Zheyou 17	半冬性Semi-winter	中国浙江Zhejiang, China
46	华航901 Huahang 901	半冬性Semi-winter	中国湖北Hubei, China
47	Wesreo	春性Spring	澳大利亚Australia
48	南川长角 Nanchuansiliqua	半冬性Semi-winter	中国重庆Chongqing, China
49	J-917	半冬性Semi-winter	中国湖北Hubei, China
50	浙双6号 Zheshuang 6	半冬性Semi-winter	中国浙江Zhejiang, China
51	荣选 Rongxuan	半冬性Semi-winter	中国江苏Jiangsu, China
52	SWU106	半冬性Semi-winter	中国重庆Chongqing, China
编号 Number	材料名称 Accessions	生态型 Ecotype	来源 Source
53	D2	春性Spring	丹麦Denmark
54	豫油1号 Yuyou 1	半冬性Semi-winter	中国重庆Chongqing, China
55	WH-37	半冬性Semi-winter	中国湖北Hubei, China
56	J-951	半冬性Semi-winter	中国湖北Hubei, China
57	全紫油菜 Quanzi rape	春性Spring	中国江苏Jiangsu, China
58	SWU69	半冬性Semi-winter	中国重庆Chongqing, China
59	SWU60	半冬性Semi-winter	中国重庆Chongqing, China
60	丰油9号 Fengyou 9	半冬性Semi-winter	中国河南Henan, China
61	宁油1号 Ningyou 1	半冬性Semi-winter	中国湖北Hubei, China
62	SWU80	半冬性Semi-winter	中国重庆Chongqing, China
63	10-C29	半冬性Semi-winter	中国湖北Hubei, China
64	秦油5号 Qinyou 5	半冬性Semi-winter	中国陕西Shaanxi, China
65	Sophia	春性Spring	德国Germany
66	WaseChousen	春性Spring	朝鲜DPRK
67	Korina	春性Spring	德国Germany
68	J-915	半冬性Semi-winter	中国湖北Hubei, China
69	Bienvenu	半冬性Semi-winter	法国France
70	SWU102	半冬性Semi-winter	中国重庆Chongqing, China
71	漕泾胜利 Caojingshengli	半冬性Semi-winter	中国上海Shanghai, China
72	563	半冬性Semi-winter	中国湖南Hunan, China
73	皖油15号 Wanyou 15	半冬性Semi-winter	中国安徽Anhui, China
74	阳光198 Yangguang 198	半冬性Semi-winter	中国湖北Hubei, China
75	湘油13号 Xiangyou 13	半冬性Semi-winter	中国湖南Hunan, China
76	皖油16号 Wanyou 16	半冬性Semi-winter	中国安徽Anhui, China
77	华油13号 Huayou 13	半冬性Semi-winter	中国湖北Hubei, China
78	湘油15号 Xiangyou 15	半冬性Semi-winter	中国湖南Hunan, China
79	Tapidor	冬性Winter	法国France
80	10-C24	半冬性Semi-winter	中国湖北Hubei, China
81	圣光77 Shengguang 77	半冬性Semi-winter	中国湖北Hubei, China
82	史力丰 Shilifeng	半冬性Semi-winter	中国江苏Jiangsu, China
83	沪油3号 Huyou 3	半冬性Semi-winter	中国上海Shanghai, China
84	Santana	半冬性Semi-winter	中国China
85	10-C34	半冬性Semi-winter	中国湖北Hubei, China
86	11-Y7-117	半冬性Semi-winter	中国湖北Hubei, China
87	SWU99	半冬性Semi-winter	中国重庆Chongqing, China
88	宁油12 Ningyou 12	半冬性Semi-winter	中国江苏Jiangsu, China
89	Comet	春性Spring	瑞典Sweden
90	WH-20	半冬性Semi-winter	中国湖北Hubei, China
91	扬J6711 Yang J6711	半冬性Semi-winter	中国江苏Jiangsu, China
92	7191	半冬性Semi-winter	中国湖北Hubei, China
93	中双9号 Zhongshuang 9	半冬性Semi-winter	中国湖北Hubei, China
94	Daechosen	半冬性Semi-winter	朝鲜DPRK
95	Monty	半冬性Semi-winter	澳大利亚Australia
96	纬隆88 Weilong 88	半冬性Semi-winter	中国陕西Shanxi, China
编号 Number	材料名称 Accessions	生态型 Ecotype	来源 Source
97	沪油14 Huyou 14	半冬性Semi-winter	中国上海Shanghai, China
98	A117	半冬性Semi-winter	中国陕西Shaanxi, China
99	WH-15	半冬性Semi-winter	中国湖北Hubei, China
100	2011-7103	半冬性Semi-winter	中国湖北Hubei, China
101	SWU68	半冬性Semi-winter	中国重庆Chongqing, China
102	浙油18 Zheyou 18	半冬性Semi-winter	中国四川Zhejiang, China
103	Yan 81-2	半冬性Semi-winter	中国重庆Chongqing, China
104	2012-K8053	半冬性Semi-winter	中国湖北Hubei, China
105	淮油6号 Huaiyou 6	半冬性Semi-winter	中国江苏Jiangsu, China
106	2012-3546	半冬性Semi-winter	中国湖北Hubei, China
107	wx 10296	半冬性Semi-winter	中国湖南Hunan, China
108	2012-8380	半冬性Semi-winter	中国湖北Hubei, China
109	SWU92	半冬性Semi-winter	中国重庆Chongqing, China
110	农林42 Nonglin 42	半冬性Semi-winter	日本Japan
111	大花球 Dahuaqiu	半冬性Semi-winter	中国江苏Jiangsu, China
112	华油6号 Huayou 6	半冬性Semi-winter	中国湖北Hubei, China
113	CY12Q95406	半冬性Semi-winter	中国四川Sichuan, China
114	SWU49	半冬性Semi-winter	中国重庆Chongqing, China
115	SWU70	半冬性Semi-winter	中国重庆Chongqing, China
116	华双128 Huashuang 128	半冬性Semi-winter	中国湖北Hubei, China
117	皖油早 Wanyouzao	半冬性Semi-winter	中国安徽Anhui, China
118	宁油12 Ningyou 12	半冬性Semi-winter	中国江苏Jiangsu, China
119	滁油1号 Chuyou 1	半冬性Semi-winter	中国安徽Anhui, China
120	10-JP3	半冬性Semi-winter	中国湖北Hubei, China
121	2359	半冬性Semi-winter	中国湖北Hubei, China
122	宁油8号 Ningyou 8	半冬性Semi-winter	中国江苏Jiangsu, China
123	CY21PXW-84	半冬性Semi-winter	中国四川Sichuan, China
124	SWU88	半冬性Semi-winter	中国重庆Chongqing, China
125	Sida	春性Spring	加拿大Canada
126	川油20 Chuanyou 20	半冬性Semi-winter	中国四川Sichuan, China
127	沪油19 Huyou 19	半冬性Semi-winter	中国上海Shanghai, China
128	WH-62	半冬性Semi-winter	中国湖北Hubei, China
129	华油14 Huayou 14	半冬性Semi-winter	中国湖北Hubei, China
130	CY12GJ-1	半冬性Semi-winter	中国四川Sichuan, China
131	湘油11号 Xiangyou 11	半冬性Semi-winter	中国湖南Hunan, China
132	浙油601 Zheyou 601	半冬性Semi-winter	中国浙江Zhejiang, China
133	SWU108	半冬性Semi-winter	中国重庆Chongqing, China
134	CY14PXW-18	半冬性Semi-winter	中国四川Sichuan, China
135	Nca	半冬性Semi-winter	中国湖北Hubei, China
136	甘油5号 Ganyou 5	半冬性Semi-winter	中国湖北Hubei, China
137	SWU94	半冬性Semi-winter	中国重庆Chongqing, China
138	中油821 Zhongyou 821	半冬性Semi-winter	中国湖北Hubei, China
139	川油18 Chuanyou 18	半冬性Semi-winter	中国四川Sichuan, China
140	wx 10213	半冬性Semi-winter	中国湖北Hunan, China

Table S1

Table 1

Table 2

Fig. 1

Fig. 2

Fig. 3

Table 3

Fig. 4

Fig. 5

Fig. 6

Table 4

Candidate genes of the traits correlated with zinc stress treatment in B. napus "

候选基因 Candidate genes	物理位置 Physical position	拟南芥同源基因 Homologs in Arabidopsis	基因注释 Gene annotation	差异倍数 log₂ (Fold change)
BnaA02g30040D	Chr.A02: 21813781-21815282	AT5G48250	B-box型锌指蛋白 B-box type zinc finger protein with CCT domain	2.18
BnaA02g30270D	Chr.A02: 21934212-21936672	AT5G48560	bHLH转录因子 Basic helix-loop-helix (bHLH) DNA-binding protein	-6.62
BnaA07g27330D	ChrA07: 19877781-19879164	AT1G68670	MYB转录因子 MYB-like transcription factor family protein	2.15
BnaA07g27340D	Chr.A07: 19884616-19887579	AT1G68690	蛋白激酶家族 Protein kinase superfamily protein	4.55
BnaA07g27500D	Chr.A07: 19996402-19997781	AT1G68850	过氧化物酶家族蛋白 Peroxidase superfamily protein	-2.06
BnaA07g27840D	Chr.A07: 20196357-20198149	AT1G69310	WRKY57转录因子 WRKY DNA-binding protein 57	2.64
BnaA07g28000D	Chr.A07: 20266703-20267687	AT1G69490	NAC转录因子 NAC-like, activated by AP3/PI (NAP)	2.01
BnaA07g31860D	Chr.A07: 22136736-22137327	AT1G74930	ERF转录因子 ORA47	3.71
BnaA07g34210D	Chr.A07: 23311591-23312410	AT1G78360	谷胱甘肽转移酶 (GSTU21) Glutathione S-transferase TAU 21 (GSTU21)	-3.13
BnaA07g35030D	Chr.A07: 23695006-23698790	AT1G79610	Na⁺/H⁺逆向转运蛋白 Na⁺/H⁺ antiporter 6 (NHX6)	2.29
BnaA07g35090D	Chr.A07: 23714116-23714860	AT1G79680	类细胞壁相关激酶WALL ASSOCIATED KINASE (WAK)-LIKE 10 (WAKL10)	6.52
BnaA07g35350D	Chr.A07: 23800896-23801571	AT1G80730	锌指蛋白 Zinc-finger protein 1 (ZFP1)	-7.08
BnaC04g06210D	Chr.C04: 4439046-4439940	AT3G55090	ABC转运蛋白 ABC-2 type transporter family protein	2.10
BnaC04g06300D	Chr.C04: 4503767-4505873	AT2G39210	主要协助转运蛋白超家族 Major facilitator superfamily protein (MFS)	3.11
BnaC06g38840D	Chr.C06: 36254140-36254958	AT1G78360	谷胱甘肽转移酶(GSTU21) Glutathione S-transferase TAU 21 (GSTU21)	-4.29
BnaC06g38850D	Chr.C06: 36255467-36256984	AT1G78360	谷胱甘肽转移酶(GSTU21) Glutathione S-transferase TAU 21 (GSTU21)	-2.35
BnaC06g39970D	Chr.C06: 36849441-36853390	AT1G79610	Na⁺/H⁺逆向转运蛋白 Na⁺/H⁺ antiporter 6 (NHX6)	4.01
BnaC06g40020D	Chr.C06: 36867031-36869575	AT1G69730	细胞壁相关激酶蛋白 Wall-associated kinase family protein	4.43
BnaC06g40250D	Chr.C06: 36958965-36959628	AT1G80730	锌指蛋白 Zinc-finger protein 1 (ZFP1)	-2.49

Table 4

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品种 Accessions	Zn(NO₃)₂溶液浓度 Concentration of Zn(NO₃)₂ solutions (mg L^-1)
品种 Accessions	0	5	10	15	20	30	50	70
1	5.76	4.46	4.74	5.82	3.78	2.54	2.54	1.68
2	4.38	4.38	4.02	3.16	2.38	2.54	2.52	2.08
3	6.80	6.64	5.02	6.02	4.34	2.62	2.24	2.34
4	7.60	7.66	6.64	5.20	4.20	3.14	2.76	2.14
5	6.70	6.28	5.24	4.32	3.24	3.20	2.84	1.80
6	6.25	5.88	5.13	4.90	3.59	2.81	2.58	2.01
7	7.90	6.30	8.40	6.52	5.88	5.46	4.84	2.60
8	5.90	7.98	8.64	4.50	4.08	4.58	4.64	2.40
9	6.30	7.90	7.10	5.60	6.54	4.50	3.74	2.40
10	6.96	7.08	8.06	5.73	6.01	4.86	4.94	2.91
平均值 Mean (cm)	6.45	6.46	6.30	3.78	3.58	2.48	3.36	2.24
标准差SD (cm)	1.00	1.29	1.68	1.17	1.25	0.87	1.07	0.37
变异系数 CV (%)	0.155	0.200	0.267	0.309	0.349	0.352	0.319	0.166

性状	最小值	最大值	均值±标准差	变异系数	偏度	峰度
Trait	Min.(cm)	Max.(cm)	Mean±SD	CV (%)	Skewness	Kurtosis
CHL	3.66	7.99	5.77±0.92	15.85	-0.13	0.83
THL	2.28	6.47	4.24±0.80	18.84	0.41	0.02
RHL	0.38	1.08	0.73±0.13	17.57	0.28	0.15

染色体 Chr.	位置 Position (bp)	P值 P-value	显著性 -log₁₀ (P)	贡献率 R² (%)
A02	22,075,111	2.97E-06	5.53	24.62
A07	20,094,111	3.97E-06	5.40	22.11
A07	22,001,673	3.49E-06	5.46	21.99
A07	23,402,490	7.70E-06	5.11	19.90
A07	23,555,825	2.92E-06	5.53	22.06
A07	23,580,640	7.50E-08	7.13	33.18
C04	4,456,230	3.12E-06	5.51	24.66
C06	36,835,784	2.55E-06	5.59	24.45

Genome-wide association analysis reveals zinc-tolerant loci of rapeseed at germination stage

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