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作物学报

作物学报 ›› 2021, Vol. 47 ›› Issue (2): 262-274.doi: 10.3724/SP.J.1006.2021.04037

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

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

魏丽娟(), 申树林, 黄小虎, 马国强, 王曦彤, 杨怡玲, 李洹东, 王书贤, 朱美晨, 唐章林, 卢坤, 李加纳*(), 曲存民*()   

  1. 西南大学农学与生物科技学院 / 油菜工程研究中心 / 西南大学现代农业科学研究院, 重庆 400715
  • 收稿日期:2020-02-18 接受日期:2020-04-15 出版日期:2021-02-12 网络出版日期:2020-12-25
  • 通讯作者: 李加纳,曲存民
  • 作者简介:魏丽娟, E-mail: lijuan525888@163.com
  • 基金资助:
    国家自然科学基金项目(31701460);中央高校基本科研业务费(XDJK2019C041);中央高校基本科研业务费(XDJK2020D023);重庆市基础科学与创新研究项目(cstc2016shms-ztzx80010);重庆市基础科学与创新研究项目(cstc2017jcyjAX0321);国家现代农业产业技术体系建设专项(CARS-12);高等学校学科创新引智基地111项目(B12006)

Genome-wide association analysis reveals zinc-tolerant loci of rapeseed at 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*()   

  1. College of Agronomy and Biotechnology, Southwest University / Chongqing Engineering Research Center for Rapeseed / Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
  • Received:2020-02-18 Accepted:2020-04-15 Published:2021-02-12 Published online:2020-12-25
  • Contact: LI Jia-Na,QU Cun-Min
  • Supported by:
    National Natural Science Foundation of China(31701460);Fundamental Research Funds for the Central Universities(XDJK2019C041);Fundamental Research Funds for the Central Universities(XDJK2020D023);Chongqing Basic Scientific and Advanced Technology Research(cstc2016shms-ztzx80010);Chongqing Basic Scientific and Advanced Technology Research(cstc2017jcyjAX0321);China Agricultural Research System(CARS-12);Intellectual Base for Discipline Innovation in Colleges and Universities(B12006)

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摘要：

锌(Zn)是重要的微量元素之一, 但土壤中过量的锌累积会影响植物的生长发育。本研究以不同遗传来源的140份甘蓝型油菜为材料, 利用芸薹属60K SNP芯片对锌胁迫下(30 mg L-1)甘蓝型油菜发芽期相对下胚轴长(RHL)进行全基因组关联分析, 筛选与甘蓝型油菜发芽期下胚轴长度显著关联的SNP位点及候选基因。群体结构分析表明, 供试的140份甘蓝型油菜被分为2个亚群, 其中89%材料间亲缘关系小于0.1, 说明供试群体材料亲缘关系比较远。GWAS分析共检测到8个与RHL显著关联的SNP位点, 单个SNP位点分别可解释22.0%~33.2%的表型变异。转录组分析获得的差异基因GO富集分析结果表明, 上调表达基因主要参与氧化还原反应、离子转运、胁迫反应、防御反应和硫化合物转运。综合全基因组关联分析和转录组测序结果, 共鉴定到19个与锌胁迫相关的候选基因, 包括编码锌指蛋白家族成员(B-box型和ZFP1)、谷胱甘肽转移酶GSTU21、过氧化物酶家族蛋白、ABC和MFS转运蛋白及细胞壁相关激酶蛋白和一些重要的转录因子(BnaA07g27330D、BnaA02g30270D、BnaA07g27840D、BnaA07g31860D和BnaA07g28000), 为深入解析油菜锌胁迫分子机制提供了参考。

关键词: 甘蓝型油菜, 重金属, 锌胁迫, 全基因组关联分析, 发芽期

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

附表1

140份甘蓝型油菜材料信息"

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

表1

不同Zn(NO3)2溶液浓度下油菜下胚轴长度"

品种
Accessions		 Zn(NO3)2溶液浓度 Concentration of Zn(NO3)2 solutions (mg L-1)
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

表2

锌胁迫下甘蓝型油菜发芽期性状统计分析"

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

图1

锌胁迫下甘蓝型油菜相对下胚轴长频率分布图"

图2

基于SNP标记估算群体结构关系图和亲缘关系图 A: lnP(D)和ΔK变化关系图; B: K = 2时群体结构图; C: 140份甘蓝型油菜亲缘关系图。"

图3

锌胁迫下甘蓝型油菜相对下胚轴长QQ图和曼哈顿图"

表3

锌胁迫下甘蓝型油菜发芽期相对下胚轴长显著关联的SNP位点"

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

图4

甘蓝型油菜染色体不同物理距离的LD分布(A)和共线性分析(B)"

图5

油菜锌胁迫后上调和下调转录因子基因数目"

图6

油菜锌胁迫后差异表达上调(A)和下调基因(B) GO富集分析"

表4

甘蓝型油菜锌胁迫下相关性状候选基因"

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
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