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作物学报 ›› 2018, Vol. 44 ›› Issue (8): 1105-1113.doi: 10.3724/SP.J.1006.2018.01105

• 作物遗传育种·种质资源·分子遗传学 •    下一篇

整合GWAS和WGCNA分析挖掘甘蓝型油菜黄籽微效作用位点

鲜小华1,**(),王嘉1,2,**(),徐新福1,曲存民1,卢坤1,李加纳1,刘列钊1,*()   

  1. 1 西南大学农学与生物科技学院 / 西南大学农业科学研究院, 重庆 400715
    2 南充市农业科学院, 四川南充 637000
  • 收稿日期:2018-01-29 接受日期:2018-06-09 出版日期:2018-08-10 网络出版日期:2018-06-11
  • 通讯作者: 鲜小华,王嘉,刘列钊
  • 基金资助:
    本研究由国家自然科学基金项目(31771830);重庆市科委项目(cstc2016shmszx80083);中央高校基本科研业务费专项(XDJK2017A009)

Mining Yellow-seeded Micro Effect Loci in B. napus by Integrated GWAS and WGCNA Analysis

Xiao-Hua XIAN1,**(),Jia WANG1,2,**(),Xin-Fu XU1,Cun-Min QU1,Kun LU1,Jia-Na LI1,Lie-Zhao LIU1,*()   

  1. 1 College of Agronomy and Biotechnology / Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
    2 Nanchong Academy of Agricultural Sciences, Nanchong 637000, Sichuan, China
  • Received:2018-01-29 Accepted:2018-06-09 Published:2018-08-10 Published online:2018-06-11
  • Contact: Xiao-Hua XIAN,Jia WANG,Lie-Zhao LIU
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31771830);the Science and Technology Committee of Chongqing(cstc2016shmszx80083);the Fundamental Research Funds for the Central Universities(XDJK2017A009)

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摘要：

甘蓝型油菜是世界上最重要的油料作物之一, 黄籽是提高品质的重要育种目标。本研究以520份具有代表性的甘蓝型油菜品种(系)为材料, 结合种子发育过程中8个时期的转录组数据, 采取整合全基因组关联分析(GWAS)和权重基因共表达网络分析(WGCNA)的策略, 挖掘油菜黄籽性状微效作用位点, 2年共检测到199个SNP位点, 在SNP位点附近共挖掘出1826个名义候选基因。利用R语言中的WGCNA软件包构建了8个共表达模块, 基因功能富集分析显示, turquoise模块和blue模块与黄籽表型相关。苯丙烷代谢途径、类黄酮途径的关键基因BnATCAD4、BnF3H以及BnANS为turquoise模块的枢纽基因(hub gene)。通过已知的黄籽相关基因, 挖掘出了一部分黄籽微效作用基因, 这些基因多参与苯丙烷、类黄酮以及原花青素代谢途径。本研究挖掘的这些位点和候选基因可作为影响油菜黄籽形成的重要候选区域和基因, 有助于探究甘蓝型油菜黄籽基因资源信息、揭示油菜黄籽性状的遗传基础和分子机制、丰富分子育种理论以及提高油菜品质。

关键词: 甘蓝型油菜, 黄籽, 全基因组关联分析, 权重基因共表达网络分析

Abstract:

Brassica napus is one of the most important oil crops in the world, and developing yellow-seeded B. napus with improved qualities is a major breeding goal. The yellow-seeded minor genes were mined by genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) with 520 representative varieties (or lines) and the transcriptional data at eight time points during the seed development. The 199 SNPs and 1826 nominally significant GWAS candidate genes were detected. Weighted gene co-expression network analysis was performed using the WGCNA R package to construct the resulting network composing eight distinct gene modules. Among them, the turquoise module and the blue module were related to the seed coat color based on gene function enrichment analysis. BnATCAD4, BnF3H, and BnANS, the key enzymes genes of phenylpropane metabolic pathway and flavonoid metabolic pathway were found in turquoise module. Through the characterization of module content and topology, we mined a number of micro effect genes based on known yellow-seed related genes mainly involved in the phenylpropanoid metabolic process, flavonoid metabolic process and proanthocyanidin biosynthetic process. This information of minor loci and candidate genes should be useful in the breeding for yellow-seeded B. napus.

Key words: Brassica napus, yellow-seeded, GWAS, WGCNA

图1

甘蓝型油菜黄籽表型全基因组关联分析结果的曼哈顿图 灰色的虚线为Bonferroni校正阈值线, 红色为FDR校正阈值线。"

图2

基因共表达网络构建结果 A: 基因的聚类与模块构建; B: 特征与模块相关性分析。"

表1

各模块GO富集情况(部分)"

模块
Module		 基因数目
Number of genes		 GO 每个模块显著富集的term
Top term for each module		 P值
P-value		 FDR
Black 68 GO:0004499 N,N-二甲基苯胺单加氧酶活性
N,N-dimethylaniline monooxygenase activity		 2.38E-03 1.26E-01
Blue 303 GO:0045551 肉桂醇脱氢酶活性
Cinnamyl-alcohol dehydrogenase activity		 1.53E-04 3.37E-02
GO:0052747 芥子醇脱氢酶活性
Sinapyl alcohol dehydrogenase activity		 1.53E-04 3.37E-02
GO:0009698 苯丙烷代谢过程
Phenylpropanoid metabolic process		 1.40E-06 2.01E-03
GO:0009699 苯丙烷生物合成过程
Phenylpropanoid biosynthetic process		 4.27E-06 3.06E-03
GO:0019748 次生代谢过程
Secondary metabolic process		 9.92E-05 3.56E-02
Brown 157 GO:0044699 单一的生物过程
Single-organism process		 4.78E-05 5.30E-02
Green 82 GO:0008107 α-1,2岩藻糖基转移酶活性
Galactoside 2-alpha-L-fucosyltransferase activity		 4.89E-04 4.74E-02
Pink 49 GO:0016886 形成磷酸酯键的连接酶活性
Ligase activity, forming phosphoric ester bonds		 4.32E-05 7.04E-03
Red 79 GO:0043170 大分子代谢过程
Macromolecule metabolic process		 3.86E-05 2.51E-02
Turquoise 473 GO:0009699 苯丙烷生物合成过程
Phenylpropanoid biosynthetic process		 6.06E-07 1.47E-04
GO:0010023 原花青素的生物合成过程
Proanthocyanidin biosynthetic process		 1.11E-04 7.92E-03
GO:0009809 木质素的生物合成过程
Lignin biosynthetic process		 1.23E-04 8.13E-03
GO:0009698 苯丙烷代谢过程
Phenylpropanoid metabolic process		 2.90E-04 1.36E-02
GO:0009808 木质素代谢过程
Lignin metabolic process		 3.68E-04 1.65E-02
GO:0009812 类黄酮代谢过程
Flavonoid metabolic process		 5.93E-04 2.18E-02
GO:0009813 类黄酮生物合成过程
Flavonoid biosynthetic process		 6.35E-04 2.27E-02
Yellow 142 GO:0050619 还原酶活性
Phytochromobilin: ferredoxin oxidoreductase activity		 5.33E-03 2.78E-01

图3

turquoise模块的KEGG富集分析"

图4

turquoise模块内的基因共表达网络"

图5

枢纽基因相关的局部调控网络 红圈强调的基因参与类黄酮-原花青素途径。A: turquoise模块; B: blue模块。"

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