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作物学报

作物学报 ›› 2023, Vol. 49 ›› Issue (3): 672-686.doi: 10.3724/SP.J.1006.2023.23017

所属专题： 玉米：遗传育种·种质资源·分子遗传学

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

利用WGCNA鉴定玉米非生物胁迫相关基因共表达网络

邓照(), 蒋环琪, 程丽沙, 刘睿, 黄敏, 李曼菲(), 杜何为()   

  1. 长江大学生命科学学院, 湖北荆州 434025
  • 收稿日期:2022-02-22 接受日期:2022-06-07 出版日期:2023-03-12 网络出版日期:2022-07-08
  • 通讯作者: 李曼菲,杜何为
  • 作者简介:邓照, E-mail: 282175698@qq.com第一联系人：**同等贡献
  • 基金资助:
    国家自然科学基金项目(31771801);国家自然科学基金项目(32072069);湖北省高等学校优秀中青年创新团队项目(2017T04);湖北省大学生创新创业项目(Yz2021220)

Identification of abiotic stress-related gene co-expression networks in maize by WGCNA

DENG Zhao(), JIANG Huan-Qi, CHENG Li-Sha, LIU Rui, HUANG Min, LI Man-Fei(), DU He-Wei()   

  1. College of Life Sciences, Yangtze University, Jingzhou 434025, Hubei, China
  • Received:2022-02-22 Accepted:2022-06-07 Published:2023-03-12 Published online:2022-07-08
  • Contact: LI Man-Fei,DU He-Wei
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    National Natural Science Foundation of China(31771801);National Natural Science Foundation of China(32072069);Outstanding Young and Middle-aged Innovation Team Project of Hubei Province(2017T04);College Students’ Innovation and Entrepreneurship Training Program of Hubei Province(Yz2021220)

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摘要：

加权基因共表达网络分析(weighted gene co-expression network analysis, WGCNA)是一种经典的系统生物学分析方法, 可用来鉴定协同表达的基因模块, 探索模块与目标性状的生物学相关性, 并挖掘模块网络中的核心基因。本文收集了低温胁迫、高温胁迫、干旱胁迫和盐胁迫处理下玉米(Zea mays L.)根、茎、叶等组织的58份转录组数据, 利用WGCNA方法鉴定玉米非生物胁迫的基因共表达网络模块。过滤转录组数据中12,552个低表达基因后, 利用余下27,204个高表达基因构建共表达网络, 分析得到25个模块。根据玉米中已报道非生物胁迫相关基因与差异表达基因在模块中的分布, 筛选出与低温胁迫、高温胁迫、干旱胁迫和盐胁迫最相关的mediumpurple4、ivory、coral2、darkseagreen4模块和响应多种胁迫的green模块。随后对这5个模块的基因进行GO富集分析, 发现在这些模块内与非生物胁迫相关基因的在非生物胁迫调控相关功能显著富集, 如胁迫响应、过氧化物酶活性等。对这5个模块作相关性分析, 预测出Zm00001eb072870、Zm00001eb320970、Zm00001eb037640、Zm00001eb423300和Zm00001eb265310等10个非生物胁迫相关的核心基因。本研究为玉米非生物胁迫相关基因的挖掘和非生物胁迫调控网络研究等提供了新思路。

关键词: 玉米, 非生物胁迫, WGCNA, 核心基因

Abstract:

Weighted Gene Co-expression Network Analysis (WGCNA) is a classic systems biology analysis method, which can be used to identify coexpressed gene modules and explore the biological correlation between modules and target traits, and mine core genes in module networks. In this study, 58 transcriptome data of roots, stems, leaves, and other tissues under low temperature stress, high temperature stress, drought stress, and salt stress in maize (Zea mays L.) were collected, and the gene co-expression network of maize abiotic stress was identified by WGCNA method. After filtering the 12,552 low-expression genes from transcriptome data, the co-expression network was constructed using the remaining 27,204 high-expression genes, and 25 modules were obtained. According to the distribution of abiotic stress-related genes and different expression genes in the modules reported in maize, the mediumpurple4, ivory, coral2, darkseagreen4 modules most related to low temperature stress, high temperature stress, drought and salt stresses, and green modules responding to various stresses were screened out. Subsequently, GO enrichment of the genes in these five modules revealed that genes with functions related to abiotic stress were significantly enriched in these modules, such as stress response, peroxidase activity. Correlation analysis showed that 10 abiotic stress-related core genes were predicted, including Zm00001eb072870, Zm00001eb320970, Zm00001eb037640, Zm00001eb423300, and Zm00001eb265310. This study provides new ideas for the mining of abiotic stress-related genes and the research of abiotic stress regulatory networks in maize.

Key words: maize, abiotic stress, WGCNA, core gene

图1

软阈值的选择"

图2

基因聚类树和模块分割 A: 样品的参差聚类树; B: dynamic tree cut表示根据各个基因的表达量计算划分的模块; C: merged dynamic是根据dynamic tree cut合并相似模块的结果。"

图3

报道基因分布情况 图中英文表示模块颜色, 百分数表示各模块已报道非生物胁迫基因数与已报道基因总数的比值。"

图4

各模块中胁迫相关差异表达基因的数目 横坐标为模块颜色, 纵坐标为基因个数, 粉色部分表示差异表达基因个数, 灰色部分表示模块中非差异表达基因的个数。A: 低温胁迫差异表达基因占比最多的5个模块; B: 高温胁迫差异表达基因占比最多的5个模块; C: 干旱胁迫差异表达基因占比最多的5个模块; D: 盐胁迫差异表达基因占比最多的5个模块。"

表1

模块GO富集情况(部分)"

胁迫
Stress		 模块
Module		 基因数目
Number of genes		 GO 显著富集的项目
Significantly enriched term		 P值
P-value
寒冷 Mediumpurple4 6 GO:0007623 昼夜节律 0.0000043
Cold Circadian rhythm
7 GO:0009738 脱落酸激活的信号通路 0.0002
Abscisic acid-activated signaling pathway
7 GO:0009266 对温度刺激的响应 0.0088
Response to temperature stimulus
7 GO:0071215 脱落酸刺激的细胞响应 0.00024
Cellular response to abscisic acid stimulus
高温 Ivory 50 GO:0009408 对热的响应 9.90E-58
Heat Response to heat
21 GO:0034605 细胞对热的响应 9.50E-24
Cellular response to heat
69 GO:0006950 对压力的响应 7.90E-22
Response to stress
76 GO:0050896 对刺激的响应 5.00E-12
Response to stimulus
47 GO:0051082 未折叠蛋白质结合 1.80E-45
Unfolded protein binding
干旱 Coral2 236 GO:0055114 氧化还原过程 0.00000077
Drought Oxidation-reduction process
193 GO:0009056 分解代谢过程 0.00031
Catabolic process
43 GO:0006979 氧化应激响应 0.0014
Response to oxidative stress
26 GO:0042744 过氧化氢分解代谢过程 0.00051
Hydrogen peroxide catabolic process
盐 Darkseagreen4 103 GO:0016054 有机酸分解代谢过程 6.90E-09
Salt Organic acid catabolic process
139 GO:0055114 氧化还原过程 5.50E-13
Oxidation-reduction process
25 GO:0009605 对外源刺激的响应 0.00038
Response to external stimulus
13 GO:0015849 有机酸转运 0.00031
Organic acid transport

图5

非生物胁迫相关的共表达网络 标红色的基因代表该共表达网络的核心基因。"

表2

模块核心基因功能注释"

模块分类
Module name		 基因名称
Gene name		 玉米中基因注释
Annotation in maize		 水稻同源基因名称
Homologous gene in rice		 水稻中基因注释
Annotation in rice
Mediumpurple4 Zm00001eb072870 MYB转录因子20
MYB-related-transcription factor 20		 LOC_Os04g49450 MYB 家族转录因子
MYB family transcription factor
Zm00001eb320970 单加氧酶/氧化还原酶
Monooxygenase/
oxidoreductase		 LOC_Os09g37620 含黄素的单加氧酶家族蛋白
Flavin-containing monooxygenase family protein
Ivory Zm00001eb037640 90 kD热休克蛋白 ATPase 的激活剂
Activator of 90 kD heat shock protein ATPase		 LOC_Os08g36150 90 kD热休克蛋白ATPase同源物的激活剂
Activator of 90 kD heat shock protein ATPase homolog
Zm00001eb423300 IV类热休克蛋白
Class IV heat shock protein		 LOC_Os04g36750 Hsp20/alpha晶状体蛋白家族蛋白
Hsp20/alpha crystallin family protein
Coral2 Zm00001eb265310 类WAK家族受体蛋白激酶
WAK family receptor-like protein kinase		 LOC_Os10g07556 类细胞壁相关受体激酶样22前体
Wall-associated receptor kinase-like 22 precursor
Zm00001eb058250 过氧化物酶16
Peroxidase 16		 LOC_Os03g55410 过氧化物酶前体
Peroxidase precursor
Darkseagreen4 Zm00001eb401330 富含CHP的锌指蛋白样
CHP-rich zinc finger protein-like		 LOC_Os07g42070 含有DC1结构域的蛋白质
DC1 domain-containing protein
Zm00001eb147030 含NAC结构域的蛋白质90
NAC domain-containing protein 90		 LOC_Os01g64310 没有顶端分生组织蛋白
No apical meristem protein
Green Zm00001eb375120 2-酮戊二酸(2OG)和Fe (II)依赖性加氧酶超家族蛋白
2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase superfamily protein		 LOC_Os06g08023 黄酮醇合成酶/黄烷酮3-羟化酶
Flavonol synthase/flavanone 3-hydroxylase
Zm00001eb323090 异柠檬酸裂解酶1
Isocitrate lyase1		 LOC_Os07g34520 异柠檬酸裂解酶
Isocitrate lyase

图6

非生物胁迫的差异表达基因 图中英文表示胁迫类型, 数字表示差异表达基因个数。"

图7

共表达基因在模块中的分布 图中数字代表共表达基因个数, 5个部分分别代表基因个数较多的4个模块和剩下的基因所占的比例。"

表3

Green模块GO富集情况(部分)"

分类
Class		 GO分类
GO term		 显著富集的项目
Significantly enriched term		 P值
P-value
细胞组分 GO:0005886 质膜 0.0000046
Cellular component Plasma membrane
GO:0071944 细胞外围 0.0000072
Cell periphery
GO:0005634 核 0.023
Nucleus
分子功能 GO:0004674 蛋白质丝氨酸/苏氨酸激酶活性 0.00000063
Molecular function Protein serine/threonine kinase activity
GO:0004672 蛋白激酶活性 0.00000082
Protein kinase activity
GO:0005516 钙调蛋白结合 0.0002
Calmodulin binding
GO:0030246 碳水化合物结合 0.000057
Carbohydrate binding
GO:0016301 激酶活性 0.0001
Kinase activity
GO:0042887 酰胺跨膜转运蛋白活性 0.0024
Amide transmembrane transporter activity
GO:0005342 有机酸跨膜转运蛋白活性 0.038
Organic acid transmembrane transporter activity
GO:0046943 羧酸跨膜转运蛋白活性 0.038
Carboxylic acid transmembrane transporter activity
生物学过程 GO:0006355 转录调控, DNA模板化 0.0000023
Biological process Regulation of transcription, DNA-templated
GO:2001141 调节RNA生物合成过程 0.0000031
Regulation of RNA biosynthetic process
GO:1903506 调节核酸模板化转录 0.0000031
Regulation of nucleic acid-templated transcription
分类
Class		 GO分类
GO term		 显著富集的项目
Significantly enriched term		 P值
P-value
GO:2000022 调节茉莉酸介导的信号通路 0.00087
Regulation of jasmonic acid mediated signaling pathway
GO:0015849 有机酸运输 0.045
Organic acid transport
GO:0009755 激素介导的信号通路 0.049
Hormone-mediated signaling pathway
GO:0006796 含磷酸盐化合物代谢过程 0.0022
Phosphate-containing compound metabolic process
GO:0009753 对茉莉花酸的响应 0.0027
Response to jasmonic acid
GO:0009867 茉莉酸介导的信号通路 0.0047
Jasmonic acid mediated signaling pathway
GO:0071395 细胞对茉莉酸刺激的响应 0.0056
Cellular response to jasmonic acid stimulus
GO:0080134 调节对压力的响应 0.019
Regulation of response to stress
GO:0071229 细胞对酸性化学物质的响应 0.025
Cellular response to acid chemical
GO:0043207 对外部生物刺激的响应 0.03
Response to external biotic stimulus
GO:0051707 对其他微生物的响应 0.03
Response to other organism
GO:0003333 氨基酸跨膜转运 0.03
Amino acid transmembrane transport
GO:1903825 有机酸跨膜转运 0.031
Organic acid transmembrane transport
GO:1905039 羧酸跨膜转运 0.031
Carboxylic acid transmembrane transport
GO:0009733 对生长素的响应 0.043
Response to auxin

图8

非生物胁迫处理后核心基因的相对表达量 黑色柱子表示基因的相对表达量, X轴下方单词表示表示对应的处理。图A和图B表示低温胁迫后mediumpurple4模块中的Zm00001eb072870和Zm00001eb320970的相对表达量; 图C和图D表示高温胁迫后ivory模块中的Zm00001eb037640和Zm00001eb423300的相对表达量; 图E和图F表示干旱胁迫后coral2模块中的Zm00001eb265310和Zm00001eb058250的相对表达量; 图G和图H表示盐胁迫后darkseagreen4模块中的Zm00001eb375120和Zm00001eb323090的相对表达量。**: P < 0.05。"

图9

同时响应多种非生物胁迫的核心基因相对表达量 图中黑色柱子表示正常处理下该基因的相对表达量, 灰色柱子表示非生物胁迫处理后该基因的相对表达量, X轴下方单词代表不同胁迫处理。图A和图B分别表示green模块中的Zm00001eb401330和Zm00001eb147030在低温胁迫、高温胁迫、干旱胁迫和盐胁迫下的相对表达量。**: P < 0.05。"

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