利用WGCNA鉴定玉米非生物胁迫相关基因共表达网络

doi:10.3724/SP.J.1006.2023.23017

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

• 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()

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()

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)

摘要/Abstract

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

邓照, 蒋环琪, 程丽沙, 刘睿, 黄敏, 李曼菲, 杜何为. 利用WGCNA鉴定玉米非生物胁迫相关基因共表达网络[J]. 作物学报, 2023, 49(3): 672-686.

DENG Zhao, JIANG Huan-Qi, CHENG Li-Sha, LIU Rui, HUANG Min, LI Man-Fei, DU He-Wei. Identification of abiotic stress-related gene co-expression networks in maize by WGCNA[J]. Acta Agronomica Sinica, 2023, 49(3): 672-686.

图/表 12

图1

图2

图3

图4

表1

图5

表2

图6

图7

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

表3

图8

图9

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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

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

利用WGCNA鉴定玉米非生物胁迫相关基因共表达网络

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

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