利用WGCNA鉴定非生物胁迫相关基因共表达网络

doi:10.3724/SP.J.1006.2019.82061

Abstract

Abstract:

Weighted Gene Co-expression Network Analysis (WGCNA) is a systematic biological method describing gene association patterns among different samples. It can be used to identify synergistically altered gene sets. In this study, 47 transcriptome data of rice tissues specimens were used to explore the regulation relationship between genes under harsh environmental conditions (cold, drought, and salt) try WGCNA method. By filtering the low expressed genes, the co-expression matrix was finally constructed using the screened 30,339 expressed genes. Subsequently, 15 modules were obtained. The reports of cloned key genes under those three stresses existed in each module, so the GO enrichment analysis was performed on the predicted target genes. The differentially expressed genes were analyzed by transcriptome data under harsh conditions, and combined with the reported stress-related genes, two stress-related modules were selected to construct the gene regulatory network. In consideration of a large number of genes related to the mentioned harsh situations in the green module, the GO functional enrichment analysis was carried out for the three kinds of stress genes under the green module, and the gene regulatory network was constructed for the common genes. In summary, 2599 harsh environmental situations-related genes were mined. Meanwhile, 25 key genes related to stress resistance were predicted. Our results on stress resistance and comprehensive stress resistance open a new window for future studies.

Key words: rice, drought stress, cold stress, salt stress, Weighted Gene Co-Expression Network (WGCNA)

LI Xu-Kai,LI Ren-Jian,ZHANG Bao-Jun. Identification of rice stress-related gene co-expression modules by WGCNA[J].Acta Agronomica Sinica, 2019, 45(9): 1349-1364.

Figures/Tables 11

Fig. 1

Fig. 2

Table 1

GO enrichments of network modules (part) "

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
干旱 Drought	Lightgreen	33	GO:0009062		脂肪酸分解过程 Fatty acid catabolic process	0
		330	GO:1901700		对含氧化合物的响应 Response to oxygen-containing compound	0
		65	GO:0000302		活性氧的响应 Response to reactive oxygen species	1.11E-16
		132	GO:0009737		脱落酸响应 Response to abscisic acid	1.38E-10
		160	GO:0006970		渗透胁迫响应 Response to osmotic stress	6.47E-13
		103	GO:0009415		对水的响应 Response to water	5.72E-09
	Green	23	GO:0043069		程序性细胞死亡的负调控 Negative regulation of programmed cell death	8.84E-09
		203	GO:0006979		氧化应激反应 Response to oxidative stress	4.41E-12
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
冷 Cold	Green	25	GO:0010857	钙依赖性蛋白激酶活性 Calcium-dependent protein kinase activity		1.12E-08
		31	GO:0044106	细胞酰胺代谢过程 Cellular amine metabolic process		2.16E-07
		20	GO:0060548	细胞死亡负调控 Negative regulation of cell death		2.21E-07
		14	GO:0003714	转录辅阻遏活性 Transcription corepressor activity		2.64E-07
		16	GO:2000022	茉莉酸介导的信号转导通路的调控 Regulation of jasmonic acid mediated signaling pathway		3.58E-06
	Darkmagenta	70	GO:0008299	异戊二烯生物合成过程 Isoprenoid biosynthetic process		0
		167	GO:0009266	温度刺激响应 Response to temperature stimulus		0
		167	GO:0006091	前体代谢物和能量的产生 Generation of precursor metabolites and energy		0
		32	GO:0016116	类胡萝卜素代谢过程 Carotenoid metabolic process		2.22E-16
盐 Salt	Green	261	GO:0009651	盐胁迫响应 Response to salt stress		3.81E-11
		586	GO:0009719	内源性刺激响应 Response to endogenous stimulus		1.94E-08
		547	GO:0009725	激素应答 Response to hormone		2.68E-07
	Lightgreen	244	GO:1901575	有机物分解代谢过程 Organic substance catabolic process		0
		10	GO:0046487	乙醛酸代谢过程 Glyoxylate metabolic process		1.04E-08

Table 1

Fig. 3

Table 2

Functional annotation of modular hub genes"

模块分类 Module name			基因名称 Gene name			水稻中基因注释 Annotation in rice				拟南芥同源基因注释 Homologous gene in A. thaliana		功能注释 Gene function
Darkmagnenta			LOC_Os03g08570			胺氧化酶 Amine oxidase				AT4G14210		一种在类胡萝卜素生物合成过程中催化八氢番茄红素致zeta-胡萝卜素去饱和的酶 An enzyme that catalyzes the desaturation of phytoene to zeta-carotene during carotenoid biosynthesis
			LOC_Os01g01420			表达蛋白 Expressed protein				AT3G54360		编码一个过氧化氢酶活性相关的过氧化氢酶伴侣, 可响应多重胁迫 Encodes a catalase chaperon that is essential for catalase activity. Required for multiple stress responses.
			LOC_Os04g39970			含有结构域的液泡分选蛋白9 Vacuolar sorting protein 9 domain-containing protein
模块分类 Module name		基因名称 Gene name			水稻中基因注释 Annotation in rice				拟南芥同源基因注释 Homologous gene in A. thaliana		功能注释 Gene function
		LOC_Os05g34040			单加氧酶 Monooxygenase				AT4G30720		编编码在叶绿体基质中检测到的推定的氧化还原酶/电子载体 Encodes a putative oxidoreductase/electron carrier detected in the chloroplast stroma
		LOC_Os02g40860			酪蛋白激酶1 CK1_CaseinKinase_1
		LOC_Os09g21250			表达蛋白 Expressed protein				AT5G23040		编码一种蛋白质, 使原卟啉抗体能够与pPORA的转运序列结合, 调节pPORA向质体基质的易位, 并阻止易位多肽链运回细胞质 Encodes a protein that enables protochlorophillide's binding to pPORA’s transit sequence, regulating Ppora’s translocation into the plastid stroma, and blocking movement of the translocating polypeptide chain back into the cytosol.
		LOC_Os09g02270			环化酶家族蛋白 Cyclase family protein				AT4G35220		环化酶家族蛋白 Cyclase family protein
		LOC_Os01g54540			核糖体蛋白L13 Ribosomal protein L13				AT1G78630		核糖体蛋白L13家族蛋白 Ribosomal protein L13 family protein
Lightgreen		LOC_Os10g28600			PPR重复结构域含有蛋白质 PPR repeat domain containing protein				AT4G31850		编码含有27个五肽-重复序列(PPR)基序的蛋白质。 Encodes a protein containing 27 pentatrico-peptide repeat (PPR) motifs.
		LOC_Os01g07120			含有AP2结构域的蛋白质 AP2 domain containing protein				AT2G40340		编码ERF/AP2转录因子家族的DREB亚家族A-2的成员。DREB2A和DREB2B参与对干旱的反应。 Encodes a member of the DREB subfamily A-2 of ERF/AP2 transcription factor family. DREB2A and DREB2B that are involved in response to drought.
		LOC_Os08g43210			含有AP2结构域的蛋白质 AP2 domain containing protein
		LOC_Os08g43334			含有HSF型DNA结合域的蛋白质 HSF-type DNA-binding domain containing protein				AT4G11660		热应激转录因子(HSF)家族成员 Member of Heat Stress Transcription Factor (Hsf) family
		LOC_Os03g41390			ZOS3-15-C2H2锌指蛋白 ZOS3-15-C2H2 zinc finger protein				AT1G27730		与高等植物中的Cys2/HIS2型锌指蛋白有关。结果表明, ZAT10产生的耐盐性部分依赖于EnA1/PMR2。 Related to Cys2/His2-type zinc-finger proteins found in higher plants. responses. Salt tolerance produced by ZAT10 appeared to be partially dependent on ENA1/PMR2
	LOC_Os12g39400			ZOS2-02-C2H2锌指蛋白 ZOS12-09-C2H2 zinc finger protein
	LOC_Os05g34830			无顶端分生组织蛋白 No apical meristem protein
模块分类 Module name	基因名称 Gene name			水稻中基因注释 Annotation in rice			拟南芥同源基因注释 Homologous gene in A. thaliana	功能注释 Gene function
	LOC_Os01g42860			抑制剂I家族蛋白 Inhibitor I family protein
	LOC_Os02g09830			BZIP转录因子结构域蛋白 bZIP transcription factor domain containing protein
	LOC_Os08g38880			WD40重复家族蛋白 WD-40 repeat family protein
	LOC_Os07g47100			质子逆向转运蛋白-2家族 Proton antiporter-2 family			AT3G05030	编码液泡K⁺/H⁺交换器, 该交换器对液泡膜上活跃的K⁺摄取必不可少, 并参与调节气孔关闭。 Encodes a vacuolar K⁺/H⁺ exchanger essential for active K⁺ uptake at the tonoplast and involved in regulating stomatal closure.

Table 2

Fig. 4

Fig. 5

Table 3

Annotation of functions of various stress regulating genes"

候选基因 Candidate gene	转录因子 Transcription factor				冷胁迫 Cold			干旱 Drought	盐 Salt
LOC_Os11g05160					AT-hook蛋白 AT-hook content nuclear localized protein			AT-hook蛋白 AT-hook content nuclear localized protein	AT-hook蛋白 AT-hook content nuclear localized protein
LOC_Os03g17700					丝裂原活化蛋白激酶 Mitogen-activated protein kinase			丝裂原活化蛋白激酶 Mitogen-activated protein kinase	丝裂原活化蛋白激酶 Mitogen-activated protein kinase
LOC_Os01g66120	NAC				NAC转录因子 NAC domain transcription factor			NAC转录因子 NAC domain transcription factor	NAC转录因子 NAC domain transcription factor
LOC_Os03g12820					SRO蛋白基因 Similar to RCD1 gene			SRO蛋白基因 Similar to RCD1 gene
候选基因 Candidate gene	转录因子 Transcription factor			冷胁迫 Cold			干旱 Drought		盐 Salt
LOC_Os03g60560	C2H2			TFIIIA型锌指蛋白基因 TFIIIA-type zinc finger protein gene			TFIIIA型锌指蛋白基因 TFIIIA-type zinc finger protein gene
LOC_Os02g33820				ABA-胁迫-成熟诱导基因 ABA, stress, ripening gene			ABA-胁迫-成熟诱导基因 ABA, stress, ripening gene
LOC_Os07g39870				TFIIIA型锌指蛋白基因 TFIIIA-type zinc finger protein gene			TFIIIA型锌指蛋白基因 TFIIIA-type zinc finger protein gene
LOC_Os06g36670				ABA受体 Pyrabactin resistance-like abscisic acid receptor			ABA受体 Pyrabactin resistance-like abscisic acid receptor
LOC_Os06g43660				液泡膜质子转运无机焦磷酸酶 H⁺-pyrophosphatase in tonoplasts			液泡膜质子转运无机焦磷酸酶 H⁺-pyrophosphatase in tonoplasts
LOC_Os07g03710							病程相关蛋白 Pathogenesis-related protein 1a		病程相关蛋白 Pathogenesis-related protein 1a
LOC_Os02g03410							钙依赖性蛋白激酶 Calcium-dependent protein Kinase		钙依赖性蛋白激酶 Calcium-dependent protein kinase
LOC_Os03g53200							钙调素 Calmodulin		钙调素 Calmodulin
LOC_Os08g39450							A20/AN1型锌指蛋白 A20/AN1 zinc-finger protein		A20/AN1型锌指蛋白 A20/AN1 zinc-finger protein
LOC_Os01g74410	MYB						MYB转录因子 MYB family transcription factor		MYB转录因子 MYB family transcription factor
LOC_Os02g52780	bZIP						bZIP转录因子 bZIP transcription factor		bZIP转录因子 bZIP transcription factor
LOC_Os03g60080	NAC						胁迫响应的NAC转录因子基因 Stress-responsive NAC 1		胁迫响应的NAC转录因子基因 Stress-responsive NAC 1
LOC_Os02g52780	bZIP						bZIP转录因子 bZIP transcription factor		bZIP转录因子 bZIP transcription factor
LOC_Os11g08210	NAC						NAC转录因子 NAC domain transcription factor		NAC转录因子 NAC domain transcription factor
LOC_Os04g50060	GRAS						GRAS转录因子 GRAS transcription factor gene		GRAS转录因子 GRAS transcription factor gene
LOC_Os01g74410	MYB						MYB转录因子 MYB family transcription factor		MYB转录因子 MYB family transcription factor
LOC_Os03g53200							钙调蛋白 Calmodulin		钙调蛋白 Calmodulin
LOC_Os02g50970							丝裂原活化蛋白激酶 Mitogen-activated protein kinase		丝裂原活化蛋白激酶Mitogen-activated protein kinase
候选基因 Candidate gene	转录因子 Transcription factor		冷胁迫 Cold			干旱 Drought			盐 Salt
LOC_Os07g03710						病程相关蛋白 Pathogenesis-related protein 1a			病程相关蛋白 Pathogenesis-related protein 1a
LOC_Os01g32660			丝裂原活化蛋白激酶 Mitogen activated protein kinase						丝裂原活化蛋白激酶 Mitogen activated protein kinase
LOC_Os01g73770		ERF	AP2/EREBP转录因子基因 AP2/EREBP transcription factor gene						AP2/EREBP转录因子基因 AP2/EREBP transcription factor gene

Table 3

Table 4

Fig. 6

Table 5

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分类 Class	GO分类 GO term	显著富集的term Significantly enriched term	P值 P-value
分子功能 Molecular function	GO:0005198	结构分子活性 Structural molecule activity	0
	GO:0003735	核糖体的结构组成 Structural constituent of ribosome	0
	GO:0016491	氧化还原酶活性 Oxidoreductase activity	5.69E-13
	GO:0004601	过氧化物酶活性 Peroxidase activity	1.07E-11
	GO:0016684	氧化还原酶活性对过氧化物作为受体的作用 Oxidoreductase activity, acting on peroxide as acceptor	3.13E-11
	GO:0016209	抗氧化活性 Antioxidant activity	4.28E-11
	GO:0020037	血红素结合 Heme binding	4.68E-09
细胞组分 Cellular component	GO:0022625	胞浆大核糖体亚基 Cytosolic large ribosomal subunit	0
	GO:0071944	细胞外周 Cell periphery	0
	GO:0044391	核糖体亚基 Ribosomal subunit	0
	GO:0044445	胞质部分 Cytosolic part	0
	GO:0015934	大核糖体亚基 Large ribosomal subunit	0
	GO:0005840	核糖体 Ribosome	0
生物学过程 Biological process	GO:0043604	酰胺生物合成过程 Amide biosynthetic process	0
	GO:0043603	细胞酰胺代谢过程 Cellular amide metabolic process	2.22E-16
	GO:0042744	过氧化氢分解代谢过程 Hydrogen peroxide catabolic process	2.34E-10
	GO:0055114	氧化还原过程 Oxidation-reduction process	3.03E-09
	GO:0072593	过氧化氢代谢过程 Reactive oxygen species metabolic process	1.05E-06
	GO:0009698	苯丙烷代谢过程 Phenylpropanoid metabolic process	4.01E-05
	GO:0009808	木质素代谢过程 Lignin metabolic process	6.62E-05
	GO:0006970	对渗透压的反应 Response to osmotic stress	4.15E-04
	GO:0009404	毒素代谢过程 Toxin metabolic process	4.23E-04
	GO:0043069	细胞程序性死亡负调节Negative regulation of programmed cell death	5.87E-04
	GO:0044248	细胞分解代谢过程 Cellular catabolic process	0.00136054

候选基因 Candidate gene	候选基因在水稻中注释 Annotation of candidate genes in rice	候选基因在玉米同源基因 Homology gene in maize	基因功能 Gene function
LOC_Os02g30900	激酶结构域蛋白 Protein kinase domain containing protein	GRMZM2G137468	蛋白激酶APK1A Protein kinase APK1A
LOC_Os11g28990	TBC结构域蛋白质 TBC domain containing protein	GRMZM2G122935	含有RabGAP/TBC结构域的蛋白质 RabGAP/TBC domain-containing protein
LOC_Os09g32040	无顶端分生组织蛋白 No apical meristem protein	GRMZM2G004531	N-乙酰-L-蛋氨酸/N-乙酰-L-甲硫氨酸 Nam 7
LOC_Os07g35750	DUF26激酶 DUF26 kinases	GRMZM2G075438	受体激酶RK20-1 Receptor kinase RK20-1
LOC_Os05g45210	呼吸爆发氧化酶 Respiratory burst oxidase	GRMZM2G043435	呼吸爆发氧化酶C Respiratory burst oxidase C
候选基因 Candidate gene	候选基因在水稻中注释 Annotation of candidate genes in rice	候选基因在玉米同源基因 Homology gene in maize	基因功能 Gene function
LOC_Os01g58150	表达蛋白质 Expressed protein	GRMZM2G139460	功能未知的保守基因 Conserved gene of unknown function
LOC_Os03g13300	谷氨酸脱羧酶 Glutamate decarboxylase	GRMZM2G098875	谷氨酸脱羧酶 Glutamate decarboxylase

Identification of rice stress-related gene co-expression modules by WGCNA

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