摘要：

权重基因共表达网络分析(weighted gene co-expression network analysis, WGCNA)是系统生物学的一种研究方法, 在挖掘生物学数据与特定性状之间的生物学关系方面具有十分重要的作用。本研究利用玉米( Zea mays L.)自交系B73的14份不同发育阶段的转录组数据, 筛选掉低表达丰度的基因, 最终得到了22,426个高表达的基因用于创建基因表达矩阵; 利用不同组织作为性状, 创建表型矩阵。然后利用R软件中的WGCNA包建立了共表达网络, 共得到20个模块。本研究将与组织相关性高于0.65的模块定义为组织特异性模块, 最终鉴定到14个组织特异性模块。利用在线网站Agrigo对组织特异性模块中的基因进行GO (gene ontology)富集分析, 发现14个模块中均可以得到富集种类。开花作为玉米生育周期中的一个重要生理过程, 不仅代表着植物从营养生长到生殖生长的转变, 也关系到产量、株高和抗逆性等农艺性状。本研究发现8个组织特异性模块中的基因可以富集到与开花调控的代谢通 。此外, 有17个已经报道过的开花时间调控基因存在于共表达模块中, 并且主要分布在Blue模块和Darkmagenta模块, 因此本研究重点关注了这2个模块内部的基因调控网络。本研究通过计算不同组织中的基因表达丰度, 并联合权重基因共表达网络分析的方法, 鉴定到了具有生物学意义的共表达基因模块, 挖掘到了数个开花相关的模块, 有助于揭示玉米开花调控的遗传机制。

Abstract:

Weighted gene co-expression network analysis (WGCNA) is one of the research methods in systematic biology. It can effectively analyze the complex samples, and has been extensively used in the analysis of complicated traits for many samples. Weighted gene co-expression network has the characteristics of scale-free distribution and could construct the scale free network. The genes with similar expression level can be clustered and assigned to a module, then the relationships between co-expression modules and specific tissues can be furtherly analyzed. Our research utilized the transcriptome data of 14 different tissues of maize ( Zea mays L.) inbred line B73, and calculated the gene expression level of the whole genome. Through filtering out the genes with low expression level we finally got 22,426 genes with high expression level to construct the gene expression matrix. We utilized the different tissues as the trait to construct the trait matrix. The weighted gene co-expression network analysis packages of R software was used to perform the co-expression network analysis, and 20 co-expression modules were identified. We finally obtained 14 tissue specific modules which were highly correlated with traits ( r > 0.65). The enrichment analysis tool Agrigo was taken to perform the GO enrichment of the tissue specific module genes, all the 14 tissues could be enriched in GO terms. Flowering is one of the important agronomic traits in the life cycle of maize controlled by external environment signals and genetic factors. Maize flowering not only represents the transition from the vegetative growth to reproductive growth, also relates to grain yield, plant height and resistance. In our research, we detected eight tissue specific modules, which could be obtained within flowering time related pathways. In addition, 17 flowering genes which have been reported in the literatures were assigned to the co-expression modules, and mainly assigned to the Blue and Darkmagenta modules. Therefore, we focused on the network of Blue and Darkmagenta modules. Our research calculated the gene expression abundances, and detected several flowering time related modules, which will contribute to revealing the genetic mechanism of maize flowering time regulation.

Key words: maize, weighted gene co-expression network, development regulation, flowering, transcriptome

Darkmagenta模块和Blue模块中候选开花基因的功能注释。"

模块 Module	开花基因 Flowering gene	候选开花基因 Candidate flowering gene	候选基因在拟南 芥同源基因 Homologous gene in A. thaliana	基因功能 Gene function
Blue	ZCN8	GRMZM2G450273	FPF1	编码调节开花的小蛋白质并参与赤霉素信号传导途径, 在开花的光周期诱导后, 在顶端分生组织中表达 Encodes a small protein that regulates flowering and is involved in gibberellin signalling pathway. It is expressed in apical meristems immediately after the photoperiodic induction of flowering
	ZCN7	GRMZM2G455413	PSBA	编码叶绿素结合蛋白D1, 属于光系统II反应中心 Encodes chlorophyll binding protein D1, belonging to photosystem II reaction center core
	COL1	GRMZM2G128212	ZFP8	编码锌指蛋白 Encodes a zinc finger protein
	PhyB1	GRMZM5G800407	PMAT2	编码消除酚类毒素的丙二酰转移酶 Encodes a malonyltransferase that may play a role in phenolic xenobiotic detoxification
	D8	GRMZM2G338809	AMT2	编码高亲和性的铵转运蛋白 Encodes a high-affinity ammonium transporter
	D9	GRMZM2G429322	LHT1	编码一个在细胞间转运氨基酸的高亲和力蛋白 Encoding a high affinity protein that translocation amino acids between cells
	ZmCCA1	GRMZM6G435553	PMI1	响应蓝光和渗透压胁迫 Response to blue light and osmotic stress
Darkmagenta	GIGZ1B	GRMZM2G333183	ABCB1	ATP结合蛋白, 调节生长素转运 ATP-binding protein, regulates the transport of auxin
	PhyC2	GRMZM2G038846	AT1G19320	与发病机制相关的超家族蛋白 Pathogenesis-related thaumatin superfamily protein
	GIGZ1A	GRMZM2G104269	OASC	参与花粉管生长和受精 Involved in pollen tube growth and fertilization
	ZmFKF1b	GRMZM2G041065	ATAVP3	无机H焦磷酸酶家族蛋白, 在分生组织和花器官原基表达 Inorganic H pyrophosphatase family protein. Expressed in meristems and floral organ primordium
	ZmFKF1a	GRMZM2G027673	FAB2	植物硬脂酰酰基载体蛋白去饱和酶家族蛋白 Plant stearoyl-acyl-carrier-protein desaturase family protein
	ZmPRR59	GRMZM2G107945	FKF1	编码黄素结合的F-box蛋白, 调节花期转变 Encodes flavin-binding F-box protein, regulates transition to flowering
	ZmPRR59	GRMZM2G106363	LKP2	编码F-box蛋白, 响应红光和蓝光, 参与光周期途径 Encodes a member of F-box proteins, response to red and blue light, involved in photoperiod pathway

组织特异性模块的GO富集分析结果(部分)"

模块 Module	GO条目 GO term	本体 Ontology	描述 Description	P 值 P -value
Darkorange2	GO: 0009889	BP	生物合成过程调节Regulation of biosynthetic process		6.90E-07
Darkorange2	GO: 0006355	BP	DNA依赖的转录调节Regulation of transcription, DNA-dependent		4.40E-07
Darkorange2	GO: 0015267	MF	通道活性Channel activity		0.00068
Darkorange2	GO: 0022838	MF	底物特异性通道活性Substrate-specific channel activity		0.00068
Blue	GO: 0009628	BP	非生物刺激的反应Response to abiotic stimulus		3.60E-10
Blue	GO: 0009416	BP	光刺激响应Response to light stimulus		1.60E-08
Blue	GO: 0003700	MF	转录因子活性Transcription factor activity		0.00017
Blue	GO: 0009535	CC	叶绿体类囊体膜Chloroplast thylakoid membrane		0.00022
Darkred	GO: 0051186	BP	辅因子代谢过程Cofactor metabolic process		1.20E-19
Darkred	GO: 0004252	MF	丝氨酸型肽链内切酶活性Serine-type endopeptidase activity		0.00015
Darkred	GO: 0009543	CC	叶绿体类囊体腔 Chloroplast thylakoid lumen		4.40E-13
Darkslateblue	GO: 0016051	BP	碳水化合物生物合成过程Carbohydrate biosynthetic process		5.60E-05
Darkslateblue	GO: 0016830	MF	碳-碳裂解酶活性Carbon-carbon lyase activity		3.40E-06
Darkslateblue	GO: 0042651	CC	类囊体膜Thylakoid membrane		0.00013
Turquoise	GO: 0060560	BP	形态发生发育Developmental growth involved in morphogenesis		1.70E-11
Turquoise	GO: 0015299	MF	溶质: 氢反向转运蛋白活性Solute: hydrogen antiporter activity		4.60E-05
Turquoise	GO: 0031224	CC	内膜Intrinsic to membrane		8.50E-06
Darkmagenta	GO: 0010927	BP	涉及形态发生的内膜组装 Cellular component assembly involved in morphogenesis		4.10E-09
Darkmagenta	GO: 0004553	MF	水解酶活性, 水解O-糖基化合物 Hydrolase activity, hydrolyzing O-glycosyl compounds		7.60E-06
Darkmagenta	GO: 0030312	CC	高尔基体Golgi apparatus		0.0004
Bisque4	GO: 0042180	BP	细胞酮代谢过程Cellular ketone metabolic process		3.00E-08
Bisque4	GO: 0044281	BP	小分子代谢过程Small molecule metabolic process		9.90E-06
Bisque4	GO: 0042221	BP	相应化学刺激Response to chemical stimulus		0.00032
Darkgrey	GO: 0010033	BP	对有机物质的反应Response to organic substance		1.60E-07
Darkgrey	GO: 0004553	MF	水解酶活性, 水解O-糖基化合物 Hydrolase activity, hydrolyzing O-glycosyl compounds		4.40E-10
Darkgrey	GO: 0005740	CC	线粒体包膜Mitochondrial envelope		7.40E-05
Floralwhite	GO: 0006412	BP	蛋白质翻译Translation		9.10E-07
Floralwhite	GO: 0005198	MF	结构分子活性Structural molecule activity		5.80E-08
Floralwhite	GO: 0043227	CC	膜有界细胞器Membrane-bounded organelle		0.0085
Darkolivegreen	GO: 0010022	BP	分生组织决定Meristem determinacy		6.10E-07
模块 Module	GO条目 GO term	本体 Ontology	描述 Description	P 值 P -value
Darkolivegreen	GO: 0003700	MF	转录因子活性Transcription factor activity		5.50E-05
Orange	GO: 0042542	BP	过氧化氢反应Response to hydrogen peroxide		2.90E-05
Orange	GO: 0009526	CC	质体Plastid		9.60E-09
Yellow	GO: 0009605	BP	响应外界刺激Response to external stimulus		8.40E-10
Yellow	GO: 0022892	MF	底物特异性转运体活性Substrate-specific transporter activity		0.00013
Plum2	GO: 0048437	BP	花器官发育Floral organ development		9.20E-05
Plum2	GO: 0005576	CC	胞外区Extracellular region		9.70E-05
Greenyellow	GO: 0034220	BP	离子跨膜转运Ion transmembrane transport		5.00E-13
Greenyellow	GO: 0032561	MF	鸟苷酸核糖核酸结合Guanyl ribonucleotide binding		2.40E-10
Greenyellow	GO: 0043231	CC	内细胞器膜Organelle inner membrane		1.20E-17

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