中国农业科技导报 ›› 2022, Vol. 24 ›› Issue (4): 52-62.DOI: 10.13304/j.nykjdb.2020.0783
周雨青1,2(), 杨永飞1,2, 葛常伟2, 沈倩2, 张思平2, 刘绍东2, 马慧娟2, 陈静2, 刘瑞华2, 李士丛2, 赵新华2, 李存东1(
), 庞朝友2(
)
收稿日期:
2020-09-07
接受日期:
2021-03-03
出版日期:
2022-04-15
发布日期:
2022-04-20
通讯作者:
李存东,庞朝友
作者简介:
周雨青 E-mail: zhouyuqing0803@163.com
基金资助:
Yuqing ZHOU1,2(), Yongfei YANG1,2, Changwei GE2, Qian SHEN2, Siping ZHANG2, Shaodong LIU2, Huijuan MA2, Jing CHEN2, Ruihua LIU2, Shicong LI2, Xinhua ZHAO2, Cundong LI1(
), Chaoyou PANG2(
)
Received:
2020-09-07
Accepted:
2021-03-03
Online:
2022-04-15
Published:
2022-04-20
Contact:
Cundong LI,Chaoyou PANG
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,在多样本转录组数据中挖掘与目标性状相关的基因模块应用较广泛。为深入探究棉花应对冷害胁迫的分子机制,以4 ℃低温处理不同时间点的2个棉花品种(新陆中16和新陆中32)幼苗子叶转录组数据为基础,过滤低表达量基因, 最终利用筛选的22 083个表达的基因来构建共表达矩阵, 得到9个共表达模块,其中2个为抗冷相关特异性模块(Blue模块与低温处理0、1和3 h时间点正相关,Brown模块与低温处理9和12 h时间点正相关)。GO和KEGG富集分析表明, 特异性模块可以富集到对刺激反应的调节(GO:0048583)、对胁迫反应的调节(GO:0080134)、对油菜素类固醇的反应(GO:0009741)等抗逆相关通路。通过计算模块内基因的连通性挖掘网络中的核心基因,功能注释表明这些基因可能在棉花抗冷过程中发挥着重要作用。该结果为进一步研究棉花抗冷调控机理提供数据支持。
中图分类号:
周雨青, 杨永飞, 葛常伟, 沈倩, 张思平, 刘绍东, 马慧娟, 陈静, 刘瑞华, 李士丛, 赵新华, 李存东, 庞朝友. 基于WGCNA的棉花子叶抗冷相关共表达模块鉴定[J]. 中国农业科技导报, 2022, 24(4): 52-62.
Yuqing ZHOU, Yongfei YANG, Changwei GE, Qian SHEN, Siping ZHANG, Shaodong LIU, Huijuan MA, Jing CHEN, Ruihua LIU, Shicong LI, Xinhua ZHAO, Cundong LI, Chaoyou PANG. Identification of Cold-related Co-expression Modules in Cotton Cotyledon by WGCNA[J]. Journal of Agricultural Science and Technology, 2022, 24(4): 52-62.
基因 ID Gene ID | 正向引物 Forward primer (5'-3') | 反向引物 Reverse primer(5'-3') |
---|---|---|
Gh_A11G0969 | GAAGGCATTCCACCTGACCAAC | CTTGACCTTCTTCTTCTTGTGCTTG |
Gh_A05G1931 | TGCCCAATGGTGGAAAACCACT | CGGCTCATGCAGAACCCTTCAA |
Gh_D13G0160 | CGAACATGATGCCAACCGATGC | TGCAATCGAGCTTCCGTAGGTG |
Gh_A13G2112 | CCACAAGAGTTTCCCTACGGGC | CGTGGTTTCTTGGTCGGCAATG |
Gh_A05G0483 | GCCGAGTGTGAGGATTATGCCA | TTCTTGACGGGACAACTTGGGG |
Gh_A12G2357 | CGTGGCAGCTATAGCACTGA | TTCTGAAAGTCTCCGCCACC |
Gh_D09G1773 | AATAGGGCTACCGAGGCTGGTT | AGCCCTCCCGTTGTAAAACACC |
Gh_D05G2642 | GCAGCAACCCCAAAATCCCAAC | CCACATCCCCGTATTCAGCACC |
Gh_A05G1554 | GCCTCAAGAGGAGGTGATCG | GCTGCTGCTATCTGATCGGT |
Gh_D05G0600 | AAGGGCTTACGTCCGCACAAAT | GCACTTGAAGTATGCCCTCGGA |
Gh_A13G0138 | AGGGTGCATGTCCTAAGGGTGA | GACCTCGGTGAAGGCATAGCAG |
表1 qRT-PCR 所用基因引物序列
Table 1 Specific primers for the selected genes
基因 ID Gene ID | 正向引物 Forward primer (5'-3') | 反向引物 Reverse primer(5'-3') |
---|---|---|
Gh_A11G0969 | GAAGGCATTCCACCTGACCAAC | CTTGACCTTCTTCTTCTTGTGCTTG |
Gh_A05G1931 | TGCCCAATGGTGGAAAACCACT | CGGCTCATGCAGAACCCTTCAA |
Gh_D13G0160 | CGAACATGATGCCAACCGATGC | TGCAATCGAGCTTCCGTAGGTG |
Gh_A13G2112 | CCACAAGAGTTTCCCTACGGGC | CGTGGTTTCTTGGTCGGCAATG |
Gh_A05G0483 | GCCGAGTGTGAGGATTATGCCA | TTCTTGACGGGACAACTTGGGG |
Gh_A12G2357 | CGTGGCAGCTATAGCACTGA | TTCTGAAAGTCTCCGCCACC |
Gh_D09G1773 | AATAGGGCTACCGAGGCTGGTT | AGCCCTCCCGTTGTAAAACACC |
Gh_D05G2642 | GCAGCAACCCCAAAATCCCAAC | CCACATCCCCGTATTCAGCACC |
Gh_A05G1554 | GCCTCAAGAGGAGGTGATCG | GCTGCTGCTATCTGATCGGT |
Gh_D05G0600 | AAGGGCTTACGTCCGCACAAAT | GCACTTGAAGTATGCCCTCGGA |
Gh_A13G0138 | AGGGTGCATGTCCTAAGGGTGA | GACCTCGGTGAAGGCATAGCAG |
图2 基因聚类树和模块划分A:基于拓扑重叠构建的基因聚类树;B:动态剪切树法得到的基因模块,颜色代表模块;C:表达模式相似模块合并后的共表达模块
Fig.2 Gene cluster dendrograms and module divisionA: Clustering of genes based on the topological overlap; B: Gene modules obtained from the dynamic tree cut, and different colors represent different modules; C: Merged co-expression modules with similar expression pattern
图4 基因共表达网络模块与不同样本的关联热图注:红色和绿色格分别代表性状与模块具有正相关性和负相关性。
Fig.4 Association analysis of gene co-expression network modules with different samplesNote: Red and green lattice represent positive correlation and negative correlation, respectively.
图5 不同模块两两之间 ME 的相关性注:红色和绿色格分别代表性状与模块具有正相关性和负相关性。格中数值代表模块与性状之间的相关系数和相应的P值(括号中)。
Fig.5 ME correlation between different modulesNote : Red and green lattice represent positive correlation and negative correlation, respectively. The numbers in the lattice show correlation coefficient and the corresponding P value (in the bracket).
模块 Module | GO条目 GO term | 基因本体 Ontology | 描述 Description | 基因数目 Genes No. | P值 P value |
---|---|---|---|---|---|
蓝色 Blue | GO:0048583 | P | 对刺激反应的调节Regulation of response to stimulus | 538 | 0.001 08 |
GO:0080134 | P | 对胁迫反应的调节Regulation of response to stress | 282 | 0.000 45 | |
GO:0031347P | P | 对防御反应的调节Regulation of defense response | 216 | 0.000 15 | |
GO:0009738 | P | 脱落酸激活的信号通路 Abscisic acid-activated signaling pathway | 216 | 0.000 32 | |
GO:0010200 | P | 对几丁质的反应Response to chitin | 166 | 0.000 15 | |
GO:0009741 | P | 对油菜素类固醇的反应Response to brassinosteroid | 114 | 0.001 47 | |
GO:0003700 | F | 转录因子活性,特异性DNA序列结合 Transcription factor activity, sequence-specific DNA binding | 1 275 | 0.000 68 | |
GO:0005623 | C | 细胞Cell | 12 853 | 1.05e-06 | |
GO:0043227 | C | 膜结合细胞器Membrane-bounded organelle | 10 326 | 7.51e-06 |
表2 特异性模块的部分GO富集分析结果
Table 2 Partial GO enrichment analysis of target module
模块 Module | GO条目 GO term | 基因本体 Ontology | 描述 Description | 基因数目 Genes No. | P值 P value |
---|---|---|---|---|---|
蓝色 Blue | GO:0048583 | P | 对刺激反应的调节Regulation of response to stimulus | 538 | 0.001 08 |
GO:0080134 | P | 对胁迫反应的调节Regulation of response to stress | 282 | 0.000 45 | |
GO:0031347P | P | 对防御反应的调节Regulation of defense response | 216 | 0.000 15 | |
GO:0009738 | P | 脱落酸激活的信号通路 Abscisic acid-activated signaling pathway | 216 | 0.000 32 | |
GO:0010200 | P | 对几丁质的反应Response to chitin | 166 | 0.000 15 | |
GO:0009741 | P | 对油菜素类固醇的反应Response to brassinosteroid | 114 | 0.001 47 | |
GO:0003700 | F | 转录因子活性,特异性DNA序列结合 Transcription factor activity, sequence-specific DNA binding | 1 275 | 0.000 68 | |
GO:0005623 | C | 细胞Cell | 12 853 | 1.05e-06 | |
GO:0043227 | C | 膜结合细胞器Membrane-bounded organelle | 10 326 | 7.51e-06 |
模块 Module | 核心基因编号 Hub gene ID | 模块内连通性 Connectivity | 拟南芥同源基因编号 Homologous gene ID in A. thaliana | 基因功能 Gene function |
---|---|---|---|---|
蓝色Blue | Gh_A05G1931 | 4 300.865 | AT4G08950 | 磷酸盐反应1家族蛋白 Phosphate-responsive 1 family protein |
Gh_D13G0160 | 4 218.162 | AT2G40140 | 锌指(C3H型)蛋白家族 Zinc finger (C3H-type) family protein | |
Gh_A13G2112 | 3 944.263 | AT1G27730 | 耐盐锌指Salt tolerance zinc finger | |
Gh_A05G0483 | 3 864.472 | AT1G80840 | WRKY DNA结合蛋白40 WRKY DNA-binding protein 40 | |
Gh_A12G2357 | 3 096.27 | AT5G51990 | C重复结合因子4 C-repeat-binding factor 4 | |
棕色 Brown | Gh_D09G1773 | 628.545 | AT3G49530 | 含有NAC结构域的蛋白质62 NAC domain containing protein 62 |
Gh_D05G2642 | 601.582 | AT3G56400 | WRKY DNA结合蛋白70 WRKY DNA-binding protein 70 | |
Gh_A05G1554 | 557.708 | AT1G20440 | 低温调节47 Cold-regulated 47 | |
Gh_D05G0600 | 550.86 | AT1G80840 | WRKY DNA结合蛋白40 WRKY DNA-binding protein 40 | |
Gh_A13G0138 | 517.077 | AT2G40140 | 锌指(C3H型)蛋白家族 Zinc finger (C3H-type) family protein 图8 核心基因的表达模式 Fig.8 Expression pattern of hub genes 图9 核心基因的 RT-qPCR 验证 Fig.9 qRT-PCR validation of hub genes |
表3 目标模块中核心基因的功能注释
Table 3 Annotation of hub genes in target module
模块 Module | 核心基因编号 Hub gene ID | 模块内连通性 Connectivity | 拟南芥同源基因编号 Homologous gene ID in A. thaliana | 基因功能 Gene function |
---|---|---|---|---|
蓝色Blue | Gh_A05G1931 | 4 300.865 | AT4G08950 | 磷酸盐反应1家族蛋白 Phosphate-responsive 1 family protein |
Gh_D13G0160 | 4 218.162 | AT2G40140 | 锌指(C3H型)蛋白家族 Zinc finger (C3H-type) family protein | |
Gh_A13G2112 | 3 944.263 | AT1G27730 | 耐盐锌指Salt tolerance zinc finger | |
Gh_A05G0483 | 3 864.472 | AT1G80840 | WRKY DNA结合蛋白40 WRKY DNA-binding protein 40 | |
Gh_A12G2357 | 3 096.27 | AT5G51990 | C重复结合因子4 C-repeat-binding factor 4 | |
棕色 Brown | Gh_D09G1773 | 628.545 | AT3G49530 | 含有NAC结构域的蛋白质62 NAC domain containing protein 62 |
Gh_D05G2642 | 601.582 | AT3G56400 | WRKY DNA结合蛋白70 WRKY DNA-binding protein 70 | |
Gh_A05G1554 | 557.708 | AT1G20440 | 低温调节47 Cold-regulated 47 | |
Gh_D05G0600 | 550.86 | AT1G80840 | WRKY DNA结合蛋白40 WRKY DNA-binding protein 40 | |
Gh_A13G0138 | 517.077 | AT2G40140 | 锌指(C3H型)蛋白家族 Zinc finger (C3H-type) family protein 图8 核心基因的表达模式 Fig.8 Expression pattern of hub genes 图9 核心基因的 RT-qPCR 验证 Fig.9 qRT-PCR validation of hub genes |
模块 Module | GO条目 GO term | 基因本体 Ontology | 描述 Description | 基因数目 Genes No. | P值 P value |
---|---|---|---|---|---|
棕色 Brown | GO:0050896 | P | 对刺激的反应Response to stimulus | 644 | 6.16e-10 |
GO:0006950 | P | 对胁迫的反应Response to stress | 365 | 1.39e-05 | |
GO:0009719 | P | 对内源性刺激的反应Response to endogenous stimulus | 269 | 7.26e-14 | |
GO:0009628 | P | 对非生物刺激的反应Response to abiotic stimulus | 263 | 2.57e-07 | |
GO:1901700 | P | 对含氧化合物的反应Response to oxygen-containing compound | 253 | 3.61e-14 | |
GO:0009725 | P | 对激素的反应Response to hormone | 233 | 1.08e-08 | |
GO:0048583 | P | 对刺激反应的调节Regulation of response to stimulus | 106 | 3.83e-08 | |
GO:0009737 | P | 对脱落酸的反应Response to abscisic acid | 103 | 3.37e-08 | |
GO:0009723 | P | 对乙烯的反应Response to ethylene | 68 | 6.83e-08 | |
GO:0080134 | P | 对胁迫反应的调节Regulation of response to stress | 66 | 3.94e-09 | |
GO:0010200 | P | 对几丁质的反应Response to chitin | 64 | 2.87e-20 | |
GO:0009751 | P | 对水杨酸的反应Response to salicylic acid | 47 | 4.46e-08 | |
GO:0031347 | P | 对防御反应的调节Regulation of defense response | 47 | 1.41e-06 | |
GO:0009753 | P | 对茉莉酸的反应Response to jasmonic acid | 46 | 2.71e-05 | |
GO:0003700 | F | 转录因子活性,特异性DNA序列结合 Transcription factor activity, sequence-specific DNA binding | 262 | 3.74e-20 | |
GO:0005634 | C | 核nucleus | 797 | 1.94e-06 | |
GO:0005887 | C | 质膜的组成部分Integral component of plasma membrane | 24 | 0.024 88 |
表2 特异性模块的部分GO富集分析结果 (续表Continued)
Table 2 Partial GO enrichment analysis of target module
模块 Module | GO条目 GO term | 基因本体 Ontology | 描述 Description | 基因数目 Genes No. | P值 P value |
---|---|---|---|---|---|
棕色 Brown | GO:0050896 | P | 对刺激的反应Response to stimulus | 644 | 6.16e-10 |
GO:0006950 | P | 对胁迫的反应Response to stress | 365 | 1.39e-05 | |
GO:0009719 | P | 对内源性刺激的反应Response to endogenous stimulus | 269 | 7.26e-14 | |
GO:0009628 | P | 对非生物刺激的反应Response to abiotic stimulus | 263 | 2.57e-07 | |
GO:1901700 | P | 对含氧化合物的反应Response to oxygen-containing compound | 253 | 3.61e-14 | |
GO:0009725 | P | 对激素的反应Response to hormone | 233 | 1.08e-08 | |
GO:0048583 | P | 对刺激反应的调节Regulation of response to stimulus | 106 | 3.83e-08 | |
GO:0009737 | P | 对脱落酸的反应Response to abscisic acid | 103 | 3.37e-08 | |
GO:0009723 | P | 对乙烯的反应Response to ethylene | 68 | 6.83e-08 | |
GO:0080134 | P | 对胁迫反应的调节Regulation of response to stress | 66 | 3.94e-09 | |
GO:0010200 | P | 对几丁质的反应Response to chitin | 64 | 2.87e-20 | |
GO:0009751 | P | 对水杨酸的反应Response to salicylic acid | 47 | 4.46e-08 | |
GO:0031347 | P | 对防御反应的调节Regulation of defense response | 47 | 1.41e-06 | |
GO:0009753 | P | 对茉莉酸的反应Response to jasmonic acid | 46 | 2.71e-05 | |
GO:0003700 | F | 转录因子活性,特异性DNA序列结合 Transcription factor activity, sequence-specific DNA binding | 262 | 3.74e-20 | |
GO:0005634 | C | 核nucleus | 797 | 1.94e-06 | |
GO:0005887 | C | 质膜的组成部分Integral component of plasma membrane | 24 | 0.024 88 |
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