基于WGCNA的谷子苗期冷胁迫应答基因网络构建与核心因子发掘

doi:10.13304/j.nykjdb.2023.0108

中国农业科技导报 ›› 2023, Vol. 25 ›› Issue (10): 22-34.DOI: 10.13304/j.nykjdb.2023.0108

基于WGCNA的谷子苗期冷胁迫应答基因网络构建与核心因子发掘

张会¹^,²(), 王越越²^,³, 赵波²^,³, 张丽玲³, 郄倩茹³, 韩渊怀²^,³, 李旭凯¹^,²()

^1.山西农业大学生命科学学院, 山西太谷 030801
^2.山西农业大学山西省后稷实验室, 太原 030031
^3.山西农业大学农学院, 山西太谷 030801

收稿日期:2023-02-17 接受日期:2023-06-14 出版日期:2023-10-15 发布日期:2023-10-27
通讯作者: 李旭凯
作者简介:张会 E-mail：huizhang@sxau.edu.cn；
基金资助:
杂粮种质资源创新与分子育种国家实验室（筹）自主研发项目(202204010910001-02);山西省基础研究计划（自由探索类）青年项目(202203021222147);山西省博士毕业生、博士后研究人员来晋工作奖励经费科研项目(SXBYKY2022059);山西农业大学博士科研启动项目(2021BQ112);国家自然科学基金项目(32001608)

Identification of Co-expression Genes Related to Cold Stress in Foxtail Millet by WGCNA

Hui ZHANG¹^,²(), Yueyue WANG²^,³, Bo ZHAO²^,³, Liling ZHANG³, Qianru QIE³, Yuanhuai HAN²^,³, Xukai LI¹^,²()

^1.College of Life Sciences，Shanxi Agricultural University，Shanxi Taigu 030801，China
^2.Houji Laboratory in Shanxi Province，Shanxi Agricultural University，Taiyuan 030031，China
^3.College of Agriculture，Shanxi Agricultural University，Shanxi Taigu 030801，China

Received:2023-02-17 Accepted:2023-06-14 Online:2023-10-15 Published:2023-10-27
Contact: Xukai LI

摘要/Abstract

摘要：

研究植物响应低温胁迫的分子基础及选育与种植耐冷作物品种对于保障粮食安全具有重要的现实意义，但目前谷子（Setaria italica）耐冷相关研究比较匮乏。为深入研究谷子苗期响应低温胁迫的分子机制，利用谷子33份不同发育阶段和不同冷处理时间的RNA-Seq数据，筛选获得32 017个高表达基因并构建基因表达矩阵。利用R软件的WGCNA包构建共表达网络，进一步将网络划分为44个模块，发现谷子冷胁迫应答基因分布于多个模块中。选取包含冷胁迫基因数目排名前3的模块进一步分析，对预测到的靶基因进行GO富集分析，并对此3个模块进行基因调控网络的构建及核心基因注释，发现大多候选基因与非生物胁迫响应相关。以上结果为谷子抗逆研究提供了新思路，发掘的冷胁迫关键基因为谷子耐冷新品种选育提供了基因资源。

关键词: 谷子, 冷胁迫, 加权基因共表达网络

Abstract:

It is of great practical significance to study the molecular basis of plant response to low temperature stress and breed new varieties of cold-tolerant for ensuring food security. However， the study is relatively scarce about cold resistance of foxtail millet （Setaria italica）. To further explore the molecular mechanism of millet responsing to low temperature stress at seedling， 33 RNA-Seq data of foxtail millet at different development stages and different cold stress times were used. Gene expression matrix was constructed using 32 017 highly expressed genes. WGCNA package of R software was used to construct a co-expression network， which was further divided into 44 modules. The genes related to cold stress of foxtail millet were existed in several modules. Here， 3 modules with most cold stress genes were selected for GO enrichment analysis to annotate the function of target genes， and it was found that most candidate genes were related to abiotic stress responses. Above results provided new ideas for stress resistance of foxtail millet， and the key genes of cold stress provided effective resources for breeding the new variety of cold tolerance in foxtail millet.

Key words: foxtail millet, cold stress, weighted gene co-expression network

中图分类号:

S515

张会, 王越越, 赵波, 张丽玲, 郄倩茹, 韩渊怀, 李旭凯. 基于WGCNA的谷子苗期冷胁迫应答基因网络构建与核心因子发掘[J]. 中国农业科技导报, 2023, 25(10): 22-34.

Hui ZHANG, Yueyue WANG, Bo ZHAO, Liling ZHANG, Qianru QIE, Yuanhuai HAN, Xukai LI. Identification of Co-expression Genes Related to Cold Stress in Foxtail Millet by WGCNA[J]. Journal of Agricultural Science and Technology, 2023, 25(10): 22-34.

图/表 9

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基因 Gene	上游引物 Forward primer （5’-3’）	下游引物 Reverse primer （5’-3’）
Actin	TGCTCAGTGGAGGCTCAACA	CCAGACACTGTACTTGCGCTC
Si2g38970	GCCGGATGTTCTGGTGGTAT	CCTTGAAACTGCGTTCACCG
Si3g02940	TATACCGCACCAGCGATGAC	TCCTTTGGGACCTGATTGCC
Si3g08050	CTCCGACACCGACTCATTCT	AAGAAGATGACCGACACCCG
Si5g36480	CAGCATCCCCAGAGAGCAAA	GCACCTTGGGAACTGTGTCT
Si6g03220	GAGCATCGTGCTGTCAGAGG	CGTTGGGTCCAGGAACAGAT
Si9g50340	CCTCACAGACATGCCCATCG	TCGACATCGACTCAGTTGCC

基因 Gene	上游引物 Forward primer （5’-3’）	下游引物 Reverse primer （5’-3’）
Actin	TGCTCAGTGGAGGCTCAACA	CCAGACACTGTACTTGCGCTC
Si2g38970	GCCGGATGTTCTGGTGGTAT	CCTTGAAACTGCGTTCACCG
Si3g02940	TATACCGCACCAGCGATGAC	TCCTTTGGGACCTGATTGCC
Si3g08050	CTCCGACACCGACTCATTCT	AAGAAGATGACCGACACCCG
Si5g36480	CAGCATCCCCAGAGAGCAAA	GCACCTTGGGAACTGTGTCT
Si6g03220	GAGCATCGTGCTGTCAGAGG	CGTTGGGTCCAGGAACAGAT
Si9g50340	CCTCACAGACATGCCCATCG	TCGACATCGACTCAGTTGCC

基因 Gene	水稻同源基因 Homologous gene in rice	功能注释 Function annotation	拟南芥同源基因 Homologous gene in Arabidopsis thaliana	功能注释 Function annotation
Si2g38970	LOC_Os07g42650	保守假蛋白 Conserved hypothetical protein	At4g33980	冷调控基因28 Cold-regulate gene 28
Si3g01950	LOC_Os04g58710	4-香豆酸-Co-A连接酶类蛋白 4-coumarate-Co-A ligase （4CL） like protein	At1g77230	四肽重复类超家族蛋白 Tetratricopeptide repeat （TPR）-like superfamily protein
Si3g02940	LOC_Os04g57550	多胺氧化酶，种子萌发 Polyamine oxidase （PAO2）， seed germination	At2g43020	多肽氧化酶2 Polyamine oxidase 2， ATPAO2
Si3g08050	LOC_Os05g11810	类赤霉素2-β-双加氧酶 Similar to gibberellin 2-beta-dioxygenase	At1g30040	赤霉素2-氧化酶 Gibberellin 2-oxidase
Si5g36480	LOC_Os01g60600	WRKY 转录因子 WRKY transcription factor	At5g22570	WRKY DNA 结合蛋白38 WRKY DNA-binding protein 38
Si5g39150	LOC_Os05g37060	R-R型MYB类转录因子 R-R-type MYB-like transcription factor	At5g67420	含LOB结构域的蛋白37 LOB-domain-containing protein 37
Si6g03220	LOC_Os04g52090	APETALA 2 类转录因子 APETALA-2-like transcription factor	At5g44210	ERF 结构域蛋白9 ERF domain protein- 9
Si7g06300	LOC_Os04g23550	螺旋-环-螺旋转录激活因子 Basic helix-loop-helix （bHLH） transcription activator	At4g16430	bHLH DNA 结合超家族蛋白 bHLH DNA-binding superfamily protein
Si9g50340	LOC_Os07g42370	含TIFY结构域蛋白 TIFY domain containing protein	At1g74950	TIFY结构域/发散CCT基序家族蛋白 TIFY domain/divergent CCT motif family protein

基因 Gene	水稻同源基因 Homologous gene in rice	功能注释 Function annotation	拟南芥同源基因 Homologous gene in Arabidopsis thaliana	功能注释 Function annotation
Si2g38970	LOC_Os07g42650	保守假蛋白 Conserved hypothetical protein	At4g33980	冷调控基因28 Cold-regulate gene 28
Si3g01950	LOC_Os04g58710	4-香豆酸-Co-A连接酶类蛋白 4-coumarate-Co-A ligase （4CL） like protein	At1g77230	四肽重复类超家族蛋白 Tetratricopeptide repeat （TPR）-like superfamily protein
Si3g02940	LOC_Os04g57550	多胺氧化酶，种子萌发 Polyamine oxidase （PAO2）， seed germination	At2g43020	多肽氧化酶2 Polyamine oxidase 2， ATPAO2
Si3g08050	LOC_Os05g11810	类赤霉素2-β-双加氧酶 Similar to gibberellin 2-beta-dioxygenase	At1g30040	赤霉素2-氧化酶 Gibberellin 2-oxidase
Si5g36480	LOC_Os01g60600	WRKY 转录因子 WRKY transcription factor	At5g22570	WRKY DNA 结合蛋白38 WRKY DNA-binding protein 38
Si5g39150	LOC_Os05g37060	R-R型MYB类转录因子 R-R-type MYB-like transcription factor	At5g67420	含LOB结构域的蛋白37 LOB-domain-containing protein 37
Si6g03220	LOC_Os04g52090	APETALA 2 类转录因子 APETALA-2-like transcription factor	At5g44210	ERF 结构域蛋白9 ERF domain protein- 9
Si7g06300	LOC_Os04g23550	螺旋-环-螺旋转录激活因子 Basic helix-loop-helix （bHLH） transcription activator	At4g16430	bHLH DNA 结合超家族蛋白 bHLH DNA-binding superfamily protein
Si9g50340	LOC_Os07g42370	含TIFY结构域蛋白 TIFY domain containing protein	At1g74950	TIFY结构域/发散CCT基序家族蛋白 TIFY domain/divergent CCT motif family protein

模块 Module	基因名称 Gene name	水稻Rice		拟南芥Arabidopsis thaliana
模块 Module	基因名称 Gene name	同源基因 Homologous gene	功能注释 Function annotation	同源基因 Homologous gene	功能注释 Function annotation
Darkturquoise	Si3g17990 （TCP）	LOC_Os07g05720	TCP 家族转录因子 TCP family transcription factor	At1g30210	TCP 家族24 TCP family 24
	Si7g22390	LOC_Os04g49510	CAMK-CAMK27钙/钙调素依赖性蛋白激酶 CAMK_CAMK_like.27-CAMK includes calcium/calmodulin depedent protein kinases	At2g17290	钙依赖性蛋白激酶家族蛋白 Calcium-dependent protein kinase family protein
	Si9g50120	LOC_Os03g08570	胺氧化酶，含黄素，含结构域蛋白 Amine oxidase， flavin-containing， domain containing protein	At4g14210	八氢番茄红素脱氢酶3 Phytoene desaturase 3
	Si1g03360	LOC_Os01g10840	CGMC_GSK.2-CGMC 激酶 CGMC_GSK.2-CGMC includes CDA， MAPK， GSK3， and CLKC kinases	At1g06390	GSK3/SHAGGY 类蛋白激酶1 GSK3/SHAGGY-like protein kinase 1
Turquoise	Si4g02480 （ERF）	LOC_Os09g35010	脱水反应元件结合蛋白 Dehydration-responsive element-binding protein	At5g51990	核碱、核苷、核苷酸和核酸代谢过程 Nucleobase， nucleoside， nucleotide and nucleic acid metabolic process
	Si2g28390 （ERF）	LOC_Os09g35030	脱水反应元件结合蛋白 Dehydration-responsive element-binding protein	—	—
	Si7g18940 （ERF）	LOC_Os09g20350	乙烯应答转录因子 Ethylene-responsive transcription factor	—	—
	Si3g13090	LOC_Os05g50710	晚期胚胎蛋白 Late embryogenesis abundant protein	At2g46140	晚期胚胎蛋白 Late embryogenesis abundant protein
Blue	Si4g17730 （bZIP）	LOC_Os06g45140	含bZIP转录因子结构域的蛋白 bZIP transcription factor domain containing protein	—	—
	Si2g39810 （bHLH）	LOC_Os07g43530	螺旋-环-螺旋DNA结合蛋白 Helix-loop-helix DNA-binding domain containing protein	—	—
	Si5g13680 （WRKY）	LOC_Os02g08440	WRKY71转录因子 WRKY71 transcription factor	At1g80840	病原体诱导转录因子，体外结合 W-box 序列 Pathogen-induced transcription factor. Binds W-box sequences in vitro
	Si9g43500	LOC_Os03g17690	抗坏血酸过氧化物酶1 Ascorbate peroxidase 1	At1g07890	抗坏血酸过氧化物酶1 Ascorbate peroxidase 1

基于WGCNA的谷子苗期冷胁迫应答基因网络构建与核心因子发掘

Identification of Co-expression Genes Related to Cold Stress in Foxtail Millet by WGCNA

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[1]	李瑞珍, 姚建民, 王忠祥, 高凤翔, 窦贵新, 杨瑞平, 刘钊, 张继, 张振宇. 全生物降解渗水地膜覆盖冬播谷子产量结构关系分析[J]. 中国农业科技导报, 2023, 25(5): 185-191.
[2]	焦雄飞, 于晋, 冯乐勇, 郭耀东, 樊丽生. 不同播期对谷子DUS测试性状的影响[J]. 中国农业科技导报, 2022, 24(8): 55-64.
[3]	赵晋锋, 余爱丽, 李颜方, 杜艳伟, 王高鸿, 王振华. 谷子SiCBL3对非生物胁迫响应特征分析[J]. 中国农业科技导报, 2022, 24(11): 68-75.
[4]	郭瑞锋, 任月梅, 杨忠, 刘贵山, 任广兵, 张绶, 朱文娟. 草甘膦铵盐诱导谷子雄性不育的转录组分析[J]. 中国农业科技导报, 2022, 24(10): 35-43.
[5]	鱼冰星, 王宏富, 王振华, 张鹏, 成锴, 余爱丽, 闫海丽, 鱼冰洁. 多效唑对谷子茎秆特征及抗倒性的影响[J]. 中国农业科技导报, 2021, 23(8): 37-44.
[6]	李冉, 刘宇航, 梁杉, 张敏, . 硒肥对谷子产量因子及其籽粒富硒效果的影响[J]. 中国农业科技导报, 2021, 23(6): 140-146.
[7]	张宇杰, 郭平毅, 郭美俊, 周浩, 原向阳, 董淑琦, 王玉国. 外源硒矿粉对谷子保护酶活性、产量和籽粒中硒含量的影响[J]. 中国农业科技导报, 2021, 23(5): 153-159.
[8]	岳琳祺,郭佳晖,白雄辉,施卫萍,郭平毅,郭杰. 叶面喷施硒肥对不同基因型谷子农艺性状及籽粒硒含量的影响[J]. 中国农业科技导报, 2021, 23(4): 154-163.
[9]	田岗, 刘鑫, 王玉文, 刘永忠, 李会霞, 成锴, 王振华, 刘红. 遮光处理对谷子农艺性状、小米品质及蒸煮特性的影响[J]. 中国农业科技导报, 2021, 23(11): 47-54.
[10]	相吉山1,张恒儒2,刘涵1,索良喜2,贾姝婧1,张颖1,史景奇1,胡利喆1,蔡一宁1. 不同生态区谷子种质资源表型比较分析[J]. 中国农业科技导报, 2020, 22(9): 31-41.
[11]	李会霞1§，郑植尹2§，田岗1，刘鑫1，王玉文1，刘红1，史关燕3*. 7个谷子杂交种及其亲本的抗旱性分析[J]. 中国农业科技导报, 2020, 22(7): 20-28.
[12]	李智，王宏富*，王钰云，杨净，鱼冰星，黄珊珊. 谷子大豆间作对作物光合特性及产量的影响[J]. 中国农业科技导报, 2020, 22(6): 168-175.
[13]	王钰云，王宏富*，李智，段宏凯，黄珊珊. 谷子花生间作对谷子光合特性及产量的影响[J]. 中国农业科技导报, 2020, 22(5): 153-165.
[14]	王振华,刘鑫*,余爱丽,成锴,李会霞,田岗,王玉文,陈新霞,张鹏,刘红. 不同谷子品种萌发期对干旱胁迫生理响应的变化及抗旱指标筛选[J]. 中国农业科技导报, 2020, 22(12): 39-49.
[15]	秦岭,陈二影,杨延兵,张艳亭,孔清华,张华文,王海莲,王润丰,管延安*. 干旱和复水对不同耐旱型谷子品种苗期生理指标的影响[J]. 中国农业科技导报, 2019, 21(3): 146-151.