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作物学报 ›› 2022, Vol. 48 ›› Issue (7): 1658-1668.doi: 10.3724/SP.J.1006.2022.14115

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

利用WGCNA筛选马铃薯块茎发育候选基因

荐红举1,2,3(), 张梅花1(), 尚丽娜1, 王季春1,2,3, 胡柏耿4, 吕典秋1,2,3,*()   

  1. 1西南大学农学与生物科技学院, 重庆 400715
    2南方山地农业教育部工程研究中心, 重庆 400715
    3薯类生物学与遗传育种重庆市重点实验室, 重庆 400715
    4国家马铃薯工程技术研究中心, 山东德州 253600
    5S. Seifullin Kazakh Agrotechnical University, Zhenis Avenue 010011, Astana, Republic of Kazakhstan
  • 收稿日期:2021-07-02 接受日期:2021-10-19 出版日期:2022-07-12 网络出版日期:2021-11-15
  • 通讯作者: 吕典秋
  • 作者简介:荐红举, E-mail: hjjian518@swu.edu.cn
    张梅花, E-mail: mhzhang77@163.com第一联系人：

    ** 同等贡献

  • 基金资助:
    科技部科技伙伴计划项目(KY201904016);国家重点研发计划项目(2018YFE0127900);国家自然科学基金项目(32101659);西南大学人才引进项目(SWU019008);西南大学种质创新专项研究项目资助

Screening candidate genes involved in potato tuber development using WGCNA

JIAN Hong-Ju1,2,3(), ZHANG Mei-Hua1(), SHANG Li-Na1, WANG Ji-Chun1,2,3, HU Bai-Geng4, Vadim Khassanov5, LYU Dian-Qiu1,2,3,*()   

  1. 1College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
    2State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
    3Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
    4National Engineering Research Center for Potato, Dezhou 253600, Shandong, China
    5S. Seifullin Kazakh Agrotechnical University, Zhenis Avenue 010011, Astana, Republic of Kazakhstan
  • Received:2021-07-02 Accepted:2021-10-19 Published:2022-07-12 Published online:2021-11-15
  • Contact: LYU Dian-Qiu
  • About author:First author contact:

    ** Contributed equally to this work

  • Supported by:
    Science and Technology Partnership Program, Minis-try of Science and Technology of China(KY201904016);National Key Research and Development Program of China(2018YFE0127900);National Natural Science Foundation of China(32101659);Talent Introduction Program of Southwest University Project(SWU019008);Special research project on Germplasm Innovation of Southwest University

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摘要：

块茎是马铃薯的主要经济器官, 解析其形成和发育机制对于马铃薯高产育种具有重要意义。虽然结薯相关基因已有报道, 但仍有大量参与结薯的基因有待进一步挖掘和鉴定。随着测序技术的不断革新和发展, 转录组数据愈加丰富和繁杂, 利用加权共表达网络分析(weighted gene co-expression network analysis, WGCNA)筛选特定性状、组织或发育阶段相关基因的方法被广泛应用。本研究利用WGCNA分别对马铃薯DM 1-3 516 R44 (DM)材料以及RH89-039-16 (RH)材料各15个组织器官的转录组数据进行分析, 构建共表达网络, 筛选与块茎发育相关的共表达模块。对筛选表达模块中的基因进行GO (Gene Ontology)和KEGG (Kyoto Encyclopedia of Genes and Genomes)通路富集分析。以模块中连通度前10的基因为核心基因, 用PGSC数据库和NCBI数据库进行注释, 并利用qRT-PCR进行验证。通过WGCNA分析, 在DM和RH材料中均得到13个共表达模块, 其中DM材料的Cyan模块和RH材料的Black模块与块茎显著相关。分析表明, 2个模块的基因显著富集在激素代谢、淀粉和蔗糖代谢以及细胞形成等相关过程中。此外, 在Cyan中注释到已被证实与块茎发育相关的基因StGA2ox1, 并且在共表达分析中StGA2ox1与模块中10个核心基因均相互关联。核心基因的qRT-PCR结果与RNA-Seq的结果基本一致。本研究运用WGCNA方法鉴别了2个块茎发育相关的共表达模块, 筛选出多个与块茎发育相关的候选基因, 为马铃薯高产育种奠定基础。

关键词: 马铃薯, WGCNA, 块茎发育, 调控网络, 核心基因

Abstract:

Tuber is the main economic organ of potato. It is of great significance to illustrate its formation and development mechanism for high yield breeding of potato. Although some related genes have been reported, there are still a large number of genes involved in tuber production which need to be further excavated and identified. With the continuous innovation and development of sequencing technology, transcriptome data has become more abundant and complicated. The method of screening genes related to specific traits, tissues or developmental stages using Weighted Gene Co-expression Network Analysis (WGCNA) has been widely used. In this study, to construct co-expression networks and screen co-expression modules related to tuber development, WGCNA was used to analyze transcriptome data of potato DM 1-3516 R44 (DM) material and RH89-039-16 (RH) material from 15 tissues and organs, respectively. GO and KEGG pathway enrichment were performed on the genes in the screening expression module. The top 10 genes in the module were taken as the hub genes, annotated by PGSC database and NCBI, and verified by qRT-PCR. 13 co-expression modules were obtained in both DM and RH materials, among which the Cray module in DM material analysis and the Black module in RH material analysis were significantly correlated with tubers by WGCNA. The analysis showed that the genes of the two modules were significantly enriched in related processes such as hormone metabolism, starch and sucrose metabolism, and cell formation. In addition, gene StGA2ox1, which had been proved to be related to tuber development, was noted in Cyan, and StGA2ox1 was correlated with 10 hub genes in the module in the co-expression analysis. The qRT-PCR results of the hub genes were basically consistent with the results of RNA-seq. In this study, two co-expression modules related to tuber development were identified by WGCNA, and several candidate genes related to tuber development were screened out, which laid a foundation for high yield potato breeding.

Key words: potato, WGCNA, tuber development, regulatory network, hub genes

表1

核心基因定量引物"

模块
Module		 基因编号
Gene ID		 正向引物
Forward primer (5°-3°)		 反向引物
Reverse primer (5°-3°)
Cyan PGSC0003DMG400021191 GTGCTGCTTAGGAATATGGTTG GAATGAAGATCCGAACAGCTTC
Cyan PGSC0003DMG400005704 CGACAACGATGAAGAAGATGAC ATGACGATGGTACTCTCTTCAC
Cyan PGSC0003DMG400005659 CAACGATTGGAGGCATTTCTAG GAGCTCATATGCAGTAGTTTGC
Cyan PGSC0003DMG400017696 AGTCGCAGTGATCGTGAATA CCACCACCATACCTATCATCTC
Cyan PGSC0003DMG401009395 GATGGCCGTATTCTTGTATCAT AGACCTGTTATGGTTCCAAATG
Cyan PGSC0003DMG400021095 CTTTTGGGGACTTGTGAAAGAG CTGGACATGGTGGATAGTGATT
Black PGSC0003DMG400030431 CTAAGGGTCATTACACTGAGGG CTTGTAGGCAGTCACAGTTTTC
Black PGSC0003DMG400010293 ATTTAGGCTTCTTTGTCTTGCG CGCCATCAAGTCAAATAAACCA
Black PGSC0003DMG400009401 ACAAGTGCTTACTATCGAGGAG GTCAGTATGATCTCTGAGCTCC
Black PGSC0003DMG400007997 TCCCTTCATTCCCTGTCTTA AATGTAGGCTCCACTTCCAC
Black PGSC0003DMG400008491 CTCTCCAACTGTGAAGTCTAGG AAGGAGAACATGATTTCCGTCT
Black PGSC0003DMG400012238 CAATGTCAAGGCCAAGATTCAA AAGTCGACTCTTTCTGGATGTT

图1

基因聚类树与模块构建 A: DM材料; B: RH材料。A: DM material; B: RH material."

图2

不同模块包含的基因数量 A: DM材料; B: RH材料。A: DM material; B: RH material."

图3

基因共表达网络模块与性状的关联热图 A: DM材料; B: RH材料。横轴表示不同组织, 纵轴表示每一个模块的特征向量。红色的格子代表性状与模块具有正相关性, 蓝色的格子代表性状与模块具有负相关性。"

图4

目标模块内基因GO富集分析 A: DM材料的Cyan模块; B: RH材料的Black模块。"

图5

目标模块内基因KEGG富集分析 A: DM材料的Cyan模块; B: RH材料的Black模块。"

图6

Cyan和Black模块内的基因共表达网络及其核心基因"

表2

不同模块中核心基因的功能注释"

模块
Module		 核心基因
Hub gene		 拟南芥同源基因
Homologous gene in Arabidopsis thaliana		 基因注释
Gene annotation
Cyan PGSC0003DMG400021191 AT1G30480 DNA损伤修复/耐受蛋白DRT111, 叶绿体 DNA-damage-repair/toleration protein DRT111, chloroplastic
Cyan PGSC0003DMG400004278 AT3G63390 功能未知的保守基因
Conserved gene of unknown function
Cyan PGSC0003DMG400005704 AT1G03280 转录起始因子IIE亚基α样亚型X2
Transcription initiation factor IIE subunit alpha-like isoform X2
Cyan PGSC0003DMG400005659 AT3G18165 Pre-mRNA剪接因子SPF27同源物
Pre-mRNA-splicing factor SPF27 homolog
Cyan PGSC0003DMG400031139 AT1G71780 功能未知的保守基因
Conserved gene of unknown function
Cyan PGSC0003DMG400011912 — 功能未知的基因
Gene of unknown function
Cyan PGSC0003DMG400017696 AT3G26420 RNA结合蛋白RZ-1
RNA binding protein RZ-1
Cyan PGSC0003DMG400006479 — Myb-like蛋白A同工型X2
Myb-like protein A isoform X2
Cyan PGSC0003DMG400000409 AT4G01560 RNA加工因子1
RNA processing factor 1
Cyan PGSC0003DMG401009395 AT4G28450 DDB1和CUL4相关因子13
DDB1- and CUL4-associated factor 13
Cyan PGSC0003DMG400021095 AT1G30040 赤霉素2-氧化酶1
Gibberellin 2-oxidase 1 (GA2OX1)
Black PGSC0003DMG400030431 AT2G29550 β微管蛋白2
Beta-tubulin 2
模块
Module		 核心基因
Hub gene		 拟南芥同源基因
Homologous gene in Arabidopsis thaliana		 基因注释
Gene annotation
Black PGSC0003DMG401002397 AT5G56670 核糖体蛋白S30
Ribosomal protein S30
Black PGSC0003DMG400017722 AT1G35780 功能未知的保守基因
Conserved gene of unknown function
Black PGSC0003DMG400010293 AT2G20490 H/ACA核糖核蛋白复合物亚基3-like蛋白同工型X2
H/ACA ribonucleoprotein complex subunit 3-like protein isoform X2
Black PGSC0003DMG400009401 AT5G60860 Ras相关蛋白RABA1f
Ras-related protein RABA1f
Black PGSC0003DMG400003723 AT5G39600 功能未知的保守基因
Conserved gene of unknown function
Black PGSC0003DMG400007997 AT2G34520 核糖体蛋白S14, 线粒体
Rbosomal protein S14, mitochondrial
Black PGSC0003DMG400007257 AT1G67785 功能未知的保守基因
Conserved gene of unknown function
Black PGSC0003DMG400008491 AT2G38160 内切几丁质酶A
Endochitinase A
Black PGSC0003DMG400012238 AT3G52590 泛素超群, 核糖体蛋白L40e
Ubiquitin supergroup, ribosomal protein L40e

图7

核心基因的qRT-PCR验证 RNA-Seq的相对表达量 = log10 (FPKM+1)。"

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