利用WGCNA筛选马铃薯块茎发育候选基因  

Screening candidate genes involved in potato tuber development using WGCNA

作　　者：荐红举 张梅花 尚丽娜 王季春[1,2,3] 胡柏耿 Vadim Khassanov 吕典秋 JIAN Hong-Ju;ZHANG Mei-Hua;SHANG Li-Na;WANG Ji-Chun;HU Bai-Geng;Vadim Khassanov;and LYU Dian-Qiu(College of Agronomy and Biotechnology,Southwest University,Chongqing 400715,China;State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University,Chongqing 400715,China;Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops,Chongqing 400715,China;National Engineering Research Center for Potato,Dezhou 253600,Shandong,China;S.Seifullin Kazakh Agrotechnical University,Zhenis Avenue 010011,Astana,Republic of Kazakhstan)

机构地区：[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 [5]S.Seifullin Kazakh Agrotechnical University,Zhenis Avenue 010011,Astana,Republic of Kazakhstan

出　　处：《作物学报》2022年第7期1658-1668,共11页Acta Agronomica Sinica

基　　金：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。

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 1-3516 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。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 deve-lopment 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 devel-opment,WGCNA was used to analyze transcriptome data of potato DM 1-3516 R44(DM)material and RH89-039-16(RH)mate-rial 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 de-velopment,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.

关 键 词：马铃薯 WGCNA 块茎发育 调控网络 核心基因 

分 类 号：S532[农业科学—作物学]