Screening candidate genes involved in potato tuber development using WGCNA
利用WGCNA筛选马铃薯块茎发育候选基因
Jian H.-J. Zhang M.-H. Shang L.-N. Wang J.-C. Hu B.-G. Khassanov V. Lyu D.-Q.
12 July 2022Institute of Crop Sciences
Acta Agronomica Sinica(China)
2022#48Issue 71658 - 1668 pp.
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 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.
Hub genes , Potato , Regulatory network , Tuber development , WGCNA
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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, China
S. Seifullin Kazakh Agrotechnical University, Zhenis Avenue, Astana, 010011, Kazakhstan
College of Agronomy and Biotechnology
State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University
Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops
National Engineering Research Center for Potato
S. Seifullin Kazakh Agrotechnical University
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