Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization

BMC Genomics

Guohu Chen¹  Chenggang Wang¹  Lingyun Yuan¹  Rifei Sun²  Xiao Sun²  Guoliang Li²  Shujiang Zhang²  Shifan Zhang²  Fei Li²  Hui Zhang²  Yun Dai³ 

[1] College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, 230036, Hefei, Anhui, China;Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, Changjiang West Road, NO.130, 230036, Hefei, Anhui, China;

关键词: Chinese cabbage;    Gradient-vernalization;    RNA sequencing;    Weighted gene co-expression network analysis;    Hub genes;   

DOI  :  10.1186/s12864-021-07510-8

来源: Springer

【 摘 要 】

BackgroundVernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapa L. ssp. pekinensis), this process causes their commercial value to decline. Clarifying the mechanisms of vernalization is essential for its further application. We performed RNA sequencing of gradient-vernalization in order to explore the reasons for the different bolting process of two Chinese cabbage accessions during vernalization.ResultsThere was considerable variation in gene expression between different-bolting Chinese cabbage accessions during vernalization. Comparative transcriptome analysis and weighted gene co-expression network analysis (WGCNA) were performed for different-bolting Chinese cabbage during different vernalization periods. The biological function analysis and hub gene annotation of highly relevant modules revealed that shoot system morphogenesis and polysaccharide and sugar metabolism caused early-bolting ‘XBJ’ to bolt and flower faster; chitin, ABA and ethylene-activated signaling pathways were enriched in late-bolting ‘JWW’; and leaf senescence and carbohydrate metabolism enrichment were found in the two Chinese cabbage-related modules, indicating that these pathways may be related to bolting and flowering. The high connectivity of hub genes regulated vernalization, including MTHFR2, CPRD49, AAP8, endoglucanase 10, BXLs, GATLs, and WRKYs. Additionally, five genes related to flower development, BBX32 (binds to the FT promoter), SUS1 (increases FT expression), TSF (the closest homologue of FT), PAO and NAC029 (plays a role in leaf senescence), were expressed in the two Chinese cabbage accessions.ConclusionThe present work provides a comprehensive overview of vernalization-related gene networks in two different-bolting Chinese cabbages during vernalization. In addition, the candidate pathways and hub genes related to vernalization identified here will serve as a reference for breeders in the regulation of Chinese cabbage production.

【 授权许可】

CC BY