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

文献类型： 外文期刊

第一作者： Dai, Yun

作者： Dai, Yun;Sun, Xiao;Li, Fei;Zhang, Shifan;Zhang, Hui;Li, Guoliang;Sun, Rifei;Zhang, Shujiang;Dai, Yun;Wang, Chenggang;Yuan, Lingyun;Chen, Guohu

作者机构：

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

期刊名称：BMC GENOMICS （ 影响因子：3.594； 五年影响因子：4.093 ）

ISSN： 1471-2164

年卷期： 2021 年 22 卷 1 期

页码：

收录情况： SCI

摘要： Background Vernalization 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. Results There 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. Conclusion The 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.

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