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

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

doi:10.1186/s12864-021-07510-8

Abstract

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.

Highlights

Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants
Five genes related to flower development, BBX32, sucrose synthase 1 (SUS1), PAO, TSF, and NAC029, were expressed in ‘Jin Wawa (JWW)’ MEdarkgrey and ‘Xiao Baojian (XBJ)’ MEpurple and MEblack
The results revealed that shoot system morphogenesis and polysaccharide and sugar metabolism induce early-bolting ‘XBJ’ to bolt and flower faster; chitin, abscisic acid (ABA) and ethylene-activated signaling pathways were enriched in late-bolting ‘JWW’; and leaf senescence and carbohydrate metabolism pathways were found to be enriched in the two Chinese cabbage-related modules, indicating that these may be related to bolting and flowering

Summary

Introduction

Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Rapid bolting and flowering promote the reproduction of Chinese cabbages Chinese cabbage is one of the most economically important Brassica vegetable crops cultivated in Asian countries [1]. In Europe, especially Western Europe, the area of land under cultivation for Chinese cabbage has increased [2]. This indicates that the demand for Chinese cabbage throughout the year is slowly increasing. Chinese cabbage is susceptible to low temperatures (vernalization) and long daylight hours during the spring cultivation process, which causes it to bolt and flower quickly, thereby losing its commercial value. In the breeding process, low temperature (vernalization) can be used to rapidly breed excellent varieties

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