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Brassica rapa  is an important Chinese vegetable crop that is beneficial to human health. The primary factor affecting  B. rapa  yield is low temperature, which promotes bolting and flowering, thereby lowering its commercial value. However, quickened bolting and flowering can be used for rapid breeding. Therefore, studying the underlying molecular mechanism of vernalization in  B. rapa  is crucial for solving production-related problems. Here, the transcriptome of two  B. rapa  accessions were comprehensively analyzed during different vernalization periods. During vernalization, a total of 974,584,022 clean reads and 291.28 Gb of clean data were obtained. Compared to the reference genome of  B. rapa , 44,799 known genes and 2280 new genes were identified. A self-organizing feature map analysis of 21,035 differentially expressed genes was screened in two  B. rapa  accessions, ‘Jin Wawa’ and ‘Xiao Baojian’. The analysis indicated that transcripts related to the plant hormone signal transduction, starch and sucrose metabolism, photoperiod and circadian clock, and vernalization pathways changed notably at different vernalization periods. Moreover, different expression patterns of  TPS ,  UGP ,  CDF ,  VIN1 , and seven hormone pathway genes were observed during vernalization between the two accessions. The transcriptome results of this study provide a new perspective on the changes that occur during  B. rapa  vernalization, as well as serve as an excellent reference for  B. rapa  breeding.

Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Vernalization Periods in Brassica rapa