The wucai genome and DNA methylation regulation on the inner leaves’ yellowing response to low temperature

Abstract

Wucai (Brassica rapa), a widely cultivated non-heading Chinese cabbage in autumn and winter in China, has been limited in its genetic and genomic analyses due to the lack of a reference genome. Here, we have assembled a high-quality chromosome-level genome assembly of wucai, which is 480.57 Mb in length, with a scaffold N50 of 46.53 Mb and a contig N50 of 4.45 Mb. We annotated 42 634 protein-coding genes in the B. rapa W7-2 genome and 55.08% of repetitive sequences. Additionally, we performed DNA methylome analysis to investigate the characteristic yellowing response of wucai inner leaves to low temperature. CHH methylation levels increased under low-temperature conditions, while a slight decrease was observed under normal temperatures with more hypo-differentially methylated regions. The expression levels of DNA methyltransferases BrCMT2 and BrDRM2 were significantly up-regulated under low-temperature conditions but down-regulated at normal temperature. Furthermore, chlorophyll metabolism genes, BrHemA, BrHemL, BrHemD, BrCLH2, BrCHLP, BrSGR, and BrPPD, were identified as differentially expressed, which exhibited elevated CHH methylation levels in their promoter regions across three stages. Leaves of Nicotiana benthamiana transiently overexpressing BrCLH2.1 exhibited a slight degreening phenotype compared to wild type. The application of a DNA methylation inhibitor into the inner leaves of W7-2 induced obvious bleaching, and the total chlorophyll content decreased significantly. In conclusion, the genome data of W7-2 provide a valuable resource for functional gene research and genetic breeding of non-heading Chinese cabbage.

Acknowledgments

This research was financially supported by the Natural Science Foundation of China Projects (32272703), Provincial Key Development Program for Basic Research of Anhui (2023z04020005), and Scientific Research Project of Higher Education Institution in Anhui Province (Key project: 2022AH050932).

Author contributions

L.Y. and C.W. conceived the project, designed the experiments, and were responsible for the project initiation. S.Z. and G.C. analyzed the data. J.W., H.Z., and J.H. performed the experiments and prepared figures. W.W., X.X., X.G., Y.Y., G.W., M.L., X.T., and J.W. conducted bioinformatic analyses. L.Y., J.W., and H.Z. organized, wrote, and revised the manuscript. All authors read and revised the manuscript.

Data availability

The raw sequence data reported in this paper have been deposited in the National Genomics Data Center (GSA: CRA012429, CRA012488, and CRA012487).

Conflict of interest statement

The authors declare that they have no competing interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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