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Article|02 Sep 2025|OPEN
The wucai genome and DNA methylation regulation on the inner leaves’ yellowing response to low temperature
Lingyun Yuan1,2,3 ,† , Jian Wang1,2 ,† , Haoying Zhang1,2 ,† , Jinfeng Hou1,2,3 ,† , Wenjie Wang1,2,3 , Xun Gao1,2 , Yating Yang1,2 , Gaoxia Wang1,2 , Min Li1,2 , Jianqiang Wu1,2,3 , Shidong Zhu1,2,3 , Guohu Chen1,2,3 , Xiaoyan Tang1,2,3 , Xinyu Xie1,2 , Chenggang Wang,1,2,3 ,
1Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
2Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
3Department of Vegetable Culture and Breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
*Corresponding author. E-mail: cgwang@ahau.edu.cn
†Lingyun Yuan and Jian Wang,Haoying Zhang,Jinfeng Hou contributed equally to the study.

Horticulture Research 13,
Article number: uhaf231 (2026)
doi: https://doi.org/10.1093/hr/uhaf231
Views: 59

Received: 21 Apr 2025
Accepted: 18 Aug 2025
Published online: 02 Sep 2025

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.