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Journal of Integrative Agriculture  2022, Vol. 21 Issue (6): 1620-1632    DOI: 10.1016/S2095-3119(21)63827-3
Special Issue: 园艺-分子生物合辑Horticulture — Genetics · Breeding
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
Genome-wide identification, evolutionary selection, and genetic variation of DNA methylation-related genes in Brassica rapa and Brassica oleracea

AN Feng1, 2*, ZHANG Kang2*, ZHANG Ling-kui2, LI Xing2, CHEN Shu-min2, WANG Hua-sen1, CHENG Feng2

1 Collaborative Innovation Center for Efficient and Green Production of Agriculture in Zhejiang Mountainous Areas, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, P.R.China

2 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China

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Abstract  DNA methylation plays an important role in plant growth and development, and in regulating the activity of transposable elements (TEs).  Research on DNA methylation-related (DMR) genes has been reported in Arabidopsis, but little research on DMR genes has been reported in Brassica rapa and Brassica oleracea, the genomes of which exhibit significant differences in TE content.  In this study, we identified 78 and 77 DMR genes in Brassica rapa and Brassica oleracea, respectively.  Detailed analysis revealed that the numbers of DMR genes in different DMR pathways varied in B. rapa and B. oleracea.  The evolutionary selection pressure of DMR genes in B. rapa and B. oleracea was compared, and the DMR genes showed differential evolution between these two species.  The nucleotide diversity (π) and selective sweep (Tajima’s D) revealed footprints of selection in the B. rapa and B. oleracea populations.  Transcriptome analysis showed that most DMR genes exhibited similar expression characteristics in B. rapa and B. oleracea.  This study dissects the evolutionary differences and genetic variations of the DMR genes in B. rapa and B. oleracea, and will provide valuable resources for future research on the divergent evolution of DNA methylation between B. rapa and B. oleracea.
Keywords:  DNA methylation       Brassica rapa       Brassica oleracea       evolutionary selection       genetic variation       gene expression   
Received: 15 March 2021   Accepted: 02 September 2021

The work was supported by the National Natural Science Foundation of China (NSFC; 31872105 and 31801862), the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences, and the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, China.

About author:  AN Feng, E-mail:; ZHANG Kang, E-mail:; Correspondence CHENG Feng, E-mail:; WANG Hua-sen, E-mail: * These authors contributed equally to this study.

Cite this article: 

AN Feng, ZHANG Kang, ZHANG Ling-kui, LI Xing, CHEN Shu-min, WANG Hua-sen, CHENG Feng. 2022. Genome-wide identification, evolutionary selection, and genetic variation of DNA methylation-related genes in Brassica rapa and Brassica oleracea. Journal of Integrative Agriculture, 21(6): 1620-1632.

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