Pepper (Capsicum spp.) is the most widely grown spice in the world. It has important uses in pharmaceuticals, as natural coloring and an active ingredient in most defense repellents.

 

Conventional breeding has improved key agronomic traits of pepper. However, the large and complex genome has hampered our understanding of the functional genome and rendered molecular breeding difficult. In addition, the large repertoire of repetitive sequences (over 80% of the genome) indicates a potentially intricate and diverse cis-regulatory mechanisms of gene expression in pepper. It should be noted that diversification of the cis-regulatory elements is a main driving force of evolution and domestication.

In this study entitled “Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper”, published in Genome Biology, the Yan Xue group at Peking University Institute of Advanced Agricultural Sciences / Shandong Laboratory of Advanced Agriculture Sciences in Weifang presents the first comprehensive epigenomic landscape of pepper.

 

Using the C. annuum Zhangshugang landrace as a model, the team profiled genome-wide chromatin states and predicted CREs — including promoters and enhancers — based on combinatorial histone modifications and chromatin accessibility. Promoters were defined by co-occupancy of H3K4me3, H3K27ac and open chromatin, whereas enhancers were marked primarily by open chromatin alone. The study further mined CREs associated with development and stress responses, and experimentally validated a subset of these elements.

Notably, the work reports, for the first time in pepper, intergenic regions simultaneously carrying H3K4me1 and H3K27me3 — putative “poised” regulatory elements whose molecular functions await further investigation.

 

This work was supported by Peking University Institute of Advanced Agricultural Sciences and Shandong Laboratory of Advanced Agriculture Sciences in Weifang. Hongji Yang, at Peking University Institute of Advanced Agricultural Sciences, is the first author. Dr. Yan Xue, at Peking University Institute of Advanced Agricultural Sciences, is the corresponding author. Dr. Zhenhui Zhong, at Sichuan University, and Dr. Feng Liu, at Hunan Agricultural University, are the co-corresponding authors. Other contributing authors include Guorong Yu, Zhidong Lv, Tonghui Li, Dr. Zhagnsheng Zhu, Dr. Hang He, Dr. Guochen Qin at Peking University Institute of Advanced Agricultural Sciences; Xi Wang at Hunan Agricultural University and Dr. Guangjun Guo at Jiangsu Academy of Agricultural Sciences.