Journal Article

Genome-wide identification of Brassicaceae histone modification genes and their responses to abiotic stresses in allotetraploid rapeseed

Hu, Lin-Lin, Ma, Sheng-Jie, Huang, Jin-Yong, Zhang, Kai-Yan, Zheng, Li-Wei, Zhu, Xin-Lei, Hua, Ying-Peng

2023

Overview

Background Histone modification is an important epigenetic regulatory mechanism and essential for stress adaptation in plants. However, systematic analysis of histone modification genes ( HMs ) in Brassicaceae species is lacking, and their roles in response to abiotic stress have not yet been identified. Results In this study, we identified 102 AtHMs , 280 BnaHMs , 251 BcHMs , 251 BjHMs , 144 BnHMs , 155 BoHMs , 137 BrHMs , 122 CrHMs , and 356 CsHMs in nine Brassicaceae species, respectively. Their chromosomal locations, protein/gene structures, phylogenetic trees, and syntenies were determined. Specific domains were identified in several Brassicaceae HMs , indicating an association with diverse functions. Syntenic analysis showed that the expansion of Brassicaceae HMs may be due to segmental and whole-genome duplications. Nine key BnaHMs in allotetraploid rapeseed may be responsible for ammonium, salt, boron, cadmium, nitrate, and potassium stress based on co-expression network analysis. According to weighted gene co-expression network analysis (WGCNA), 12 BnaHMs were associated with stress adaptation. Among the above genes, BnaPRMT11 simultaneously responded to four different stresses based on differential expression analysis, while BnaSDG46 , BnaHDT10 , and BnaHDA1 participated in five stresses. BnaSDG46 was also involved in four different stresses based on WGCNA, while BnaSDG10 and BnaJMJ58 were differentially expressed in response to six different stresses. In summary, six candidate genes for stress resistance ( BnaPRMT11 , BnaSDG46 , BnaSDG10 , BnaJMJ58 , BnaHDT10 , and BnaHDA1 ) were identified. Conclusions Taken together, these findings help clarify the biological roles of Brassicaceae HMs . The identified candidate genes provide an important reference for the potential development of stress-tolerant oilseed plants.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abiotic stress / Adaptation / Agricultural production / Agriculture / Allotetraploid rapeseed / allotetraploidy / Ammonium / Analysis / Biomedical and Life Sciences / Boron / Brassica napus - genetics / Brassica napus - metabolism / Brassica rapa - genetics / Brassicaceae / Cadmium / Cell cycle / Cell division / Cruciferae / Environmental aspects / Epigenetic inheritance / Epigenetics / Gene expression / gene expression regulation / Gene Expression Regulation, Plant / Genes / Genetic aspects / Genetic research / Genomes / Genomics / Growth / histone code / Histone Code - genetics / Histone modification / Histones / Life Sciences / Network analysis / nitrates / Phylogenetics / Phylogeny / Physiology / Plant growth / Plant Proteins - genetics / Plant Proteins - metabolism / Plant Sciences / potassium / Rapeseed / Regulatory mechanisms (biology) / Salt / species / stress tolerance / Stress, Physiological - genetics / Stresses / Synteny / Toxicity / Tree Biology