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Background  Jumonji C (JmjC) proteins exert critical roles in plant development and stress response through the removal of lysine methylation from histones.  Brassica napus,  which originated from spontaneous hybridization by  Brassica rapa  and  Brassica oleracea , is the most important oilseed crop after soybean. In JmjC proteins of  Brassica  species, the structure and function and its relationship with the parents and model plant  Arabidopsis thaliana  remain uncharacterized. Systematic identification and analysis for JmjC family in  Brassica  crops can facilitate the future functional characterization and oilseed crops improvement.    Methods  Basing on the conserved JmjC domain,   JmjC homologs from the three  Brassica  species,  B. rapa  (AA),  B. oleracea  (CC) and  B. napus,  were identified from the  Brassica  database. Some methods, such as phylogenic analysis, chromosomal mapping, HMMER searching, gene structure display and Logos analysis, were used to characterize relationships of the JmjC homologs. Synonymous and nonsynonymous nucleotide substitutions were used to infer the information of gene duplication among homologs. Then, the expression levels of  BnKDM5  subfamily genes were checked under abiotic stress by qRT-PCR.    Results  Sixty-five JmjC genes were identified from  B. napus  genome, 29 from  B. rapa,  and 23 from  B. oleracea . These genes were grouped into seven clades based on the phylogenetic analysis, and their catalytic activities of demethylation were predicted. The average retention rate of  B. napus JmjC  genes ( B. napus JmjC  gene from  B. rapa  (93.1%) and  B. oleracea  (82.6%)) exceeded whole genome level. JmjC sequences demonstrated high conservation in domain origination, chromosomal location, intron/exon number and catalytic sites. The gene duplication events were confirmed among the homologs. Many of the   BrKDM5  subfamily genes showed higher expression under drought and NaCl treatments, but only a few genes were involved in high temperature stress.    Conclusions  This study provides the first genome-wide characterization of JmjC genes in  Brassica  species. The  BnJmjC  exhibits higher conservation during the formation process of allotetraploid than the average retention rates of the whole  B. napus  genome. Furthermore, expression profiles of many genes indicated that  BnKDM5  subfamily genes are involved in stress response to salt, drought and high temperature.

Systematic analysis of JmjC gene family and stress­-response expression of KDM5 subfamily genes in Brassica napus

Systematic analysis of JmjC gene family and stress-response expression of KDM5 subfamily genes in Brassica napus