Genome-Wide Identification of Pakchoi (Brassica rapa ssp. chinensis) HDM Genes Family and Expression Profile Analysis Under Heat Stress
LIU Hong-Chuang, OUYANG Wen-Dong, XUE Jian-Ping, LAN Wei*
College of Life Sciences/Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, Huaibei Normal University, Huaibei 235000, China
Abstract：Pakchoi (Brassica rapa ssp. chinesis) also referred to as small bok choy, this variety belongs to the category of Shanghai white cabbage renowned for its robust resistance to heat, cold, and pests, coupled with its straightforward cultivation techniques. Histone demethylase (HDM) is one of the epigenetic factors, which participates in regulating the transcriptional expression of genes by adjusting the level of histone methylation modification. Therefore, in this study, a total of 33 BrcHDM gene members were identified, including 4 B. rapa ssp. chinensis lysine-specific demethylase 1 (BrcLSD1) genes and 29 B. rapa ssp. chinensis JmjC domain-containing histone demethylases (BrcJHDM) genes, were identified by homologous comparison based on the genome data of pakchoi. Chromosomal localization, phylogenetic tree, conserved structural domains and gene structures as well as promoter cis-acting elements were analyzed; The phylogenetic tree analysis and chromosomal localization analysis indicated that the BrcHDM proteins in B. rapa var. chinensis were classified into the LSD1 subfamily and the JHDM subfamily. These proteins were unevenly distributed across 10 chromosomes. Analysis of conserved domains revealed that the BrcHDM proteins harbored the PLN02529, PLN03000, PLN02976, and PLN02328 domains, respectively. Gene structure analysis showed that the genes within the BrcHDM family contained 1 to 25 exons. Specifically, the members of the LSD1 subfamily had 1 to 8 exons, while the members of the JHDM subfamily had 2 to 25 exons. Analysis of cis-acting elements in the promoter region indicated that the number of stress-related cis-acting elements in the promoters of BrcHDM genes was generally greater than that of hormone-related and growth-and-development-related cis-acting elements. At the same time, based on the transcriptome data of high-temperature stress, it was found that BrcJMJ1/13/26 were the candidate genes for high-temperature response of pakchoi, and BrcJMJ26 might have been the main BrcHDM gene that formed the difference in heat resistance between high-temperature resistant 'PC-fu' and sensitive 'JP20' cultivars. Subcellular localization analysis showed that BrcJMJ13 was localized in the nucleus. The results of qRT-PCR showed that the expression of BrcJMJ1/13/26 increased with the extension of high temperature treatment. This study provides important candidate histone methylation modification factors for the cultivation of high-temperature resistant pakchoi.
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