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| 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 |
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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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Received: 27 December 2024
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Corresponding Authors:
*lanwei@chnu.edu.cn
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[1] Ayyappan V, Sripathi V R, Xie S, et al.2024. Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass[J]. BMC Genomics, 25(1): 223.
[2] Banday Z Z, Nandi A K.2017. Arabidopsis thaliana GLUTATHIONE‐S‐TRANSFERASE THETA 2 interacts with RSI1/FLD to activate systemic acquired resistance[J]. Molecular Plant Pathology, 19(2): 464-475.
[3] Chen L, Wu X, Zhang M, et al.2024. Genome-Wide Identification of BrCMF Genes in Brassica rapa and their expression analysis under abiotic stresses[J]. Plants (Basel), 13(8): 1118.
[4] Cui X, Zheng Y, Lu Y, et al.2021. Metabolic control of histone demethylase activity involved in plant response to high temperature[J]. Plant Physiology, 185(4): 1813-1828.
[5] Du T T, Huang Q H.2007. The roles of histone lysine methylation in epigenetic regulation[J]. Hereditas, 29(4): 387-392.
[6] Fan S, Liu H, Liu J, et al.2020. Systematic analysis of the DNA methylase and demethylase gene families in rapeseed (Brassica napus L.) and their expression variations after salt and heat stresses[J]. The International Journal of Molecular Sciences, 21(3): 953.
[7] Guo T, Wang D, Fang J, et al.2019. Mutations in the rice OsCHR4 gene, encoding a CHD3 family chromatin remodeler, induce narrow and rolled leaves with increased cuticular wax[J]. The International Journal of Molecular Sciences, 20(10): 2567.
[8] He K, Cao X, Deng X.2021b. Histone methylation in epigenetic regulation and temperature responses[J]. Current Opinion in Plant Biology, 61: 102001.
[9] He X, Wang Q, Pan J, et al.2021a. Systematic analysis of JmjC gene family and stress-response expression of KDM5 subfamily genes in Brassica napus[J]. PeerJ, 9: e11137.
[10] Huang S, Zhang A, Jin J B, et al.2019. Arabidopsis histone H3K4 demethylase JMJ17 functions in dehydration stress response[J]. New Phytologist, 223(3): 1372-1387.
[11] Jiang D, Yang W, He Y, et al.2007. Arabidopsis relatives of the human lysine-specific demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition[J]. Plant Cell, 19(10): 2975-2987.
[12] Klose R J, Zhang Y.2007. Regulation of histone methylation by demethylimination and demethylation[J]. Nature Reviews Molecular Cell Biology, 8(4): 307-318.
[13] Liu G, Khan N, Ma X, et al.2019. Identification, evolution, and expression profiling of histone lysine methylation moderators in Brassica rapa[J]. Plants, 8(12): 516.
[14] Lu F, Li G, Cui X, et al.2008. Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice[J]. Journal of Integrative Plant Biology, 50(7): 886-896.
[15] Martin C, Zhang Y.2005. The diverse functions of histone lysine methylation[J]. Nature Reviews Molecular Cell Biology, 6(11): 838-849.
[16] Min L, Li Y, Hu Q, et al.2014. Sugar and auxin signaling pathways respond to high-temperature stress during anther development as revealed by transcript profiling analysis in cotton[J]. Plant Physiology, 164(3): 1293-1308.
[17] Mishra S K, Chaudhary C, Baliyan S, et al.2024. Heat-stress-responsive HvHSFA2e gene regulates the heat and drought tolerance in barley through modulation of phytohormone and secondary metabolic pathways[J]. Plant Cell Reports, 43(7): 172.
[18] Oberkofler V, Bäurle I.2022. Inducible epigenome editing probes for the role of histone H3K4 methylation in Arabidopsis heat stress memory[J]. Plant Physiology, 189(2): 703-714.
[19] Panara F, Fasano C, Lopez L, et al.2022. Genome-wide identification and spatial expression analysis of histone modification gene families in the rubber dandelion Taraxacum kok-saghyz[J]. Plants, 11(16): 2077.
[20] Pérez-Oliver M A, Haro J G, Pavlović I, et al.2021. Priming maritime pine megagametophytes during somatic embryogenesis improved plant adaptation to heat stress[J]. Plants (Basel), 10(3): 446.
[21] Xu H, Wang C, Shao G, et al.2022. The reference genome and full-length transcriptome of pakchoi provide insights into cuticle formation and heat adaption[J]. Horticulture Research, 9: uhac123.
[22] Yamaguchi N, Ito T.2021. JMJ histone demethylases balance H3K27me3 and H3K4me3 levels at the HSP21 Locus during heat acclimation in Arabidopsis[J]. Biomolecules, 11(6): 852.
[23] Zhao M, Yang S, Liu X, et al.2015. Arabidopsis histone demethylases LDL1 and LDL2 control primary seed dormancy by regulating DELAY OF GERMINATION 1 and ABA signaling-related genes[J]. Frontiers in Plant Science, 6: 159.
[24] Zheng S, Hu H, Ren H, et al.2019. The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor[J]. Nature Communications, 10(1): 1033.
[25] Zhou L, Yarra R, Jin L, et al.2022. Identification and expression analysis of histone modification gene (HM) family during somatic embryogenesis of oil palm[J]. BMC Genomics, 23(1): 11.
[26] Zong W, Yang J, Fu J, et al.2020. Synergistic regulation of drought-responsive genes by transcription factor OsbZIP23 and histone modification in rice[J]. The International Journal of Molecular Sciences, 62(6): 723-729. |
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