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| Identification of the HSF Gene Family in Flowering Chinese Cabbage (Brassica rapa var. parachinensis) and Its Expression Analysis Under High Temperature Stress |
| JIANG Ding1, YUAN Fan-Chong1, SUN Feng-Lin2, LI Guang-Guang2, LEI Shi-Kang1, ZHENG Yan-Song2,* |
1 Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, China;
2 Guangzhou Academy of Agricultural and Rural Sciences, Guangzhou 510335, China |
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Abstract Heat shock transcription factor (HSF) plays an important role in regulating heat response and tolerance in plants. In order to further investigate the function of HSF genes in flowering Chinese cabbage (Brassica rapa var. parachinensis), this study used bioinformatics methods to systematically identify and analyze the HSF gene family and its molecular characteristics, and analyzed the gene expression patterns under high temperature stress. The results showed that a total of 39 HSF family genes were identified at the whole genome level of flowering Chinese cabbage, with protein sequence lengths ranging from 140 to 487 aa, molecular weights ranging from 16.10~53.82 kD, and theoretical isoelectric points ranging from 4.63 to 10.08. Protein subcellular localization prediction showed that 38 HSF proteins in flowering Chinese cabbage were located in the nucleus. The gene structure of most members of the HSF gene family in flowering Chinese cabbage was relatively conserved, with most genes contained 2 exons and 1 intron, as well as highly conserved DBD domain, conserved motif, and HSF domain. The 39 HSF genes in flowering Chinese cabbage were unevenly distributed on 10 chromosomes, with chromosome 3 had the most members. In synteny analysis, there were 32 genes in flowering Chinese cabbage that had a synteny relationship with Arabidopsis thaliana. The comparative analysis of the phylogenetic relationship between the HSF genes in flowering Chinese cabbage and A. thaliana indicated that these members of the HSF gene family could be divided into 3 categories: A, B, and C, with varying numbers of groups, and there were 9 pairs of orthologous genes and 2 pairs of paralogous genes. In addition, a large number of cis-acting elements related to plant hormones and stress response were found to be widely distributed in the promoter regions of HSF genes in flowering Chinese cabbage. qRT-PCR analysis showed that high temperature stress significantly induced the specific expression of most HSF genes in flowering Chinese cabbage (P<0.05), with 37 HSF genes showed up-regulation and 2 HSF genes showed down-regulation. Ten HSF genes highly expressed in the leaves or roots of flowering Chinese cabbage seedlings were screened, suggested that these genes play an important role in regulating the response of flowering Chinese cabbage to heat shock. This study provides a theoretical basis for understanding the characteristics of the HSF gene family in flowering Chinese cabbage and analyzing the functions of HSF family members in response to high temperature stress.
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Received: 18 August 2024
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Corresponding Authors:
*yansong_zheng@163.com
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[1] 白晓璟, 王玉奎, 左同鸿, 等. 2019. 甘蓝PMEI家族基因结构、基因组分布和表达分析[J]. 园艺学报, 46(10): 1973-1988.
(Bai X J, Wang Y K, Zuo T H, et al.2019. The strcture, genome-wide distribution and expression analysis of pectin methylesterase inhibitor genes in Brassica oleracea[J]. Acta Horticulturae Sinica, 46(10): 1973-1988.)
[2] 陈汉才, 吴增祥, 林悦欣, 等. 2021. 广东菜心、芥蓝研究现状与展望[J]. 广东农业科学, 48(9): 62-71.
(Chen H C, Wu Z X, Lin Y X, et al.2021. Research status and prospect of flowering Chinese cabbage and Chinese kale in Guangdong[J]. Guangdong Agricultural Sciences, 48(9): 62-71.)
[3] 陈勇兵, 王燕, 张海利. 2015. 番茄热激转录因子(Hsf)基因家族鉴定及表达分析[J]. 农业生物技术学报, 23(4): 492-501.
(Chen Y B, Wang Y, Zhang H L.2015. Identification and expression analysis of heat shock factor (Hsf) gene family in tomato (Solanum lycopersicum)[J]. Journal of Agricultural Biotechnology, 23(4): 492-501.)
[4] 郭仰东, 张磊, 李双桃, 等. 2018. 蔬菜作物应答非生物逆境胁迫的分子生物学研究进展[J]. 中国农业科学, 51(6): 1167-1181.
(Guo Y D, Zhang L, Li S T, et al.2018. Progresses in research on molecular biology of abiotic stress responses in vegetable crops[J]. Scientia Agricultura Sinica, 51(6): 1167-1181.)
[5] 江定, 李光光, 袁凡崇, 等. 2024. 菜心响应高温胁迫的转录组分析与基因挖掘[J]. 南方农业学报, 55(3): 766-783.
(Jiang D, Li G G, Yuan F C, et al.2024. Transcriptome analysis and gene mining of flowering Chinese cabbage in response to high temperature stress[J]. Journal of Southern Agriculture, 55(3): 766-783.)
[6] 司修洋, 梁文杰, 罗澜, 等. 2020. 甜瓜热激转录因子(Hsf)基因家族鉴定及生物信息学分析[J]. 中国蔬菜, (11): 23-32.
(Si X Y, Liang W J, Luo L, et al.2020. Identification and bioinformatics analysis of heat shock transcription factor (Hsf) gene family in melon[J]. China Vegetables, (11): 23-32.)
[7] 宋想, 王璐瑶, 富博晓, 等. 2024. 高等植物启动子元件鉴定与合成研究进展[J]. 植物学报, 59(5): 691-708.
(Song X, Wang L Y, Fu B X, et al.2024. Advances in identification and synthesis of promoter elements in higher plants[J]. Chinese Bulletin of Botany, 59(5): 691-708.)
[8] 田尉婧, 殷学仁, 李鲜, 等. 2017. 热激转录因子调控植物逆境响应研究进展[J]. 园艺学报, 44(1): 179-192.
(Tian Y J, Yin X R, Li X, et al.2017. Regulation of stress responses by heat stress transcription factors (Hsfs) in plants[J]. Acta Horticulturae Sinica, 44(1): 179-192.)
[9] 徐坚, 王燕, 陈先知, 等. 2014. 大白菜热激转录因子基因家族鉴定及表达分析[J]. 核农学报, 28(4): 586-596.
(Xu J, Wang Y, Chen X Z, et al.2014. Genome-wide identification and analysis of heat shock factors family in Chinese cabbage[J]. Journal of Nuclear Agricultural Sciences, 28(4): 586-596.)
[10] 赵杨, 杨永青, 丁杨林, 等. 2024. 植物非生物逆境学科发展综述[J]. 植物生理学报, 60(2): 248-270.
(Zhao Y, Yang Y Q, Ding Y L,et al.2024. Plant abiotic stress biology: A decade update[J]. Plant Physiology Journal, 60(2): 248-270.)
[11] Chao J T, Li Z Y, Sun Y H, et al.2021. MG2C: A user-friendly online tool for drawing genetic maps[J]. Molecular Horticulture, 1(1): 16.
[12] Chen C J, Wu Y, Li J W, et al.2023. TBtools-Ⅱ: A "one for all, all for one" bioinformatics platform for biological big-data mining[J]. Molecular Plant, 16(11): 1733-1742.
[13] Cheng F, Wu J, Fang L, et al.2012. Syntenic gene analysis between Brassica rapa and other Brassicaceae species[J]. Frontiers in Plant Science, 3: 198.
[14] Chung E, Kim K M, Lee J H.2013. Genome-wide analysis and molecular characterization of heat shock transcription factor family in Glycine max[J]. Journal of Genetics and Genomics, 40(3): 127-135.
[15] Clarke S, Cristescu S, Miersch O, et al.2009. Jasmonates act with salicylic acid to confer basal thermotolerance in Arabidopsis thaliana[J]. New Phytologist, 182(1): 175-187.
[16] Finkelstein R.2013. Abscisic acid synthesis and response[J]. The Arabidopsis Book, 11: e0166.
[17] Gai W X, Yang F, Ali M, et al.2023. Pepper heat shock transcription factor A1d contributes to seed thermotolerance and germination vigor[J]. Scientia Horticulturae,311: 111786.
[18] Guo J K, Wu J, Ji Q, et al.2008. Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis[J]. Journal of Genetics Genomics, 35(2): 105-118.
[19] Guo M, Lu J P, Zhai Y F, et al.2015. Genome-wide analysis, expression profile of heat shock factor gene family (CaHsfs) and characterisation of CaHsfA2 in pepper (Capsicum annuum L.)[J]. BMC Plant Biology, 15: 151.
[20] Jiang D, Li G G, Chen G J, et al.2021. Genome-wide identification and expression profiling of 2OGD superfamily genes from three Brassica plants[J]. Genes, 12(9), 1399.
[21] Jiao S Z, Guo C, Yao W K, et al.2022. An Amur grape VaHsfC1 is involved in multiple abiotic stresses[J]. Scientia Horticulturae, 295: 110785.
[22] Larkin M A, Blackshields G, Brown N P, et al.2007. Clustal W and Clustal X version 2.0[J].?Bioinformatics, 23(21): 2947-2948.
[23] Lei S K, Li G G, Jiang D, et al.2024. The genome-wide identification of the R2R3-MYB gene family in Chinese flowering cabbage and the characterization of its response to Pectobacterium carotovorum infection[J]. Horticulturae, 10(4): 325.
[24] Li G G, Jiang D, Wang J T, et al.2023. A high-continuity genome assembly of Chinese flowering cabbage (Brassica rapa var. parachinensis) provides new insights into Brassica genome structure evolution[J]. Plants, 12(13), 2498.
[25] Lin Y X, Jiang H Y, Chu Z X, et al.2011. Genome-wide identification, classification and analysis of heat shock transcription factor family in maize[J]. BMC genomics, 12(1): 76.
[26] Liu G T, Chai F M, Wang Y, et al.2018. Genome-wide identification and classification of Hsf family in grape, and their transcriptional analysis under heat acclimation and heat stress[J]. Horticultural Plant Journal, 4(4): 133-143.
[27] Lohani N, Golicz A A, Singh M B, et al.2019. Genome-wide analysis of the Hsf gene family in Brassica oleracea and a comparative analysis of the Hsf gene family in B. oleracea, B. rapa and B. napus[J]. Functional & Integrative Genomics, 19(3): 515-531.
[28] Nie G, Zhou J, Jiang Y, et al.2022. Transcriptome characterization of candidate genes for heat tolerance in perennial ryegrass after exogenous methyl jasmonate application[J]. BMC Plant Biology, 22(1): 68.
[29] Nover L, Bharti K, Döring P, et al.2001. Arabidopsis and the heat stress transcription factor world: How many heat stress transcription factors do we need?[J]. Cell Stress & Chaperones, 6(3): 177-189.
[30] Ohama N, Sato H, Shinozaki K, et al.2017. Transcriptional regulatory network of plant heat stress response[J]. Trends in Plant Science, 22(1): 53-65.
[31] Pei Q Y, Yu T, Wu T, et al.2021. Comprehensive identification and analyses of the Hsf gene family in the whole-genome of three Apiaceae species[J]. Horticultural Plant Journal, 7(5): 457-468.
[32] Scharf K D, Berberich T, Ebersberger I, et al.2012. The plant heat stress transcription factor (Hsf) family: Structure, function and evolution[J]. Biochimica et Biophysica Acta, 1819(2): 104-119.
[33] Scharf K D, Rose S, Zott W, et al.1990. Three tomato genes code for heat stress transcription factors with a region of remarkable homology to the DNA-binding domain of the yeast HSF[J]. The EMBO Journal, 9(13) : 4495-4501.
[34] Snyman M, Cronje M J.2008. Modulation of heat shock factors accompanies salicylic acid-mediated potentiation of Hsp70 in tomato seedlings[J]. Journal of Experimental Botany, 59(8): 2125-2132.
[35] Song X M, Liu G F, Duan W K, et al.2014. Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Chinese cabbage[J]. Molecular?Genetics?and?Genomics, 289(4): 541-551.
[36] Tamura K, Stecher G, Kumar S.2021. MEGA11: Molecular evolutionary genetics analysis version 11[J]. Molecular Biology and Evolution, 38(7): 3022-3027.
[37] Wang W J, Chen Q, Singh P K, et al.2020. CRISPR/Cas9 edited HSFA6a and HSFA6b of Arabidopsis thaliana offers ABA and osmotic stress insensitivity by modulation of ROS homeostasis[J]. Plant Signaling & Behavior, 15(12): 1816321.
[38] Wang Y, Zhou Y, Wang R, et al.2022. Ethylene response factor LlERF110 mediates heat stress response via regulation of LlHsfA3A expression and interaction with LlHsfA2 in lilies (Lilium longiflorum)[J]. International Journal of Molecular Sciences, 23(24): 16135.
[39] Wang Y D, Song S W, Hao Y W, et al.2023. Role of BraRGL1 in regulation of Brassica rapa bolting and flowering[J]. Horticulture Research, 10(8): uhad119.
[40] Yu X Y, Yao Y, Hong Y H, et al.2019. Differential expression of the Hsf family in cassava under biotic and abiotic stresses[J]. Genome, 62(8): 563-569.
[41] Zhou S J, Zhang P, Jing Z G, et al.2013. Genome-wide identification and analysis of heat shock transcription factor family in cucumber (Cucumis sativus L.)[J]. Plant Omics Journal, 6(6): 449-455.
[42] Zhu X, Huang C, Zhang L, et al.2017. Systematic analysis of Hsf family genes in the Brassica napus genome reveals novel responses to heat, drought and high CO2 stresses[J]. Frontiers in Plant Science, 8: 1174. |
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