Identification and Expression Analysis of GRAS Transcription Factor Family in Rosa persica

doi:10.13560/j.cnki.biotech.bull.1985.2024-0507

Abstract

Abstract:

【Objective】Identification and functional analysis of members of the GRAS gene family in Rosa persica, laying a theoretical foundation for functional research and breeding applications of the GRAS gene family in Rosa persica. 【Method】Using the genome of Rosa persica as the research object, the member identification, structural analysis, evolutionary analysis, cis-acting element analysis, prediction of secondary and tertiary structures of GRAS protein were carried out on the GRAS gene family of Rosa persica. Combined with transcriptome analysis, gene expression analysis was conducted in tissue locations, different levels of drought and low temperature stress environments.【Result】The 42 members of the GRAS gene family were identified, distributed on 7 different chromosomes. The 42 RbGRAS genes were divided into 9 subfamilies. Gene structure analysis showed that the RbGRAS gene had a conserved N-terminus, while the C-terminus had more structural variation. The collinearity analysis of gene family members showed 4 pairs of segment repeat genes and 4 pairs of tandem repeat genes. Analysis of cis-acting elements revealed that the GRAS gene family of R. persica contained abundant hormone responsive elements and stress responsive elements. The secondary prediction structure of RbGRAS protein was mainly alpha helix and irregular curl, while the tertiary prediction results showed similar protein composition. The results of tissue-specific expression analysis showed that the GRAS gene was mainly expressed in the root and stem tissues, with lower expression levels in flowers. The RbGRAS gene also showed gene specific expression under drought and low temperature stress.【Conclusion】The 42 members of the RbGRAS family are identified, all contain stress-related elements. RbGRAS27 and RbGRAS41 respond positively to drought and low temperature stress, respectively.

Key words: Rosa persica, GRAS gene family, bioinformatics analysis, expression analysis, drought stress, low temperature stress

KONG Qing-yang, ZHANG Xiao-long, LI Na, ZHANG Chen-jie, ZHANG Xue-yun, YU Chao, ZHANG Qi-xiang, LUO Le. Identification and Expression Analysis of GRAS Transcription Factor Family in Rosa persica[J]. Biotechnology Bulletin, 2025, 41(1): 210-220.

Figures/Tables 8

Fig. 1 Phylogenetic tree analysis of the GRAS family of Rosa persica（Rb）and A. thaliana（AT）

Fig. 2 Phylogeny, conserved motifs and gene structure analysis of GRAS family proteins in R. persica The scale indicates protein sequence length（aa）and gene length（bp）, respectively

Fig. 3 Distribution of 42 GRAS genes in chromosomes of R. persica Red line indicates the tandem gene

Fig. 4 Internal collinearity analysis of GRAS gene family of R. persica and the collinearity analysis of GRAS gene family R. persica and Arabidopsis thaliana A: Collinearity analysis of the GRAS gene family in R. persica. B: Analysis of collinearity between the GRAS gene family of R. persica and Arabidopsis thaliana

Fig. 5 Distribution of cis-acting elements of GRAS gene promoter in R. persica

Fig. 6 Statistics on the number of cis-acting elements in the GRAS gene promoter of R. persica TC-rich repeats: Defense and stress response elements; ABRE: abscisic acid response element; ARE: anaerobic induction regulatory element; TGACG-motif/CGTCA-motif: methyl jasmonate response element; MBS: drought-induced element; TATC-box: gibberellin response element; LTR: low temperature response element; TCA-element: salicylic acid response element; WUN-motif: wound-responsive element

Fig. 7 Tertiary structure of 42 GRAS proteins in R. persica

Fig. 8 Heatmap of GRAS gene expression in different tissues of R. persica under different stresses Root, stem, leaf, flower, fruit: Non-stressed roots, stems, leaves, flowers and fruits; CKr, CKl: control group roots and leaves; LDr, LDl: roots and leaves under mild drought stress; SDr, SDl: roots and leaves under severe drought stress. G9-G4: Leaves from September 2021 to April 2022 in the wild environment. J9-J4: Stems from September 2021 to April 2022 in the wild environment

References 38

[1]	新疆植物志编辑委员会. 新疆植物志-第二卷, 第二分册-小檗科—蔷薇科[M]. 乌鲁木齐: 新疆科技卫生出版社, 1995.
	Editorial Committee for the Flora of Xinjiang. Flora xinjiangensis - Volume two, part two - Berberidaceae to Rosaceae[M]. Xinjiang Science, Technology and Public Health Press, 1995.
[2]	惠俊爱, 张霞, 王绍明. 新疆野生单叶蔷薇生物学特性分析[J]. 山东林业科技, 2013, 43(4): 61-63.
	Hui JA, Zhang X, Wang SM. Analysis of biological characteristics of wild Hulthemia berberifolia(pall.)dumort in Xinjiang[J]. J Shandong For Sci Technol, 2013, 43(4): 61-63.
[3]	中国科学院中国植物志编辑委员会. 中国植物志-第七十四卷[M]. 北京: 科学出版社, 1985: 370-371.
	Committee on the Flora of China, Chinese Academy of Sciences. Flora of China(37 vols)[M]. Beijing: Science Press, 1985: 370-371.
[4]	丛者福. 新疆野蔷薇果的研究[J]. 干旱区资源与环境, 1996, 10(4): 100-102.
	Cong ZF. Study on the fruit of wild rose in Xinjiang[J]. Arid Land Resour Environ, 1996, 10(4): 100-102.
[5]	范春国. 单叶蔷薇耐旱关键转录因子挖掘与功能初步验证[D]. 南京: 南京农业大学, 2021.
	Fan CG. Mining and functional verification of key transcription factors of drought tolerance in Rosa persica[D]. Nanjing: Nanjing Agricultural University, 2021.
[6]	冯策婷, 江律, 刘鑫颖, 等. 单叶蔷薇NAC基因家族鉴定及干旱胁迫响应分析[J]. 生物技术通报, 2023, 39(11): 283-296. doi: 10.13560/j.cnki.biotech.bull.1985.2023-0531
	Feng CT, Jiang L, Liu XY, et al. Identification of the NAC gene family in Rosa persica and response analysis under drought stress[J]. Biotechnol Bull, 2023, 39(11): 283-296.
[7]	Zhuang YY, Zhou LJ, Geng LF, et al. Genome-wide identification of the bHLH transcription factor family in Rosa persica and response to low-temperature stress[J]. PeerJ, 2024, 12: e16568.
[8]	Moradkhani S, Rezaei-Dehghanzadeh T, Nili-Ahmadabadi A. Rosa persica hydroalcoholic extract improves cadmium-hepatotoxicity by modulating oxidative damage and tumor necrosis factor-alpha status[J]. Environ Sci Pollut Res Int, 2020, 27(25): 31259-31268.
[9]	欧哲, 杨宇, 冯策婷, 等. 单叶蔷薇远缘杂交中花粉管生长的荧光显微观察[J]. 东北农业大学学报, 2022, 53(10): 18-26.
	Ou Z, Yang Y, Feng CT, et al. Fluorescent microscope observation on growth of pollen tube on distant hybridization in Rosa persica[J]. J Northeast Agric Univ, 2022, 53(10): 18-26.
[10]	Pysh LD, Wysocka-Diller JW, Camilleri C, et al. The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes[J]. Plant J, 1999, 18(1): 111-119. pmid: 10341448
[11]	Sun XL, Xue B, Jones WT, et al. A functionally required unfoldome from the plant Kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development[J]. Plant Mol Biol, 2011, 77(3): 205-223. doi: 10.1007/s11103-011-9803-z pmid: 21732203
[12]	Khan Y, Xiong Z, Zhang H, et al. Expression and roles of GRAS gene family in plant growth, signal transduction, biotic and abiotic stress resistance and symbiosis formation-a review[J]. Plant Biol, 2022, 24(3): 404-416.
[13]	Tian CG, Wan P, Sun SH, et al. Genome-wide analysis of the GRAS gene family in rice and Arabidopsis[J]. Plant Mol Biol, 2004, 54(4): 519-532.
[14]	Li Z, Tu QC, Lyu XG, et al. GmSTF accumulation mediated by DELLA protein GmRGAs contributes to coordinating light and gibberellin signaling to reduce plant height in soybean[J]. Crop J, 2024, 12(2): 432-442. doi: 10.1016/j.cj.2024.01.013
[15]	Helariutta Y, Fukaki H, Wysocka-Diller J, et al. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling[J]. Cell, 2000, 101(5): 555-567. doi: 10.1016/s0092-8674(00)80865-x pmid: 10850497
[16]	Wang ZM, Wong DCJ, Wang Y, et al. GRAS-domain transcription factor PAT1 regulates jasmonic acid biosynthesis in grape cold stress response[J]. Plant Physiol, 2021, 186(3): 1660-1678. doi: 10.1093/plphys/kiab142 pmid: 33752238
[17]	Zhang S, Li XW, Fan SD, et al. Overexpression of HcSCL13, a Halostachys caspica GRAS transcription factor, enhances plant growth and salt stress tolerance in transgenic Arabidopsis[J]. Plant Physiol Biochem, 2020, 151: 243-254.
[18]	Silverstone AL, Ciampaglio CN, Sun T. The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway[J]. Plant Cell, 1998, 10(2): 155-169. doi: 10.1105/tpc.10.2.155 pmid: 9490740
[19]	Dinneny JR, Benfey PN. Plant stem cell niches: standing the test of time[J]. Cell, 2008, 132(4): 553-557. doi: 10.1016/j.cell.2008.02.001 pmid: 18295573
[20]	Han H, Yan A, Li LH, et al. A signal cascade originated from epidermis defines apical-basal patterning of Arabidopsis shoot apical meristems[J]. Nat Commun, 2020, 11(1): 1214. doi: 10.1038/s41467-020-14989-4 pmid: 32139673
[21]	Morohashi K, Minami M, Takase H, et al. Isolation and characterization of a novel GRAS gene that regulates meiosis-associated gene expression[J]. J Biol Chem, 2003, 278(23): 20865-20873. doi: 10.1074/jbc.M301712200 pmid: 12657631
[22]	孙彦琳, 于超, 罗乐. 单叶蔷薇bZIP转录因子家族鉴定与表达分析[J]. 西北农林科技大学学报: 自然科学版, 2022, 50(6): 82-92.
	Sun YL, Yu C, Luo L, et al. Identification and expression analysis of bZIP transcription factor family in Rosa persica[J]. J Northwest A F Univ Nat Sci Ed, 2022, 50(6): 82-92.
[23]	于婷婷, 李欢, 宁源生, 等. 苹果GRAS全基因组鉴定及其对生长素的响应分析[J]. 园艺学报, 2023, 50(2): 397-409. doi: 10.16420/j.issn.0513-353x.2021-1039
	Yu TT, Li H, Ning YS, et al. Genome-wide identification of GRAS gene family in apple and expression analysis of its response to auxin[J]. Acta Hortic Sin, 2023, 50(2): 397-409.
[24]	Kumari P, Gahlaut V, Kaur E, et al. Genome-wide identification of GRAS transcription factors and their potential roles in growth and development of rose(Rosa chinensis)[J]. J Plant Growth Regul, 2023, 42(3): 1505-1521.
[25]	牛义岭. 番茄GRAS基因家族生物信息学分析及部分抗性相关基因鉴定分析[D]. 哈尔滨: 东北农业大学, 2017.
	Niu YL. Bioinformatics analysis of GRAS gene family in tomato and identification of some resistance-related genes[D]. Harbin: Northeast Agricultural University, 2017.
[26]	惠俊爱, 张霞, 王绍明. 新疆野生单叶蔷薇的染色体核型分析[J]. 山东林业科技, 2013, 43(4): 58-60.
	Hui JA, Zhang X, Wang SM. Karyotype analysis of Xin Jiang wild Hulthemia berberifolia(Pall.)Dumort[J]. J Shandong For Sci Technol, 2013, 43(4): 58-60.
[27]	Shaul O. How introns enhance gene expression[J]. Int J Biochem Cell Biol, 2017, 91(Pt B): 145-155. doi: S1357-2725(17)30154-1 pmid: 28673892
[28]	Cannon SB, Mitra A, Baumgarten A, et al. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana[J]. BMC Plant Biol, 2004, 4: 10.
[29]	Wei XP, Liu LY, Liu G, et al. Methyl jasmonate promotes suberin biosynthesis by stimulating transcriptional activation of AchMYC2 on AchFHT in wound healing of kiwifruit[J]. Postharvest Biol Technol, 2024, 210: 112741.
[30]	赵曼如, 胡文忠, 于皎雪, 等. 茉莉酸甲酯对果蔬抗性、抗氧化活性及品质影响的研究进展[J]. 食品工业科技, 2020, 41(4): 328-332.
	Zhao MR, Hu WZ, Yu JX, et al. Research progress on effects of methyl jasmonate on resistance, antioxidant activity and quality of fruits and vegetables[J]. Sci Technol Food Ind, 2020, 41(4): 328-332.
[31]	Feng M, Zhang A, Nguyen V, et al. A conserved graft formation process in Norway spruce and Arabidopsis identifies the PAT gene family as central regulators of wound healing[J]. Nat Plants, 2024, 10(1): 53-65.
[32]	Rivas-San Vicente M, Plasencia J. Salicylic acid beyond defence: its role in plant growth and development[J]. J Exp Bot, 2011, 62(10): 3321-3338. doi: 10.1093/jxb/err031 pmid: 21357767
[33]	龙亚芹, 王万东, 王美存, 等. 水杨酸(SA)诱导植物对病虫害产生抗性及作用机制研究[J]. 热带农业科学, 2009, 29(12): 46-50.
	Long YQ, Wang WD, Wang MC, et al. Salicylic acid induced resistance of plants against insects and diseases and its interaction mechanism[J]. Chin J Trop Agric, 2009, 29(12): 46-50.
[34]	Incarbone M, Bradamante G, Pruckner F, et al. Salicylic acid and RNA interference mediate antiviral immunity of plant stem cells[J]. Proc Natl Acad Sci U S A, 2023, 120(42): e2302069120.
[35]	Li SL, Li XN, Wei ZH, et al. ABA-mediated modulation of elevated CO₂ on stomatal response to drought[J]. Curr Opin Plant Biol, 2020, 56: 174-180.
[36]	Zhong MS, Jiang H, Cao Y, et al. MdCER2 conferred to wax accumulation and increased drought tolerance in plants[J]. Plant Physiol Biochem, 2020, 149: 277-285.
[37]	张晓龙, 邓童, 刘学森, 等. 单叶蔷薇幼苗根系对不同潜水埋深的适应机制[J]. 生态学报, 2022, 42(15): 6137-6149.
	Zhang XL, Deng T, Liu XS, et al. Adaptability mechanism of Rosa persica seedlings root in different groundwater levels[J]. Acta Ecol Sin, 2022, 42(15): 6137-6149.
[38]	Lucas M, Swarup R, Paponov IA, et al. Short-Root regulates primary, lateral, and adventitious root development in Arabidopsis[J]. Plant Physiol, 2011, 155(1): 384-398.