单叶蔷薇GRAS转录因子家族鉴定及表达分析

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

生物技术通报 ›› 2025, Vol. 41 ›› Issue (1): 210-220.doi: 10.13560/j.cnki.biotech.bull.1985.2024-0507

单叶蔷薇GRAS转录因子家族鉴定及表达分析

孔青洋(), 张晓龙, 李娜, 张晨洁, 张雪云, 于超, 张启翔, 罗乐()

北京林业大学园林学院城乡生态环境北京实验室花卉种质创新与分子育种北京市重点实验室教育部园林环境工程研究中心林木花卉遗传育种教育部重点实验室林木资源高效生产全国重点实验室国家花卉工程技术研究中心，北京 100083

收稿日期:2024-05-29 出版日期:2025-01-26 发布日期:2025-01-22
通讯作者: 罗乐，男，博士，教授，研究方向：园林植物遗传育种；E-mail: luolebjfu@163.com
作者简介:孔青洋，男，硕士，研究方向：园林植物遗传育种；E-mail: kongqingyangd@163.com
基金资助:
国家重点研发计划(2023YFD1200105);国家重点研发计划(2019YFD1001001);中央高校基本科研业务费专项资金(QNTD202306);国家自然科学基金项目(32071820)

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

KONG Qing-yang(), ZHANG Xiao-long, LI Na, ZHANG Chen-jie, ZHANG Xue-yun, YU Chao, ZHANG Qi-xiang, LUO Le()

School of Landscape Architecture, Beijing Forestry University, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, State Key Laboratory of Efficient Production of Forest Resources, National Engineering Research Center for Floriculture, Beijing 100083

Received:2024-05-29 Published:2025-01-26 Online:2025-01-22

摘要/Abstract

摘要：

【目的】对单叶蔷薇（Rosa persica）GRAS基因家族成员进行鉴定及功能分析，为单叶蔷薇GRAS基因家族功能研究及育种应用奠定理论基础。【方法】以单叶蔷薇基因组为研究对象，对单叶蔷薇GRAS基因家族进行成员鉴定、结构分析、进化分析、顺式作用元件分析、GRAS蛋白二级结构、三级结构预测，结合转录组对组织部位、不同水平干旱和低温胁迫环境中基因表达进行分析。【结果】鉴定出42个GRAS基因家族成员，分布在 7条不同的染色体上；42个RbGRAS基因可分为9个亚族；基因结构分析表明RbGRAS基因具有保守的N端，而C端在结构上较多变；对基因家族成员共线性分析显示，有4对片段重复基因和4对串联重复基因；顺式作用元件分析发现，单叶蔷薇GRAS基因家族中含有丰富的激素应答元件和胁迫响应元件；RbGRAS蛋白二级预测结构以α-螺旋以及无规则卷曲为主，三级预测结果显示蛋白组成相似；组织特异性表达分析结果显示GRAS基因主要在根系和茎组织中表达，在花中表达量较低；RbGRAS基因在干旱和低温胁迫中也存在基因特异性表达。【结论】鉴定得到42个RbGRAS家族成员，均含有逆境相关作用元件，RbGRAS27和RbGRAS41分别对干旱和低温胁迫积极响应。

关键词: 单叶蔷薇, GRAS基因家族, 生物信息学分析, 表达分析, 干旱胁迫, 低温胁迫

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

孔青洋, 张晓龙, 李娜, 张晨洁, 张雪云, 于超, 张启翔, 罗乐. 单叶蔷薇GRAS转录因子家族鉴定及表达分析[J]. 生物技术通报, 2025, 41(1): 210-220.

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.

图/表 8

图1 单叶蔷薇与拟南芥 GRAS 家族系统发育树分析

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

图2 单叶蔷薇 GRAS 家族蛋白的系统进化、保守基序及基因结构分析刻度尺分别表示蛋白序列长度（aa）和基因长度（bp）

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

图3 单叶蔷薇 42个 GRAS 基因在染色体的分布红线表示串联基因

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

图4 单叶蔷薇GRAS 基因家族内部共线性分析、单叶蔷薇与拟南芥 GRAS 基因家族共线性分析 A：单叶蔷薇GRAS基因家族共线性分析；B：单叶蔷薇与拟南芥GRAS基因家族共线性分析

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

图5 单叶蔷薇 GRAS 基因启动子顺式作用元件分布

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

图6 单叶蔷薇GRAS基因启动子顺式作用元件数量统计 TC-rich repeats：防御和应激反应元件；ABRE：脱落酸反应元件；ARE：厌氧诱导调节元件；TGACG-motif/CGTCA-motif：茉莉酸甲酯反应元件；MBS：干旱诱导元件；TATC-box：赤霉素反应元件；LTR：低温响应元件；TCA-element：水杨酸反应元件；WUN-motif：创伤响应元件

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

图7 单叶蔷薇42个GRAS蛋白的三级结构

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

图8 单叶蔷薇不同组织及不同胁迫中GRAS基因表达热图 Root、stem、leaf、flower、fruit：非胁迫下根、茎、叶、花和果实；CKr、CKl：干旱对照组根和叶；LDr、LDl：轻度干旱的根和叶；SDr、SDl：重度干旱的根和叶；G9-G4：野外环境下的2021年9月-2022年4月的叶；J9-J4：野外环境下2021年9月-2022年4月的茎

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

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