中国农业科学 ›› 2019, Vol. 52 ›› Issue (24): 4567-4581.doi: 10.3864/j.issn.0578-1752.2019.24.011

• 园艺 • 上一篇    下一篇

GRAS家族全基因组鉴定与响应UV-B的表达模式分析

李晨,赵雪惠,王庆杰,王旭旭,肖伟,陈修德,付喜玲,李玲,李冬梅()   

  1. 山东农业大学园艺科学与工程学院/作物生物学国家重点实验室/山东果蔬优质高效生产协同创新中心,山东泰安 271018
  • 收稿日期:2019-06-11 接受日期:2019-08-03 出版日期:2019-12-16 发布日期:2020-01-15
  • 通讯作者: 李冬梅
  • 作者简介:李晨,Tel:15650453756;E-mail:15650453756@163.com。
  • 基金资助:
    国家自然科学基金(31601706);山东省自然科学基金(ZR2016CM09)

Genome Identification of PpGRAS Family and Expression Pattern Analysis of Responding to UV-B in Peach

Chen LI,XueHui ZHAO,QingJie WANG,XuXu WANG,Wei XIAO,XiuDe CHEN,XiLing Fu,Ling LI,DongMei LI()   

  1. College of Horticulture Science and Engineering, Shandong Agricultural University/State Key Laboratory of Crop Biology/Shandong Collaborative Innovation Center for Fruit & Vegetable Production with High Quality and Efficiency, Taian 271018, Shandong
  • Received:2019-06-11 Accepted:2019-08-03 Online:2019-12-16 Published:2020-01-15
  • Contact: DongMei LI

摘要:

【目的】GRAS基因家族成员在调节植物生长发育中发挥着关键作用。通过生物信息学分析GRAS在桃基因组中的分布、结构及进化,研究家族成员在不同组织中的表达特异性及其对UV-B的响应,解析GRAS基因家族的生物学功能。【方法】对设施油桃‘中油5号’(Prunus persica var. nectarina cv. Zhongyou5)补充适量UV-B(Ultraviolet-B)剂量,利用Plant TFDB数据库鉴定桃GRAS基因家族成员。采用Clustal W、MEGA6.0、ProtParam tool、MCScanX、Circos、SMART、NCBI-CDD、ExPASy、GSDS和MEME等软件构建系统进化树,绘制染色体定位图,预测蛋白的相对分子质量与等电点等理化性质等,分析GRAS基因家族成员在不同组织中的表达模式,利用qRT-PCR技术检测桃GRAS在UV-B处理下的表达情况。【结果】从桃全基因组中鉴定出48个GRAS转录因子家族基因,构建系统进化树将这48个成员分为9个亚家族,PpGRAS在桃的8条染色体上呈不均匀分布。对GRAS基因家族进行理化性质分析发现,其蛋白平均长度为590.52 aa,等电点在4.36—7.56。GRAS家族基因结构分析表明,有40个基因不含内含子,8个基因含有1个内含子。保守元件分析显示,GRAS家族包含20个保守元件,其中Motif 2和4在GRAS的家族中高度保守,同一个亚家族成员含有相同的保守元件,其可能具备相似的功能。然而,有些亚家族成员的表达模式不同,这可能与其保守基序之外的序列有关。PpGRAS在不同组织中具有不同的表达模式。叶片中PpGRAS5经UV-B处理后上调表达最显著,而有多达15个基因表达量呈现下调。果实中PpGRAS13经UV-B处理后上调表达,但有9个基因表达下调。韧皮部中,UV-B处理后有14个基因上调表达,而PpGRAS16经处理后在韧皮部中表达下调最明显。【结论】从桃基因组中共鉴定出48个GRAS基因家族成员,分布于8条染色体上;多数PpGRAS能响应UV-B处理,但在不同组织中的表达不尽相同。

关键词: 桃, GRAS基因家族, 生物信息学分析, UV-B

Abstract:

【Objective】 GRAS transcription factor family genes play a key role in the regulation of plant growth and development. The objectives of this study were to analyze the distribution, structure and evolution of GRAS in the peach genome by bioinformatics, to study the expression specificity of family members in different tissues and their responses to UV-B optical signal, and to investigate the biological function of GRAS transcription factor family genes in peach. 【Method】 The facility nectarine ‘Prunus persica var. nectarina cv. Zhongyou5 was supplemented with an appropriate dose of UV-B (Ultraviolet-B). The peach GRAS gene in the peach genome was identified by using the Plant TFDB database. Phylogenetic tree, chromosome localization, relative mass and isoelectric point and other physical and chemical properties of GRAS member were analyzed with Clustal W, MEGA6.0, ProtParam tool, MCScanX, Circos, SMART, NCBI-CDD, ExPASy, GSDS2.0, and MEME, respectively. The expression pattern of GRAS gene family in different tissues was analyzed, and the expression of some members of GRAS gene family in peach treated with UV-B was detected by real-time fluorescence quantitative PCR (qRT-PCR).【Result】48 members of GRAS transcription factor family were identified from the whole genome of the peach, and they could be divided into 9 categories by constructing a phylogenetic tree. The PpGRAS gene showed uneven distribution on 8 chromosomes of peach. The theoretical isoelectric point of the family protein was ranged from 4.36 to 7.56, and the average number of amino acids encoded was 590.52. Gene’s structure analysis showed that 40 genes contained no introns, and 8 genes contained 1 intron. Conservative elemental analysis revealed that the GRAS family contains 20 conserved elements, of which Motif 2 and Motif 4 were highly conserved in the GRAS family. Members of the same subfamily contained the same conserved elements, suggesting that members of the same subfamily might have similar functions. However, some subfamily members had different expression patterns, which might be related to sequences other than the conserved motif. The PpGRAS genes had different expression patterns in different tissues; and most of PpGRAS genes could respond to UV-B treatment, but the expression changes were different in different tissues. In leaves, PpGRAS5 was up-regulated after UV-B treatment, while up to 15 genes were down-regulated. In the fruit, PpGRAS13 was up-regulated by UV-B treatment, but 9 genes were down-regulated. In the phloem, 14 genes were up-regulated after UV-B treatment, while PpGRAS16 was most down-regulated in the phloem after treatment. 【Conclusion】A total of 48 GRAS gene family members were identified from the peach genome and distributed on 8 chromosomes; most PpGRAS genes responded to UV-B treatment, but the expression changes were different in different tissues. This study laid the foundation for further analysis of the PpGRAS family of genes in response to UV-B light signals and other potential functions.

Key words: peach, GRAS gene family, bioinformatic analysis, UV-B