中国农业科学 ›› 2018, Vol. 51 ›› Issue (2): 327-340.doi: 10.3864/j.issn.0578-1752.2018.02.012

• 园艺 • 上一篇    下一篇

梨全基因组生长素反应因子(ARF)基因家族鉴定及表达分析

欧春青,姜淑苓,王斐,赵亚楠   

  1. 中国农业科学院果树研究所/农业部园艺作物种质资源利用重点实验室,辽宁兴城 125199
  • 收稿日期:2017-06-26 出版日期:2018-01-16 发布日期:2018-01-16
  • 通讯作者: 姜淑苓,E-mail:jshling@163.com
  • 作者简介:欧春青,E-mail:ochunqing@163.com
  • 基金资助:
    国家科技支撑计划(2013D02B01,2013BAD01B04-23)、中国农业科学院科技创新工程(CAAS-ASTIP-2016-RIP)、中央级公益性科研院所基本科研业务费专项(Y2016CG19 1610032012006)、辽宁省果树产业技术体系专项(LNGSCYTX-15-X)

Genome-Wide Identification and Expression Analysis of Auxin Response Factor (ARF) Gene Family in Pear

OU ChunQing, JIANG ShuLing, WANG Fei, ZHAO YaNan   

  1. Institute of Pomology, Chinese Academy of Agricultural Sciences/Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture, Xingcheng 125100, Liaoning
  • Received:2017-06-26 Online:2018-01-16 Published:2018-01-16

摘要: 【目的】明确梨ARF转录因子在梨基因组中的数量、结构和组织表达差异,为揭示ARF转录因子在梨树生长素信号途径及在矮生梨生长发育中的作用奠定理论基础。【方法】根据文献报道的苹果、拟南芥等植物中的ARF转录因子基因,利用BLAST软件鉴定梨基因组中的ARF。采用SMART、PROSITE、WebLogo 3、DNAMAN 5.0、MEME、GSDS 2.0和MEGA 5.1等软件对其蛋白和基因序列进行生物信息学分析。采用qPCR方法检测梨ARF在矮生梨‘中矮1号’不同组织器官及3个不同生长势梨品种木质部和韧皮部中的表达情况。【结果】鉴定得到31个梨ARF,所有PbARF蛋白均含有1个Auxin_resp结构域和1个B3结构域,除PbARF11、12、24、25和26外,其他序列的C末端还存在一个PB1(AUX_IAA)结构域。保守元件分析表明,PbARF基因家族包含15个保守元件,并非每个蛋白均含有所有保守元件。分组鉴定和进化树分析结果显示,PbARF蛋白可以被分为4组。基因结构分析表明,PbARF基因家族成员由2—15个外显子组成,基因结构进化高度保守。qPCR结果显示,所有PbARF在‘中矮1号’根、韧皮部、木质部、叶、花和果实中均有表达,表达模式各有不同,PbARF29在3个梨品种韧皮部中的表达表现出植株越矮表达量越高的趋势,PbARF16、17、18、27等4个基因在3个梨品种木质部中的表达表现为植株越矮表达量越低的趋势。【结论】梨基因组中含有31个ARF基因家族成员;所有PbARF蛋白均含有Auxin_resp和B3两个高度保守的结构域;PbARF结构进化高度保守;所有PbARF在‘中矮1号’不同组织器官、基砧杜梨根系及3个梨品种的木质部和韧皮部中均有表达,其中,PbARF2916、17、18、27等5个基因的表达可能与梨树植株的高矮有关。

关键词: 梨, ARF, 转录因子, 生物信息学, 基因表达

Abstract: 【Objective】The objectives of this research are to identify the auxin response factor (ARF) family genes from pear (Pyrus bretschneideri) genome, to know the profile of ARF family such as gene number, gene structure and tissue expression in pear, and to provide theoretical basis for revealing what roles the ARF play in auxin signaling pathway and in growth and development of dwarf pear.【Method】ARF genes in pear genome were identified by BLAST software based on ARF genes from apple and Arabidopsis. SMART, PROSITE, WebLogo 3, DNAMAN 5, MEME, GSDS 2 and MEGA 5.1 software were used for bioinformatics analysis of ARF protein and gene sequences. The qPCR method was used to detect the relative expression of ARF genes in different tissues of dwarf pear ‘Zhongai 1’ and in xylem and phloem of 3 pear cultivars with different growth vigor.【Result】Total of 31 ARF genes were identified from pear genome. All the PbARFs contain two domains of Auxin_resp and B3, and except for PbARF11, 12, 24, 25 and 26, the rest also contain a PB1 domain. Conservative motif analysis result showed that there are 15 motifs in PbARFs, but not every PbARF protein contains all the motifs. The PbARFs were divided into four classes based on phylogenetic analysis. Gene structure analysis result showed that there are 2-15 exons in PbARFs, The gene structure of PbARF is high conservative. The qPCR result showed that all the PbARF genes were expressed in the root, phloem, xylem, leaf, flower and fruit of ‘Zhongai 1’ pear and the expression pattern was various. The relative expression of PbARF29 in the phloem of 3 pear cultivars showed that the more dwarf the plant, the higher the expression, and the relative expression of PbARF16, 17, 18, 27 in the xylem of 3 pear cultivars showed that the more dwarf the plant, the lower the expression.【Conclusion】Auxin response factor family in pear contains 31 genes. All the 31 PbARF proteins contain both of Auxin_resp and B3 conservative domains, and were divided into four classes. The gene structure of PbARF is high conservative. All the 31 PbARFs were expressed in different tissues of ‘Zhongai 1’, root of rootstock Pyrus betulifolia and in phloem and xylem of 3 cultivars. Thereinto, the expression of PbARF29, 16, 17, 18, 27 may be relevant to pear plant height.

Key words: pear, ARF, transcription factor, bioinformatics, gene expression