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

OU ChunQing1 JIANG ShuLing1 WANG Fei1 ZHAO YaNan1

(1.Institute of Pomology, Chinese Academy of Agricultural Sciences/Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture, Xingcheng, Liaoning 125100)

【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, Web Logo 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] A total of 31 ARF genes were identified from pear genome. All the PbARFs contained two domains of Auxin_resp and B3, and except for PbARF11, 12, 24, 25 and 26, the rest also contained a PB1 domain. The conservative motif analysis result showed that there were 15 motifs in PbARFs, but not every PbARF protein contained all the motifs. The PbARFs were divided into four classes based on phylogenetic analysis. The gene structure analysis result showed that there were 2–15 exons in PbARFs. The gene structure of PbARF was 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 31PbARF proteins contain both of Auxin_resp and B3 conservative domains, and are divided into four classes. The gene structure of PbARF is high conservative. All the 31 PbARFs are 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.

【Keywords】 pear; ARF; transcription factor; bioinformatics; gene expression;

【DOI】

【Funds】 National Key Technology Research and Development Program of the Ministry of Science and Technology of China (2013D02B01, 2013BAD01B04-23) Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2016-RIP) Central Public-interest Scientific Institution Basal Research Fund of China (Y2016CG19 1610032012006) Special Project for Fruit Tree Industry Technical System of Liaoning Province, China (LNGSCYTX-15-X)

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(Translated by CHEN T)

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This Article

ISSN:0578-1752

CN: 11-1328/S

Vol 51, No. 02, Pages 327-340

January 2018

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Article Outline

Abstract

  • 0 Introduction
  • 1 Materials and methods
  • 2 Results
  • 3 Discussion
  • 4 Conclusion
  • References