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Genomewide identification and expression analysis of the ARF gene family in apple

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Abstract

Auxin response factors (ARF) are transcription factors that regulate auxin responses in plants. Although the genomewide analysis of this family has been performed in some species, little is known regarding ARF genes in apple (Malus domestica). In this study, 31 putative apple ARF genes have been identified and located within the apple genome. The phylogenetic analysis revealed that MdARFs could be divided into three subfamilies (groups I, II and III). The predicted MdARFs were distributed across 15 of 17 chromosomes with different densities. In addition, the analysis of exon–intron junctions and of the intron phase inside the predicted coding region of each candidate gene has revealed high levels of conservation within and between phylogenetic groups. Expression profile analyses of MdARF genes were performed in different tissues (root, stem, leaf, flower and fruit), and all the selected genes were expressed in at least one of the tissues that were tested, which indicated that MdARFs are involved in various aspects of physiological and developmental processes of apple. To our knowledge, this report is the first to provide a genomewide analysis of the apple ARF gene family. This study provides valuable information for understanding the classification and putative functions of the ARF signal in apple.

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Acknowledgement

This work was supported by the National Natural Science Foundation in China (Grant No. 31401822).

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Authors and Affiliations

  1. State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People’s Republic of China

    XIAO-CUI LUO, MEI-HONG SUN, HUAI-RUI SHU & SHI-ZHONG ZHANG

  2. Key Laboratory of Biology and Molecular Biology in University of Shandong, Weifang University, Weifang, Shandong, 261061, People’s Republic of China

    RUI-RUI XU

  3. Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, 271000, People’s Republic of China

    JIA-WEI WANG

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  1. XIAO-CUI LUO
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  2. MEI-HONG SUN
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  3. RUI-RUI XU
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  4. HUAI-RUI SHU
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  5. JIA-WEI WANG
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  6. SHI-ZHONG ZHANG
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Correspondence to SHI-ZHONG ZHANG.

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[Luo X.-C., Sun M.-H., Xu R.-R., Shu H.-R., Wang J.-W. and Zhang S.-Z. 2014 Genomewide identification and expression analysis of the ARF gene family in apple. J. Genet. 93, xx–xx]

Xiao-Cui Luo and Mei-Hong Sun contributed equally to this work.

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LUO, XC., SUN, MH., XU, RR. et al. Genomewide identification and expression analysis of the ARF gene family in apple. J Genet 93, 785–797 (2014). https://doi.org/10.1007/s12041-014-0462-0

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  • DOI: https://doi.org/10.1007/s12041-014-0462-0

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