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The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A

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Abstract

Completion of the whole genome sequencing of citrus enabled us to perform genome-wide identification and functional analysis of the gene families involved in agronomic traits and morphological diversity of citrus. In this study, 22 CitARF, 11 CitGH3 and 26 CitAUX/IAA genes were identified in citrus, respectively. Phylogenetic analysis revealed that all the genes of each gene family could be subdivided into three groups and showed strong evolutionary conservation. The GH3 and AUX/IAA gene families shrank and ARF gene family was highly conserved in the citrus genome after speciation from Arabidopsis thaliana. Tissue-specific expression profiles revealed that 54 genes were expressed in at least one tissue while just 5 genes including CitARF07, CitARF20, CitGH3.04, CitAUX/IAA25 and CitAUX/IAA26 with very low expression level in all tissues tested, suggesting that the CitARF, CitGH3 and CitAUX/IAA gene families played important roles in the development of citrus organs. In addition, our data found that the expression of 2 CitARF, 4 CitGH3 and 4 AUX/IAA genes was affected by IAA treatment, and 7 genes including, CitGH3.04, CitGH3.07, CitAUX/IAA03, CitAUX/IAA04, CitAUX/IAA18, CitAUX/IAA19 and CitAUX/IAA23 were related to fruitlet abscission. This study provides a foundation for future studies on elucidating the precise role of citrus ARF, GH3 and AUX/IAA genes in early steps of auxin signal transduction and open up a new opportunity to uncover the molecular mechanism underlying citrus fruitlet abscission.

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Abbreviations

ARF:

Auxin response factor

GH3:

Gretchen Hagen3

AUX/IAA:

Auxin/indole-3-acetic acid protein

AZ A:

Abscission zone A

RT-PCR:

Semi-quantitative reverse transcription polymerase chain reaction

qPCR:

Quantitative real-time PCR

DBD:

DNA-binding domain

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Acknowledgments

We thank Dr. Li Jing and Chris for critical reading of the manuscript. This work was funded by NSFC (31301743), the National Science-technology Support Plan Projects (2013BAD02B00), the Planning Subject of ‘the twelfth five-year-plan’ in National Science and Technology for the Rural Development in China (2014BAD16B00), Chongqing Application and Development Projects (cstc2013yykfB80001), and Chongqing “121” demonstrative project of science and technology support (cstc2014fazktjcsf80031).

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    Authors and Affiliations

    1. Citrus Research Institute, Chinese Academy of Agricultural Science/Southwest University, Beibei, Chongqing, 400712, China

      Rangjin Xie, Shaoping Pang, Yanyan Ma, Lie Deng, Shaolan He, Shilai Yi, Qiang Lv & Yongqiang Zheng

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    1. Rangjin Xie
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    Correspondence to Rangjin Xie.

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    Communicated by S. Hohmann.

    R. Xie and S. Pang are contributed equally to this work.

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    Xie, R., Pang, S., Ma, Y. et al. The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A. Mol Genet Genomics 290, 2089–2105 (2015). https://doi.org/10.1007/s00438-015-1063-1

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