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Identification, isolation and expression analysis of auxin response factor (ARF) genes in Solanum lycopersicum

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Abstract

Auxin response factors (ARFs) encode transcriptional factors that bind specifically to the TGTCTC-containing auxin response elements found in the promoters of primary/early auxin response genes that regulate plant development. In this study, investigation of the tomato genome revealed 21 putative functional ARF genes (SlARFs), a number comparable to that found in Arabidopsis (23) and rice (25). The full cDNA sequences of 15 novel SlARFs were isolated and delineated by sequencing of PCR products. A comprehensive genome-wide analysis of this gene family is presented, including the gene structures, chromosome locations, phylogeny, and conserved motifs. In addition, a comparative analysis between ARF family genes in tomato and maize was performed. A phylogenetic tree generated from alignments of the full-length protein sequences of 21 OsARFs, 23 AtARFs, 31 ZmARFs, and 21 SlARFs revealed that these ARFs were clustered into four major groups. However, we could not find homologous genes in rice, maize, or tomato with AtARF12-15 and AtARF20-23. The expression patterns of tomato ARF genes were analyzed by quantitative real-time PCR. Our comparative analysis will help to define possible functions for many of these newly isolated ARF-family genes in plant development.

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Abbreviations

ARF:

Auxin response factor

SlARF:

Solanum lycopersicum auxin response factor

ZmARF:

Zea mays auxin response factor

AtARF:

Arabidopsis thaliana auxin response factor

OsARF:

Oryza sativa auxin response factor

qRT-PCR:

quantitative Real-time PCR

SOL:

The International Solanaceae Project

PCR:

Polymerase chain reaction

BlASTN:

Search a nucleotide database using a nucleotide query

MaizeGDB:

The Maize Genetics and Genomics Database

TBLASTN:

Search translated nucleotide database using a protein query

ORF:

Open reading frame

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Acknowledgments

This work was supported by the State Key Basic Research and Development Plan of China (2009CB119000), the National Natural Science Foundation of China (30771470 and 31071804) and the Zhejiang Province Research Project of China (2009C32025).

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Authors and Affiliations

  1. Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Hangzhou, 310058, People’s Republic of China

    Jian Wu, Feiyan Wang, Lin Cheng, Fuling Kong, Zhen Peng, Songyu Liu, Xiaolin Yu & Gang Lu

  2. Department of Horticulture, Zhejiang University, Hangzhou, 310058, People’s Republic of China

    Jian Wu, Feiyan Wang, Lin Cheng, Fuling Kong, Zhen Peng, Songyu Liu, Xiaolin Yu & Gang Lu

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  1. Jian Wu
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  2. Feiyan Wang
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  5. Zhen Peng
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  6. Songyu Liu
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  7. Xiaolin Yu
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  8. Gang Lu
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Correspondence to Gang Lu.

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Communicated by C. Quiros.

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Wu, J., Wang, F., Cheng, L. et al. Identification, isolation and expression analysis of auxin response factor (ARF) genes in Solanum lycopersicum . Plant Cell Rep 30, 2059–2073 (2011). https://doi.org/10.1007/s00299-011-1113-z

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  • DOI: https://doi.org/10.1007/s00299-011-1113-z

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