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Genome-wide analysis of auxin response factor (ARF) gene family from tomato and analysis of their role in flower and fruit development

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Abstract

Auxin response transcription factors have been widely implicated in auxin-mediated responses during various developmental processes ranging from root and shoot development to flower and fruit development in plants. In order to use them for improvement of agronomic traits related to fruit, we need to have better understanding of their role during fruit development. In this study, 17 SlARF genes have been identified from tomato (Solanum lycopersicum), using various publically available tomato EST databases. Phylogenetic analysis of the 23 AtARF and 17 SlARF proteins results in formation of three major classes and a total of 14 sister pairs, including seven SlARF–AtARF, four SlARF–SlARF and three AtARF–AtARF sister pairs, providing insights into various orthologous relationships between AtARFs and SlARFs. Further, search for orthologs of these SlARFs resulted in identification of nine, ten, four and three ARF genes from potato, tobacco, N. benthemiana and pepper, respectively. A phylogenetic analysis of these genes, along with their orthologs from Solanaceae species, suggests the presence of a common set of the ARF genes in this family. Comparison of the expression of these SlARF genes in wild type and rin mutant provides an insight into their role during different stages of flower and fruit development. This study suggests that ARF genes may play diverse role during flower and fruit development. Comprehensive data generated here will provide a platform for identification of ARF genes and elucidation of their function during reproductive development stages in Solanaceae in general and fruit development in tomato, in particular.

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Acknowledgments

This work was financially supported by grants received from the Department of Biotechnology, Government of India. RK acknowledges CSIR for the fellowship granted during his tenure as a research fellow. Authors also acknowledge use of the draft tomato genome sequence, which was generated by the International Tomato Genome Sequencing Consortium (http://solgenomics.net/tomato/).

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Authors and Affiliations

  1. Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India

    Rahul Kumar, Akhilesh K. Tyagi & Arun K. Sharma

  2. National Institute of Plant Genome Research, New Delhi, 110067, India

    Akhilesh K. Tyagi

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  1. Rahul Kumar
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  2. Akhilesh K. Tyagi
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Correspondence to Arun K. Sharma.

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Communicated by A. Schnittger.

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List of primers used for QPCR analysis (XLSX 10 kb)

Amino acid sequence comparison between the predicted full-length auxin response factor (SlARF) genes (XLS 32 kb)

438_2011_602_MOESM3_ESM.doc

Multiple alignment profile of full SlARF proteins obtained with the ClustalX program. All the sequences show high level of amino acids conservation. Gaps (marked with dashes) have been introduced to maximize the alignments (DOC 1074 kb)

Protein sequences of ARF family genes in tomato and other Solanaceae members (DOC 54 kb)

438_2011_602_MOESM5_ESM.xls

Summary and taxonomic hierarchy of conserved motifs identified from SlARF proteins. MEME Suite version 4.0.0 (Optimum width 6-200 AA; Any number of repetitions; Maximum number of motifs 25) was used to identify conserved motifs in SlARFs. BLAST search was performed in NCBI database, using conserved motif sequences as probes, to find homologous sequences from other plants and non-plant organisms to study taxonomic hierarchy of these motifs. Comparison of motifs in other orthologous ARF proteins of Arabidopsis and other Solanaceae members has also been represented (XLS 155 kb)

438_2011_602_MOESM6_ESM.ppt

Phylogenetic analysis of tomato ARF proteins. The unrooted tree was generated using the ClustalX program by neighbor-joining method and viewed in FigTree v1.2.2. Scale bar represents 0.1 amino acid substitutions per site (PPT 105 kb)

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Kumar, R., Tyagi, A.K. & Sharma, A.K. Genome-wide analysis of auxin response factor (ARF) gene family from tomato and analysis of their role in flower and fruit development. Mol Genet Genomics 285, 245–260 (2011). https://doi.org/10.1007/s00438-011-0602-7

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