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

• Published in: Molecular genetics and genomics : MGG 2011-03, Vol.285 (3), p.245-260
• Main Authors: Kumar, Rahul, Tyagi, Akhilesh K, Sharma, Arun K
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Animal Genetics and Genomics; ARF gene; Auxin; Base Sequence; Biochemistry; Biomedical and Life Sciences; Cell division; Chromosome Mapping; Cluster Analysis; Computational Biology; Conserved Sequence - genetics; Flowers - genetics; Flowers - growth & development; Fruit - genetics; Fruit - growth & development; Genes; Genome-Wide Association Study; Genomes; Genomics; Human Genetics; Indoleacetic Acids - metabolism; Indoleacetic Acids - pharmacology; Life Sciences; Lycopersicon esculentum; Lycopersicon esculentum - drug effects; Lycopersicon esculentum - genetics; Lycopersicon esculentum - growth & development; Microbial Genetics and Genomics; Molecular Sequence Data; Multigene Family - drug effects; Multigene Family - genetics; Original Paper; Phylogenetic analysis; Phylogenetics; Phylogeny; Plant Genetics and Genomics; Polymerase Chain Reaction; QPCR; rin Mutant; Sequence Analysis, DNA; Solanaceae; Solanum; Solanum tuberosum; Species Specificity; tomatoes; Transcription factors; Transcription Factors - classification; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 1617-4615; 1617-4623
• DOI: 10.1007/s00438-011-0602-7

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.