Auxin response factor gene family in Brassica rapa: genomic organization, divergence, expression, and evolutionReport as inadecuate

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Molecular Genetics and Genomics

, Volume 287, Issue 10, pp 765–784

First Online: 24 August 2012Received: 11 April 2012Accepted: 03 August 2012


Completion of the sequencing of the Brassica rapa genome enabled us to undertake a genome-wide identification and functional study of the gene families related to the morphological diversity and agronomic traits of Brassica crops. In this study, we identified the auxin response factor ARF gene family, which is one of the key regulators of auxin-mediated plant growth and development in the B. rapa genome. A total of 31 ARF genes were identified in the genome. Phylogenetic and evolutionary analyses suggest that ARF genes fell into four major classes and were amplified in the B. rapa genome as a result of a recent whole genome triplication after speciation from Arabidopsis thaliana. Despite its recent hexaploid ancestry, B. rapa includes a relatively small number of ARF genes compared with the 23 members in A. thaliana, presumably due to a paralog reduction related to repetitive sequence insertion into promoter and non-coding transcribed region of the genes. Comparative genomic and mRNA sequencing analyses demonstrated that 27 of the 31 BrARF genes were transcriptionally active, and their expression was affected by either auxin treatment or floral development stage, although 4 genes were inactive, suggesting that the generation and pseudogenization of ARF members are likely to be an ongoing process. This study will provide a fundamental basis for the modification and evolution of the gene family after a polyploidy event, as well as a functional study of ARF genes in a polyploidy crop species.

KeywordsBrassica rapa Auxin response factor Genome organization mRNA sequencing Evolution Communicated by Y. Van de Peer.

J.-H. Mun and H.-J. Yu contributed equally to this work.

Electronic supplementary materialThe online version of this article doi:10.1007-s00438-012-0718-4 contains supplementary material, which is available to authorized users.

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Author: Jeong-Hwan Mun - Hee-Ju Yu - Ja Young Shin - Mijin Oh - Hyun-Ju Hwang - Hee Chung


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