Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

Haitao Li,Jing Wang,Kede Liu,Graham J King,Qinghua Zhang,Bo Wang

doi:10.1186/s12870-017-1165-5

Haitao Li, Jing Wang + Show 4 more

Open Access

https://doi.org/10.1186/s12870-017-1165-5

Copy DOI

Abstract

BackgroundAuxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development. Although the Aux/IAA gene family has been identified in many plants, within allotetraploid Brassica napus little is known.ResultsIn this study, a total of 119 Aux/IAA genes were found in the genome of B. napus. They were distributed non-randomly across all 19 chromosomes and other non-anchored random scaffolds, with a symmetric distribution in the A and C subgenomes. Evolutionary and comparative analysis revealed that 111 (94.1%) B. napus Aux/IAA genes were multiplied due to ancestral Brassica genome triplication and recent allotetraploidy from B. rapa and B. oleracea. Phylogenetic analysis indicated seven subgroups containing 29 orthologous gene sets and two Brassica-specific gene sets. Structures of genes and proteins varied across different genes but were conserved among homologous genes in B. napus. Furthermore, analysis of transcriptional profiles revealed that the expression patterns of Aux/IAA genes in B. napus were tissue dependent. Auxin-responsive elements tend to be distributed in the proximal region of promoters, and are significantly associated with early exogenous auxin up-regulation.ConclusionsMembers of the Aux/IAA gene family were identified and analyzed comprehensively in the allotetraploid B. napus genome. This analysis provides a deeper understanding of diversification of the Aux/IAA gene family and will facilitate further dissection of Aux/IAA gene function in B. napus.

Highlights

Auxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development
Genome-wide identification and chromosomal distribution of Aux/IAA genes in B. napus In order to identify all the Aux/IAA gene members in B. napus, 101,040 available protein sequences were obtained from the B. napus database. 182 non-redundant genes were extracted as candidate Aux/IAA members by a Hidden Markov Model (HMM)-based search with Aux/IAA domain (PF02309) and BLASTP with 29 A. thaliana Aux/IAA genes as queries
The number of Aux/IAA gene family members in B. napus is much higher than that in A. thaliana (29 members), B. rapa (55 members) and B. oleracea (60 members). These observations suggest that the expansion of the B. napus Aux/IAA gene family may be independent of tandem duplication, and only affected by segmental duplication resulting from Brassica whole genome triplication (WGT) and allopolyploidy

Summary

Introduction

Auxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development. Auxins are able to regulate many aspects of plant growth and development, including cell division and elongation, as well as organ development at both cellular and whole plant level. They play a role in regulating plant responses to environment such as phototropism, gravitropism, thigmotropism, and shade avoidance [1, 2]. Domain II contains a conserved degron GWPPV motif that interacts with the SCFTIR1/AFB complex [13, 14] and confers instability to the proteins in the presence of auxin [15]. Domains III and IV contain a carboxyterminal PB1 (Phox and Bem1) domain that is located in the carboxy-terminal of ARFs, and are responsible for homo- and hetero-dimerization between Aux/IAA and ARF proteins [4, 16]

Objectives

Methods

Results

Discussion

Conclusion