Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus.

Hongtao Cheng,Jia Liu,Li Fu,Hui Wang,Mengyu Hao,Chaobo Tong,Desheng Mei,Wenxiang Wang,Qiong Hu

doi:10.1186/s12870-016-0852-y

Abstract

BackgroundSBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological processes, information of SBP-box genes in the third most important oilseed crop Brassica napus is largely undefined.ResultsIn the present study, by whole genome bioinformatics analysis and transcriptional profiling, 58 putative members of SBP-box gene family in oilseed rape (Brassica napus L.) were identified and their expression pattern in different tissues as well as possible interaction with miRNAs were analyzed. In addition, B. napus lines with contrasting branch angle were used for investigating the involvement of SBP-box genes in plant architecture regulation. Detailed gene information, including genomic organization, structural feature, conserved domain and phylogenetic relationship of the genes were systematically characterized. By phylogenetic analysis, BnaSBP proteins were classified into eight distinct groups representing the clear orthologous relationships to their family members in Arabidopsis and rice. Expression analysis in twelve tissues including vegetative and reproductive organs showed different expression patterns among the SBP-box genes and a number of the genes exhibit tissue specific expression, indicating their diverse functions involved in the developmental process. Forty-four SBP-box genes were ascertained to contain the putative miR156 binding site, with 30 and 14 of the genes targeted by miR156 at the coding and 3′UTR region, respectively. Relative expression level of miR156 is varied across tissues. Different expression pattern of some BnaSBP genes and the negative correlation of transcription levels between miR156 and its target BnaSBP gene were observed in lines with different branch angle.ConclusionsTaken together, this study represents the first systematic analysis of the SBP-box gene family in Brassica napus. The data presented here provides base foundation for understanding the crucial roles of BnaSBP genes in plant development and other biological processes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0852-y) contains supplementary material, which is available to authorized users.

Highlights

SQUAMOSA promoterbinding protein (SBP)-box genes belong to one of the largest families of transcription factors
Identification of SBP genes in B. napus All Arabidopsis SBP protein sequences were used as queries for TBLASTN
All SBP-box genes in B. napus are designated as BnaSBP and named according to the order of closest orthologues in Arabidopsis

Summary

Introduction

SBP-box genes belong to one of the largest families of transcription factors Though members of this family have been characterized to be important regulators of diverse biological processes, information of SBP-box genes in the third most important oilseed crop Brassica napus is largely undefined. Besides the important roles reported in dicot plants, SBP-box genes in monocot plant, such as rice and maize, were shown to modulate essential developmental processes. Higher expression of OsSPL14 in the reproductive stage promotes panicle branching and higher grain yield in rice, suggesting the important roles of SPL genes in plant architecture regulation [22, 23]. Maize transcription factors unbranched and unbranched encoding SBP-box proteins alter plant architecture and affect yield traits by regulating the rate of lateral primordia initiation [24]

Methods

Results

Conclusion