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



In 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.



Taken 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.
Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
Hongtao
H
Cheng
Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
Mengyu
M
Hao
Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
Wenxiang
W
Wang
Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
Desheng
D
Mei
Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
Chaobo
C
Tong
Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
Hui
H
Wang
Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
Jia
J
Liu
Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China.
Li
L
Fu
Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture,, No.2 Xudong 2nd Road, Wuhan, 430062, People's Republic of China. huqiong01@caas.cn.
Qiong
Q
Hu
D029688:Brassica napus / Q000235:genetics* / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D035683:MicroRNAs / Q000378:metabolism*; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant; D014157:Transcription Factors
Brassica napus; SBP-box; SQUAMOSA promoter binding protein; Transcription factor