Cheng Hongtao, Hao Mengyu, Wang Wenxiang, Mei Desheng, Tong Chaobo, Wang Hui, Liu Jia, Fu Li, Hu Qiong
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.
BMC Plant Biol. 2016 Sep 8;16(1):196. doi: 10.1186/s12870-016-0852-y.
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.
SBP-box基因属于最大的转录因子家族之一。尽管该家族成员已被证明是多种生物学过程的重要调节因子，但在第三大重要油料作物甘蓝型油菜中，SBP-box基因的信息大多尚未明确。
在本研究中，通过全基因组生物信息学分析和转录谱分析，鉴定出了甘蓝型油菜（Brassica napus L.）中SBP-box基因家族的58个推定成员，并分析了它们在不同组织中的表达模式以及与miRNA可能的相互作用。此外，利用具有不同分枝角度的甘蓝型油菜品系研究SBP-box基因在植物结构调控中的作用。系统地描述了详细的基因信息，包括基因的基因组组织、结构特征、保守结构域和系统发育关系。通过系统发育分析，BnaSBP蛋白被分为八个不同的组，表明它们与拟南芥和水稻中的家族成员具有明确的直系同源关系。在包括营养器官和生殖器官在内的十二个组织中的表达分析表明，SBP-box基因之间存在不同的表达模式，许多基因表现出组织特异性表达，表明它们在发育过程中具有多种功能。确定有44个SBP-box基因含有推定的miR156结合位点，其中30个和14个基因分别在编码区和3'UTR区域被miR156靶向。miR156的相对表达水平在不同组织中有所不同。在具有不同分枝角度的品系中，观察到一些BnaSBP基因的不同表达模式以及miR156与其靶标BnaSBP基因转录水平之间的负相关。
综上所述，本研究首次对甘蓝型油菜中的SBP-box基因家族进行了系统分析。这里提供的数据为理解BnaSBP基因在植物发育和其他生物学过程中的关键作用奠定了基础。
