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

View Article: PubMed Central - PubMed

ABSTRACT

Background: 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.

Results: 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.

Conclusions: 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.

Electronic supplementary material: The online version of this article (doi:10.1186/s12870-016-0852-y) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Expression patterns of BnaSBP genes in twelve different tissue samples. Color scale bar at the top of map represents log2 transformed FPKM values, which represents low and high expression, respectively. Tissues used for expression profiling are indicated at the top of each column. The genes are on right of expression bar
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Fig7: Expression patterns of BnaSBP genes in twelve different tissue samples. Color scale bar at the top of map represents log2 transformed FPKM values, which represents low and high expression, respectively. Tissues used for expression profiling are indicated at the top of each column. The genes are on right of expression bar

Mentions: A wide range of SBP genes play important roles in plant development process. In the absence of SBP gene mutants, the expression pattern may provide a clue to elucidate the potential role of the different SBP genes in B. napus. The expression level of BnaSBP genes in twelve tissues were shown by heat map representation (Fig. 7, Additional file 3: Table S2). Transcript of BnaSBP6c was zero in all twelve tissue samples and only very low expression level of BnaSBP4c in leaf was detected. Based on the hierarchical clustering analysis, the BnaSBP genes could be divided into eight categories. The transcription of a large number of BnaSBP genes was enriched in bud, stamen and pericarp. By contrast, most of BnaSBP genes exhibit low expression level in ovule and petal. Eight BnaSBP genes, BnaSBP1a, 1b, 11e, 14a, 14b, 14c, 16a and 16b seemed to be expressed constitutively, from root to pericarp. It should be noted that all these genes, excluding BnaSBP11e, are not predicted to be targeted by the miR156. BnaSBP4c, 4d, 5c, 5d, 10d and 13d sustained low expression level in most tissues. The expression level of BnaSBP3a and 3d was not detected in most tissue samples, but reached clearly higher levels in pericarp. A relative higher expression level of BnaSBP2b and 11d could also be discerned in root tissue. Compared with the SBP genes not bound by miRNA, the BnaSBP genes have the target site represent more divergent expression pattern. We also performed RT-PCR to confirm the expression levels of some BnaSBPs in eight different tissues (Fig. 8). Thirty-nine BnaSBPs were selected to verify the result of RNA-seq data. Results showed that RT-PCR data was generally consistent with RNA-seq data for relative expression of BnaSBPs in most of the tissues. For example, expression level of BnaSBP1a, 1b and 11e could be detected in most tissues (Fig. 8). Though BnaSBPs were expressed at least in one of the tissues, distinction of expression patterns were observed across the gene groups. Some BnaSBPs belongs to a same group exhibited similar expression pattern, such as BnaSBP1a and 1b in group IV, BnaSBP15a and 15b in group III, indicating redundant roles of BnaSBPs in the same group. Therefore, the oilseed rape SBP transcription factors have diverse expression patterns and may be redundant in biological function with each individual in charge of certain physiological processes.Fig. 7


Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus
Expression patterns of BnaSBP genes in twelve different tissue samples. Color scale bar at the top of map represents log2 transformed FPKM values, which represents low and high expression, respectively. Tissues used for expression profiling are indicated at the top of each column. The genes are on right of expression bar
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5017063&req=5

Fig7: Expression patterns of BnaSBP genes in twelve different tissue samples. Color scale bar at the top of map represents log2 transformed FPKM values, which represents low and high expression, respectively. Tissues used for expression profiling are indicated at the top of each column. The genes are on right of expression bar
Mentions: A wide range of SBP genes play important roles in plant development process. In the absence of SBP gene mutants, the expression pattern may provide a clue to elucidate the potential role of the different SBP genes in B. napus. The expression level of BnaSBP genes in twelve tissues were shown by heat map representation (Fig. 7, Additional file 3: Table S2). Transcript of BnaSBP6c was zero in all twelve tissue samples and only very low expression level of BnaSBP4c in leaf was detected. Based on the hierarchical clustering analysis, the BnaSBP genes could be divided into eight categories. The transcription of a large number of BnaSBP genes was enriched in bud, stamen and pericarp. By contrast, most of BnaSBP genes exhibit low expression level in ovule and petal. Eight BnaSBP genes, BnaSBP1a, 1b, 11e, 14a, 14b, 14c, 16a and 16b seemed to be expressed constitutively, from root to pericarp. It should be noted that all these genes, excluding BnaSBP11e, are not predicted to be targeted by the miR156. BnaSBP4c, 4d, 5c, 5d, 10d and 13d sustained low expression level in most tissues. The expression level of BnaSBP3a and 3d was not detected in most tissue samples, but reached clearly higher levels in pericarp. A relative higher expression level of BnaSBP2b and 11d could also be discerned in root tissue. Compared with the SBP genes not bound by miRNA, the BnaSBP genes have the target site represent more divergent expression pattern. We also performed RT-PCR to confirm the expression levels of some BnaSBPs in eight different tissues (Fig. 8). Thirty-nine BnaSBPs were selected to verify the result of RNA-seq data. Results showed that RT-PCR data was generally consistent with RNA-seq data for relative expression of BnaSBPs in most of the tissues. For example, expression level of BnaSBP1a, 1b and 11e could be detected in most tissues (Fig. 8). Though BnaSBPs were expressed at least in one of the tissues, distinction of expression patterns were observed across the gene groups. Some BnaSBPs belongs to a same group exhibited similar expression pattern, such as BnaSBP1a and 1b in group IV, BnaSBP15a and 15b in group III, indicating redundant roles of BnaSBPs in the same group. Therefore, the oilseed rape SBP transcription factors have diverse expression patterns and may be redundant in biological function with each individual in charge of certain physiological processes.Fig. 7

View Article: PubMed Central - PubMed

ABSTRACT

Background: 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.

Results: 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.

Conclusions: 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.

Electronic supplementary material: The online version of this article (doi:10.1186/s12870-016-0852-y) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus