Limits...
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.


The expression patterns of miR156 in different tissue samples. Relative expression levels of mature miR156 in different tissues were analyzed by qRT-PCR. a The expression level of miR156 in the different tissue samples of Zhongshuang11. The value was normalized to the root at the seedling stage. R, root; St, stem; L, leaf; B, bud; Sl1, silique 15 days after flowering; Sl2, silique 18 days after flowering; Sl3, silique 20 days after flowering; Sl4, silique 23 days after flowering. b The expression level of miR156 in five tissue samples of Puler and 6098B respectively. The value was normalized to 6098B at the bolting stage. L, leaf; B, bud; St, stem; Bs1, branch site at the bolting stage; Bs2, branch site at the early flowering stage. Asterisks indicate a significant difference was detected between Purler and 6098B in the same tissue sample by t-test at *P < 0.01
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig11: The expression patterns of miR156 in different tissue samples. Relative expression levels of mature miR156 in different tissues were analyzed by qRT-PCR. a The expression level of miR156 in the different tissue samples of Zhongshuang11. The value was normalized to the root at the seedling stage. R, root; St, stem; L, leaf; B, bud; Sl1, silique 15 days after flowering; Sl2, silique 18 days after flowering; Sl3, silique 20 days after flowering; Sl4, silique 23 days after flowering. b The expression level of miR156 in five tissue samples of Puler and 6098B respectively. The value was normalized to 6098B at the bolting stage. L, leaf; B, bud; St, stem; Bs1, branch site at the bolting stage; Bs2, branch site at the early flowering stage. Asterisks indicate a significant difference was detected between Purler and 6098B in the same tissue sample by t-test at *P < 0.01

Mentions: Several BnaSBP genes carry the complementary sequences to miR156. MiR156 was thus expected to be an important determinant for the expression of these BnaSBP genes. The expression level of miR156 was mostly abundant in bud and silique of Zhongshuang 11 at different developmental stages (Fig. 11a). Relative low levels were found in leaf sample. Meanwhile, the expression level of miR156 in 6098B and Purler was also determined. It was showed that the abundance of miR156 decreased significantly at early flowering time compared to bolting time (Fig. 11b). Besides the stem sample of two materials, the transcription of miR156 was stronger in Purler than in 6098B of the other tissues.Fig. 11


Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus
The expression patterns of miR156 in different tissue samples. Relative expression levels of mature miR156 in different tissues were analyzed by qRT-PCR. a The expression level of miR156 in the different tissue samples of Zhongshuang11. The value was normalized to the root at the seedling stage. R, root; St, stem; L, leaf; B, bud; Sl1, silique 15 days after flowering; Sl2, silique 18 days after flowering; Sl3, silique 20 days after flowering; Sl4, silique 23 days after flowering. b The expression level of miR156 in five tissue samples of Puler and 6098B respectively. The value was normalized to 6098B at the bolting stage. L, leaf; B, bud; St, stem; Bs1, branch site at the bolting stage; Bs2, branch site at the early flowering stage. Asterisks indicate a significant difference was detected between Purler and 6098B in the same tissue sample by t-test at *P < 0.01
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig11: The expression patterns of miR156 in different tissue samples. Relative expression levels of mature miR156 in different tissues were analyzed by qRT-PCR. a The expression level of miR156 in the different tissue samples of Zhongshuang11. The value was normalized to the root at the seedling stage. R, root; St, stem; L, leaf; B, bud; Sl1, silique 15 days after flowering; Sl2, silique 18 days after flowering; Sl3, silique 20 days after flowering; Sl4, silique 23 days after flowering. b The expression level of miR156 in five tissue samples of Puler and 6098B respectively. The value was normalized to 6098B at the bolting stage. L, leaf; B, bud; St, stem; Bs1, branch site at the bolting stage; Bs2, branch site at the early flowering stage. Asterisks indicate a significant difference was detected between Purler and 6098B in the same tissue sample by t-test at *P < 0.01
Mentions: Several BnaSBP genes carry the complementary sequences to miR156. MiR156 was thus expected to be an important determinant for the expression of these BnaSBP genes. The expression level of miR156 was mostly abundant in bud and silique of Zhongshuang 11 at different developmental stages (Fig. 11a). Relative low levels were found in leaf sample. Meanwhile, the expression level of miR156 in 6098B and Purler was also determined. It was showed that the abundance of miR156 decreased significantly at early flowering time compared to bolting time (Fig. 11b). Besides the stem sample of two materials, the transcription of miR156 was stronger in Purler than in 6098B of the other tissues.Fig. 11

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&prime;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.