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Sugarcane genes associated with sucrose content.

Papini-Terzi FS, Rocha FR, Vêncio RZ, Felix JM, Branco DS, Waclawovsky AJ, Del Bem LE, Lembke CG, Costa MD, Nishiyama MY, Vicentini R, Vincentz MG, Ulian EC, Menossi M, Souza GM - BMC Genomics (2009)

Bottom Line: Sucrose content is a highly desirable trait in sugarcane as the worldwide demand for cost-effective biofuels surges.Genes associated with sucrose content were extensively validated by qRT-PCR, which highlighted several protein kinases and transcription factors that are likely to be regulators of sucrose accumulation.Moreover, sucrose-associated genes were shown to be directly responsive to short term sucrose stimuli, confirming their role in sugar-related pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil. flastal@yahoo.com.br

ABSTRACT

Background: Sucrose content is a highly desirable trait in sugarcane as the worldwide demand for cost-effective biofuels surges. Sugarcane cultivars differ in their capacity to accumulate sucrose and breeding programs routinely perform crosses to identify genotypes able to produce more sucrose. Sucrose content in the mature internodes reach around 20% of the culms dry weight. Genotypes in the populations reflect their genetic program and may display contrasting growth, development, and physiology, all of which affect carbohydrate metabolism. Few studies have profiled gene expression related to sugarcane's sugar content. The identification of signal transduction components and transcription factors that might regulate sugar accumulation is highly desirable if we are to improve this characteristic of sugarcane plants.

Results: We have evaluated thirty genotypes that have different Brix (sugar) levels and identified genes differentially expressed in internodes using cDNA microarrays. These genes were compared to existing gene expression data for sugarcane plants subjected to diverse stress and hormone treatments. The comparisons revealed a strong overlap between the drought and sucrose-content datasets and a limited overlap with ABA signaling. Genes associated with sucrose content were extensively validated by qRT-PCR, which highlighted several protein kinases and transcription factors that are likely to be regulators of sucrose accumulation. The data also indicate that aquaporins, as well as lignin biosynthesis and cell wall metabolism genes, are strongly related to sucrose accumulation. Moreover, sucrose-associated genes were shown to be directly responsive to short term sucrose stimuli, confirming their role in sugar-related pathways.

Conclusion: Gene expression analysis of sugarcane populations contrasting for sucrose content indicated a possible overlap with drought and cell wall metabolism processes and suggested signaling and transcriptional regulators to be used as molecular markers in breeding programs. Transgenic research is necessary to further clarify the role of the genes and define targets useful for sugarcane improvement programs based on transgenic plants.

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Real Time PCR (qRT-PCR) analysis of drought and ABA-responsive gene expression. The y axis refers to the relative expression ratio between target mRNA versus the reference mRNA (polyubiquitin SCCCST2001G02.g; GAPDH Gene ID: 542367; UBE2 SCBGLR1002D06.g) in sugarcane plants treated with ABA for 12 h or drought conditions for 24, 72 or 120 h. The reactions for the target mRNA and reference mRNA were carried out in parallel and each reaction was performed in triplicates. Error bars were calculated as described previously [31]. The transcript levels for the reference genes were verified to not vary in response to the treatments. The values of P correspond to the probability Pr (Treated>Control) and Pr (Treated<Control) for up- and down-regulated genes, respectively. The SAS was considered differentially expressed when P ≥ 0.95.
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Figure 4: Real Time PCR (qRT-PCR) analysis of drought and ABA-responsive gene expression. The y axis refers to the relative expression ratio between target mRNA versus the reference mRNA (polyubiquitin SCCCST2001G02.g; GAPDH Gene ID: 542367; UBE2 SCBGLR1002D06.g) in sugarcane plants treated with ABA for 12 h or drought conditions for 24, 72 or 120 h. The reactions for the target mRNA and reference mRNA were carried out in parallel and each reaction was performed in triplicates. Error bars were calculated as described previously [31]. The transcript levels for the reference genes were verified to not vary in response to the treatments. The values of P correspond to the probability Pr (Treated>Control) and Pr (Treated<Control) for up- and down-regulated genes, respectively. The SAS was considered differentially expressed when P ≥ 0.95.

Mentions: Expression data of forty-two genes was also obtained using qRT-PCR. We determined gene expression differences for pools of extreme individuals from both populations (Figure 2), in mature and immature internodes (Figure 3) and in response to drought and ABA treatment (Figure 4). The significance of the data obtained by qRT-PCR was inferred statistically by calculating values of P for expression differences against the reference sample (see Methods for details). Overall gene expression data obtained using cDNA microarrays was confirmed in qRT-PCR experiments for over 80% of the genes tested, even when the target RNA derived from a distinct biological replicate. We also investigated, using qRT-PCR, how the expression levels varied among the individual genotypes from Population 1 (Figure 5). In this case, the value of P was calculated against the average expression level across genotypes and the validation rate was around 58%. Additional file 3 lists all the values of P for the validated genes.


Sugarcane genes associated with sucrose content.

Papini-Terzi FS, Rocha FR, Vêncio RZ, Felix JM, Branco DS, Waclawovsky AJ, Del Bem LE, Lembke CG, Costa MD, Nishiyama MY, Vicentini R, Vincentz MG, Ulian EC, Menossi M, Souza GM - BMC Genomics (2009)

Real Time PCR (qRT-PCR) analysis of drought and ABA-responsive gene expression. The y axis refers to the relative expression ratio between target mRNA versus the reference mRNA (polyubiquitin SCCCST2001G02.g; GAPDH Gene ID: 542367; UBE2 SCBGLR1002D06.g) in sugarcane plants treated with ABA for 12 h or drought conditions for 24, 72 or 120 h. The reactions for the target mRNA and reference mRNA were carried out in parallel and each reaction was performed in triplicates. Error bars were calculated as described previously [31]. The transcript levels for the reference genes were verified to not vary in response to the treatments. The values of P correspond to the probability Pr (Treated>Control) and Pr (Treated<Control) for up- and down-regulated genes, respectively. The SAS was considered differentially expressed when P ≥ 0.95.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2666766&req=5

Figure 4: Real Time PCR (qRT-PCR) analysis of drought and ABA-responsive gene expression. The y axis refers to the relative expression ratio between target mRNA versus the reference mRNA (polyubiquitin SCCCST2001G02.g; GAPDH Gene ID: 542367; UBE2 SCBGLR1002D06.g) in sugarcane plants treated with ABA for 12 h or drought conditions for 24, 72 or 120 h. The reactions for the target mRNA and reference mRNA were carried out in parallel and each reaction was performed in triplicates. Error bars were calculated as described previously [31]. The transcript levels for the reference genes were verified to not vary in response to the treatments. The values of P correspond to the probability Pr (Treated>Control) and Pr (Treated<Control) for up- and down-regulated genes, respectively. The SAS was considered differentially expressed when P ≥ 0.95.
Mentions: Expression data of forty-two genes was also obtained using qRT-PCR. We determined gene expression differences for pools of extreme individuals from both populations (Figure 2), in mature and immature internodes (Figure 3) and in response to drought and ABA treatment (Figure 4). The significance of the data obtained by qRT-PCR was inferred statistically by calculating values of P for expression differences against the reference sample (see Methods for details). Overall gene expression data obtained using cDNA microarrays was confirmed in qRT-PCR experiments for over 80% of the genes tested, even when the target RNA derived from a distinct biological replicate. We also investigated, using qRT-PCR, how the expression levels varied among the individual genotypes from Population 1 (Figure 5). In this case, the value of P was calculated against the average expression level across genotypes and the validation rate was around 58%. Additional file 3 lists all the values of P for the validated genes.

Bottom Line: Sucrose content is a highly desirable trait in sugarcane as the worldwide demand for cost-effective biofuels surges.Genes associated with sucrose content were extensively validated by qRT-PCR, which highlighted several protein kinases and transcription factors that are likely to be regulators of sucrose accumulation.Moreover, sucrose-associated genes were shown to be directly responsive to short term sucrose stimuli, confirming their role in sugar-related pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil. flastal@yahoo.com.br

ABSTRACT

Background: Sucrose content is a highly desirable trait in sugarcane as the worldwide demand for cost-effective biofuels surges. Sugarcane cultivars differ in their capacity to accumulate sucrose and breeding programs routinely perform crosses to identify genotypes able to produce more sucrose. Sucrose content in the mature internodes reach around 20% of the culms dry weight. Genotypes in the populations reflect their genetic program and may display contrasting growth, development, and physiology, all of which affect carbohydrate metabolism. Few studies have profiled gene expression related to sugarcane's sugar content. The identification of signal transduction components and transcription factors that might regulate sugar accumulation is highly desirable if we are to improve this characteristic of sugarcane plants.

Results: We have evaluated thirty genotypes that have different Brix (sugar) levels and identified genes differentially expressed in internodes using cDNA microarrays. These genes were compared to existing gene expression data for sugarcane plants subjected to diverse stress and hormone treatments. The comparisons revealed a strong overlap between the drought and sucrose-content datasets and a limited overlap with ABA signaling. Genes associated with sucrose content were extensively validated by qRT-PCR, which highlighted several protein kinases and transcription factors that are likely to be regulators of sucrose accumulation. The data also indicate that aquaporins, as well as lignin biosynthesis and cell wall metabolism genes, are strongly related to sucrose accumulation. Moreover, sucrose-associated genes were shown to be directly responsive to short term sucrose stimuli, confirming their role in sugar-related pathways.

Conclusion: Gene expression analysis of sugarcane populations contrasting for sucrose content indicated a possible overlap with drought and cell wall metabolism processes and suggested signaling and transcriptional regulators to be used as molecular markers in breeding programs. Transgenic research is necessary to further clarify the role of the genes and define targets useful for sugarcane improvement programs based on transgenic plants.

Show MeSH