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Plant Mol Biol. 2016 May;91(1-2):15-35. doi: 10.1007/s11103-016-0434-2. Epub 2016 Jan 28.

Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane.

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Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil.
Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil.
Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
Departamento de Fitotecnia, Universidade Federal de Viçosa, Viçosa, Brazil.
Centro de Ciências Agrárias, Universidade Federal de São Carlos, São Carlos, Brazil.
Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.


Sugarcane is a hybrid of Saccharum officinarum and Saccharum spontaneum, with minor contributions from other species in Saccharum and other genera. Understanding the molecular basis of cell wall metabolism in sugarcane may allow for rational changes in fiber quality and content when designing new energy crops. This work describes a comparative expression profiling of sugarcane ancestral genotypes: S. officinarum, S. spontaneum and S. robustum and a commercial hybrid: RB867515, linking gene expression to phenotypes to identify genes for sugarcane improvement. Oligoarray experiments of leaves, immature and intermediate internodes, detected 12,621 sense and 995 antisense transcripts. Amino acid metabolism was particularly evident among pathways showing natural antisense transcripts expression. For all tissues sampled, expression analysis revealed 831, 674 and 648 differentially expressed genes in S. officinarum, S. robustum and S. spontaneum, respectively, using RB867515 as reference. Expression of sugar transporters might explain sucrose differences among genotypes, but an unexpected differential expression of histones were also identified between high and low Brix° genotypes. Lignin biosynthetic genes and bioenergetics-related genes were up-regulated in the high lignin genotype, suggesting that these genes are important for S. spontaneum to allocate carbon to lignin, while S. officinarum allocates it to sucrose storage. Co-expression network analysis identified 18 transcription factors possibly related to cell wall biosynthesis while in silico analysis detected cis-elements involved in cell wall biosynthesis in their promoters. Our results provide information to elucidate regulatory networks underlying traits of interest that will allow the improvement of sugarcane for biofuel and chemicals production.


Cell wall; Co-expression network; Expression profiling; Lignin; Sugarcane; Transcription factors

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