title: Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane.
abstract: 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.
authors.affiliation: Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Savio Siqueira
authors.initials: SS
authors.lastname: Ferreira
authors.affiliation: Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Carlos Takeshi
authors.initials: CT
authors.lastname: Hotta
authors.affiliation: Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil.|Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil.
authors.forename: Viviane Guzzo de Carli
authors.initials: VG
authors.lastname: Poelking
authors.affiliation: Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Debora Chaves Coelho
authors.initials: DC
authors.lastname: Leite
authors.affiliation: Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Marcos Silveira
authors.initials: MS
authors.lastname: Buckeridge
authors.affiliation: Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil.
authors.forename: Marcelo Ehlers
authors.initials: ME
authors.lastname: Loureiro
authors.affiliation: Departamento de Fitotecnia, Universidade Federal de Viçosa, Viçosa, Brazil.
authors.forename: Marcio Henrique Pereira
authors.initials: MH
authors.lastname: Barbosa
authors.affiliation: Centro de Ciências Agrárias, Universidade Federal de São Carlos, São Carlos, Brazil.
authors.forename: Monalisa Sampaio
authors.initials: MS
authors.lastname: Carneiro
authors.affiliation: Instituto de Química, Universidade de São Paulo, São Paulo, Brazil. glmsouza@iq.usp.br.
authors.forename: Glaucia Mendes
authors.initials: GM
authors.lastname: Souza
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D002244:Carbon / Q000378:metabolism; D002473:Cell Wall / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D005838:Genotype; D017705:Lignans / Q000378:metabolism; D009584:Nitrogen / Q000378:metabolism; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D040081:Protein Array Analysis; D031786:Saccharum / Q000166:cytology / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D000596:Amino Acids; D017705:Lignans; D010940:Plant Proteins; D014157:Transcription Factors; D002244:Carbon; D009584:Nitrogen
keywords: Cell wall; Co-expression network; Expression profiling; Lignin; Sugarcane; Transcription factors
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