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

Author(s)

Ferreira, Savio Siqueira ^[1] ; Hotta, Carlos Takeshi ^[1] ; de Carli Poelking, Viviane Guzzo ^{[2, 3]} ; Coelho Leite, Debora Chaves ^[4] ; Buckeridge, Marcos Silveira ^[4] ; Loureiro, Marcelo Ehlers ^[2] ; Pereira Barbosa, Marcio Henrique ^[5] ; Carneiro, Monalisa Sampaio ^[6] ; Souza, Glaucia Mendes ^[1]

Affiliation

^[1] Univ Sao Paulo, Inst Quim, Sao Paulo - Brazil

^[2] Univ Fed Vicosa, Dept Biol Vegetal, Vicosa, MG - Brazil

^[3] Univ Fed Reconcavo Bahia, Cruz Das Almas - Brazil

^[4] Univ Sao Paulo, Inst Biociencias, Sao Paulo - Brazil

^[5] Univ Fed Vicosa, Dept Fitotecnia, Vicosa, MG - Brazil

^[6] Univ Fed Sao Carlos, Ctr Ciencias Agr, BR-13560 Sao Carlos, SP - Brazil

• Document type: Journal article
• Source: Plant Molecular Biology; v. 91, n. 1-2, p. 15-35, MAY 2016.
• Web of Science Citations: 21

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 BrixA degrees 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. (AU)

• FAPESP's process: 08/52146-0 - Sugarcane signaling and regulatory networks
• Grantee: Glaucia Mendes Souza
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• FAPESP's process: 13/23048-9 - Functional analysis of sugarcane promoters and their allelic variation
• Grantee: Sávio de Siqueira Ferreira
• Support Opportunities: Scholarships in Brazil - Post-Doctoral