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Sugarcane signaling and regulatory networks

Abstract

We aim to study signaling and regulatory networks in sugarcane and to develop tools for a systems biology approach in this grass. As a starting point we intend to characterize three agronomical traits of interest: drought, brix and lignin content. We will study gene categories with a well known regulatory role (Transcription Factors, Protein Kinases and Phosphatases), conduct studies on the Transcriptome, produce transgenics, develop a database and computacional tools to integrate the several levels of information and we will initiate the whole genome sequencing of a Brazilian sugarcane cultivar. In parallel, we intend to implement ChIP-Seq technology in sugarcane, to identify TF targets and gene promoters. The results will have multiple direct consequences on breeding programs that frequently select for CREs and TF changes in search for genotypes better adapted to the environment and with increased agronomical performance. PKs activate signaling cascades in response to environmental stimuli and our studies point to a predominant role of PKs in the regulation of sucrose content and drought responses. To identify new genes associated to brix, drought and lignin content we will characterize the transcriptome of genotypes and cultivars that contrast for these traits using olinonucleotide arrays. Genes of interest will be functionally evaluated by generating transgenics altered for their expression. To integrate the immense amount of public data and that generated by this project a robust computational infrastructure and database will be developed. The SUCEST-FUN database will integrate the SUCEST sequences, promoters, CREs, expression data, agronomical, physiological and biochemical characterization of sugarcane cultivars. We will also participate in the development of the GRASSIUS database to establish sugarcane, rice, maize and sorghum regulatory networks. (AU)

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Scientific publications (12)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
SOUZA, GLAUCIA MENDES; VAN SLUYS, MARIE-ANNE; LEMBKE, CAROLINA GIMILIANI; LEE, HAYAN; MARGARIDO, GABRIEL RODRIGUES ALVES; HOTTA, CARLOS TAKESHI; GAIARSA, JONAS WEISSMANN; DINIZ, AUGUSTO LIMA; OLIVEIRA, MAURO DE MEDEIROS; FERREIRA, SAVIO DE SIQUEIRA; et al. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. GIGASCIENCE, v. 8, n. 12, . (13/07467-1, 08/52074-0, 14/50921-8, 15/22993-7, 12/51062-3, 17/02270-6, 11/50761-2, 16/17545-8, 16/06917-1, 13/23048-9, 08/52146-0)
YILMAZ, ALPER; NISHIYAMA, JR., MILTON Y.; FUENTES, BERNARDO GARCIA; SOUZA, GLAUCIA MENDES; JANIES, DANIEL; GRAY, JOHN; GROTEWOLD, ERICH. GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses. Plant Physiology, v. 149, n. 1, p. 171-180, . (08/52146-0)
WACLAWOVSKY, ALESSANDRO J.; SATO, PALOMA M.; LEMBKE, CAROLINA G.; MOORE, PAUL H.; SOUZA, GLAUCIA M.. Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content. Plant Biotechnology Journal, v. 8, n. 3, p. 263-276, . (06/57798-0, 08/52146-0, 08/54201-9)
DE SETTA, NATHALIA; MONTEIRO-VITORELLO, CLAUDIA BARROS; METCALFE, CUSHLA JANE; QUEIROGA CRUZ, GUILHERME MARCELO; DEL BEM, LUIZ EDUARDO; VICENTINI, RENATO; SILVEIRA NOGUEIRA, FABIO TEBALDI; CAMPOS, ROBERTA ALVARES; NUNES, SIDENY LIMA; GASPERAZZO TURRINI, PAULA CRISTINA; et al. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics, v. 15, . (10/05591-9, 08/54201-9, 08/52074-0, 08/58031-0, 08/52197-4, 08/52146-0)
CUNHA, CAMILA P.; ROBERTO, GUILHERME G.; VICENTINI, RENATO; LEMBKE, CAROLINA G.; SOUZA, GLAUCIA M.; RIBEIRO, RAFAEL V.; MACHADO, EDUARDO C.; LAGOA, ANA M. M. A.; MENOSSI, MARCELO. Ethylene-induced transcriptional and hormonal responses at the onset of sugarcane ripening. SCIENTIFIC REPORTS, v. 7, . (08/57495-3, 08/54201-9, 12/13920-8, 13/15576-5, 08/52146-0)
SANTINI, LUCIANE; YOSHIDA, LEONARDO; DE OLIVEIRA, KAIQUE DIAS; LEMBKE, CAROLINA GIMILIANI; DINIZ, AUGUSTO LIMA; CANTELLI, GERALDO CESAR; NISHIYAMA-JUNIOR, MILTON YUTAKA; SOUZA, GLAUCIA MENDES. Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 23, n. 19, p. 21-pg., . (08/52146-0, 20/07851-0, 20/10876-4, 14/50921-8, 18/09867-0, 17/02270-6)
SOUZA, GLAUCIA MENDES; VAN SLUYS, MARIE-ANNE; LEMBKE, CAROLINA GIMILIANI; LEE, HAYAN; MARGARIDO, GABRIEL RODRIGUES ALVES; HOTTA, CARLOS TAKESHI; GAIARSA, JONAS WEISSMANN; DINIZ, AUGUSTO LIMA; OLIVEIRA, MAURO DE MEDEIROS; FERREIRA, SAVIO DE SIQUEIRA; et al. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. GIGASCIENCE, v. 8, n. 12, p. 18-pg., . (14/50921-8, 08/52074-0, 15/22993-7, 08/52146-0, 12/51062-3, 13/07467-1, 17/02270-6, 11/50761-2, 13/23048-9, 16/06917-1, 16/17545-8)
CONTILIANI, DANYEL FERNANDES; DE OLIVEIRA NEBO, JOAO FELIPE CARLOS; RIBEIRO, RAFAEL VASCONCELOS; ANDRADE, LARISSA MARA; PEIXOTO JUNIOR, RAFAEL FAVERO; LEMBKE, CAROLINA GIMILIANI; MACHADO, RICARDO SILVERIO; SILVA, DANIEL NUNES; BELLOTI, MARIANA; DE SOUZA, GLAUCIA MENDES; et al. Leaf transcriptome profiling of contrasting sugarcane genotypes for drought tolerance under field conditions. SCIENTIFIC REPORTS, v. 12, n. 1, p. 12-pg., . (08/06446-2, 21/13478-2, 08/57923-5, 08/52146-0, 11/50661-8)
FERREIRA, SAVIO SIQUEIRA; HOTTA, CARLOS TAKESHI; DE CARLI POELKING, VIVIANE GUZZO; COELHO LEITE, DEBORA CHAVES; BUCKERIDGE, MARCOS SILVEIRA; LOUREIRO, MARCELO EHLERS; PEREIRA BARBOSA, MARCIO HENRIQUE; CARNEIRO, MONALISA SAMPAIO; SOUZA, GLAUCIA MENDES. Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane. Plant Molecular Biology, v. 91, n. 1-2, p. 15-35, . (08/52146-0, 13/23048-9)
ZHANG, JISEN; ZHANG, XINGTAN; TANG, HAIBAO; ZHANG, QING; HUA, XIUTING; MA, XIAOKAI; ZHU, FAN; JONES, TYLER; ZHU, XINGUANG; BOWERS, JOHN; et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.. Nature Genetics, v. 50, n. 11, p. 1565+, . (14/50921-8, 12/51062-3, 08/52146-0)
DOS SANTOS, FERNANDA R. C.; ZUCCHI, MARIA I.; PARK, JONG-WON; BENATTI, THIAGO R.; DA SILVA, JORGE A.; SOUZA, GLAUCIA M.; LANDELL, MARCOS G. A.; PINTO, LUCIANA R.. New Sugarcane Microsatellites and Target Region Amplification Polymorphism Primers Designed from Candidate Genes Related to Disease Resistance. SUGAR TECH, v. 19, n. 2, p. 219-224, . (05/55258-6, 08/52146-0)
NISHIYAMA, JR., MILTON YUTAKA; FERREIRA, SAVIO SIQUEIRA; TANG, PEI-ZHONG; BECKER, SCOTT; POERTNER-TALIANA, ANTJE; SOUZA, GLAUCIA MENDES. Full-Length Enriched cDNA Libraries and ORFeome Analysis of Sugarcane Hybrid and Ancestor Genotypes. PLoS One, v. 9, n. 9, . (08/52146-0)