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In silico analysis of transcriptome and genome sequences in sugarcane: SNPs identification, allele specific expression analysis and, development and characterization of microsatellite markers

Grant number: 12/11109-0
Support Opportunities:Scholarships in Brazil - Doctorate (Direct)
Effective date (Start): August 01, 2012
Effective date (End): January 31, 2015
Field of knowledge:Agronomical Sciences - Agronomy - Crop Science
Principal Investigator:Anete Pereira de Souza
Grantee:Cláudio Benício Cardoso da Silva
Host Institution: Centro de Biologia Molecular e Engenharia Genética (CBMEG). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
Associated research grant:08/52197-4 - Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection, AP.BIOEN.TEM


The sugarcane to be among the species most important economically in the world, have been a major source of sugar and alcohol production. The development of genetic markers, specific PCR, as the microsatellite (SSR) and SNPs, can generate information that will help the sugarcane breeding programs. This project proposes the continuation of work that began with the development of microsatellite markers from expressed sequence ESTs (EST-SSR) and genomics markers transcripts-associated. So far, 65 have been developed and characterized EST-SSR markers, which were published (Marconi et al., 2011) along with other markers previously characterized. Besides these, 326 were further developed SSR genomic, which were identified as being associated with a gene of sugarcane. For the continuity of this project, we propose the analysis of the transcriptome, using the RNA-Seq technology to transcripts mapping into six parents of three mapping populations in our laboratory. In order to identify differentially expressed transcripts, and subsequent identification of SNPs for these sequences. Furthermore, it is proposed that a study is designed to detect allele-specific expression. To implement this project, and all the support offered by the laboratory where the research will be carried out, it still is co-supervision with Dr. Renato Vicentini, which assists in the analysis of bioinformatics (AU)

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Scientific publications
(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)
ALMEIDA BALSALOBRE, THIAGO WILLIAN; PEREIRA, GUILHERME DA SILVA; ALVES MARGARIDO, GABRIEL RODRIGUES; GAZAFFI, RODRIGO; BARRETO, FERNANDA ZATTI; ANONI, CARINA OLIVEIRA; CARDOSO-SILVA, CLAUDIO BENICIO; COSTA, ESTELA ARAUJO; MANCINI, MELINA CRISTINA; HOFFMANN, HERMANN PAULO; et al. GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC Genomics, v. 18, . (12/25236-4, 12/11109-0, 08/52197-4, 08/57908-6)
MANTELLO, CAMILA CAMPOS; CARDOSO-SILVA, CLAUDIO BENICIO; DA SILVA, CARLA CRISTINA; DE SOUZA, LIVIA MOURA; SCALOPPI JUNIOR, ERIVALDO JOSE; GONCALVES, PAULO DE SOUZA; VICENTINI, RENATO; DE SOUZA, ANETE PEREIRA. De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways. PLoS One, v. 9, n. 7, . (07/50562-4, 12/50491-8, 12/11109-0, 12/05473-1)
BARRETO, M. A.; ROSA, J. R. B. F.; HOLANDA, I. S. A.; CARDOSO-SILVA, C. B.; VILDOSO, C. I. A.; AHNERT, D.; SOUZA, M. M.; CORREA, R. X.; ROYAERT, S.; MARELLI, J.; et al. QTL mapping and identification of corresponding genomic regions for black pod disease resistance to three Phytophthora species in Theobroma cacao L.. EUPHYTICA, v. 214, n. 10, . (12/11109-0)
Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
SILVA, Cláudio Benício Cardoso da. Transcriptome and genomic sequences analysis of commercial sugarcane varieties. 2015. Doctoral Thesis - Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia Campinas, SP.

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