Advanced search
Start date
Betweenand

Transcriptomics for the identification of commercially important genes in sugarcane

Grant number: 15/22993-7
Support type:Program for Research on Bioenergy (BIOEN) - Young Investigators Grants
Duration: August 01, 2016 - October 31, 2020
Field of knowledge:Agronomical Sciences - Agronomy - Crop Science
Principal Investigator:Gabriel Rodrigues Alves Margarido
Grantee:Gabriel Rodrigues Alves Margarido
Home Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Assoc. researchers:Anete Pereira de Souza ; Antonio Augusto Franco Garcia ; Monalisa Sampaio Carneiro
Associated scholarship(s):18/21345-0 - Comparison of sampling strategies in differential gene expression studies, BP.MS
17/06091-9 - Evaluation of proline levels in sugarcane genotypes subjected to drought, BP.IC

Abstract

Despite the economic importance of sugarcane, knowledge on the regulation of gene expression involved in controlling biological processes of commercial relevance are scanty in this species. Among such processes, the differential production of sucrose and biomass between diverse genotypes stands out, as well as the behavior of these genotypes when faced with abiotic stresses such as water deficit. The goal of this research project is to study the gene expression profiles of sugarcane genotypes, chosen based on differences in their values of these phenotypic traits, to identify differentially expressed genes responsible for the expression of phenotypes. Additionally, we will study the relationship between allele dosage in SNP variants and the relative expression level of the various alleles of each transcript, in order to identify differential allele expression. We will collect leaf, culm and root samples from various distinct genotypes, located at extremes of the phenotypic distributions of the traits of interest. We will apply the messenger RNA sequencing methodology to quantify genome-wide expression levels of the transcripts of each sample. We will perform differential gene expression analyses between groups of genotypes contrasting with regards to sucrose accumulation, biomass production and drought resistance. We hope to identify genes responsible for the distinctive performance of superior genotypes, which will contribute in elucidating molecular mechanisms involved in controlling agronomically important traits. This information will be crucial for designing molecular breeding programmes in sugarcane, in order for the bioenergy sector to satisfy current and future demands. (AU)

Scientific publications (5)
(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)
CORRER, FERNANDO HENRIQUE; HOSAKA, GUILHERME KENICHI; GOMEZ, SERGIO GREGORIO PEREZ; CIA, MARIANA CICARELLI; VITORELLO, CLAUDIA BARROS MONTEIRO; CAMARGO, LUIS EDUARDO ARANHA; MASSOLA JR, NELSON SIDNEI; CARNEIRO, MONALISA SAMPAIO; MARGARIDO, GABRIEL RODRIGUES ALVES. Time-series expression profiling of sugarcane leaves infected with Puccinia kuehnii reveals an ineffective defense system leading to susceptibility. Plant Cell Reports, v. 39, n. 7 APR 2020. Web of Science Citations: 0.
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; NISHIYAMA, MILTON YUTAKA; TEN-CATEN, FELIPE; RAGAGNIN, GEOVANI TOLFO; ANDRADE, PABLO DE MORAIS; DE SOUZA, ROBSON FRANCISCO; NICASTRO, GIANLUCCA GONCALVES; PANDYA, RAVI; KIM, CHANGSOO; GUO, HUI; DURHAM, ALAN MITCHELL; CARNEIRO, MONALISA SAMPAIO; ZHANG, JISEN; ZHANG, XINGTAN; ZHANG, QING; MING, RAY; SCHATZ, MICHAEL C.; DAVIDSON, BOB; PATERSON, ANDREW H.; HECKERMAN, DAVID. 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 DEC 2019. Web of Science Citations: 3.
DINIZ, AUGUSTO L.; FERREIRA, SAVIO S.; TEN-CATEN, FELIPE; MARGARIDO, GABRIEL R. A.; DOS SANTOS, JOAO M.; BARBOSA, GERALDO V. DE S.; CARNEIRO, MONALISA S.; SOUZA, GLAUCIA M. Genomic resources for energy cane breeding in the post genomics era. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, v. 17, p. 1404-1414, 2019. Web of Science Citations: 0.
PEREIRA, GUILHERME S.; GARCIA, ANTONIO AUGUSTO F.; MARGARIDO, GABRIEL R. A. A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids. BMC Bioinformatics, v. 19, NOV 1 2018. Web of Science Citations: 4.
DE OLIVEIRA, AMANDA AVELAR; PASTINA, MARIA MARTA; DE SOUZA, VANDER FILIPE; DA COSTA PARRELLA, RAFAEL AUGUSTO; NODA, ROBERTO WILLIANS; FERREIRA SIMEONE, MARIA LUCIA; SCHAFFERT, ROBERT EUGENE; DE MAGALHES, JURANDIR VIEIRA; BORGES DAMASCENO, CYNTHIA MARIA; ALVES MARGARIDO, GABRIEL RODRIGUES. Genomic prediction applied to high-biomass sorghum for bioenergy production. MOLECULAR BREEDING, v. 38, n. 4 APR 2018. Web of Science Citations: 5.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.