Transcriptomics for the identification of commercially important genes in sugarcane

• Grant number: 15/22993-7
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Young Investigators Grants
• Start date: August 01, 2016
• End date: June 30, 2021
• Field of knowledge: Agronomical Sciences - Agronomy - Crop Science
• Principal Investigator: Gabriel Rodrigues Alves Margarido
• Grantee: Gabriel Rodrigues Alves Margarido
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated 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

(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)

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. (14/50921-8, 16/06917-1, 15/22993-7, 17/02270-6)

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. (12/25236-4, 08/52197-4, 15/22993-7)

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, DEC 2019. (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)

AONO, ALEXANDRE HILD; GONZAGA PIMENTA, RICARDO JOSE; BASSO GARCIA, ANA LETYCIA; CORRER, FERNANDO HENRIQUE; HOSAKA, GUILHERME KENICHI; CARRASCO, MARISHANI MARIN; CARDOSO-SILVA, CLAUDIO BENICIO; MANCINI, MELINA CRISTINA; SFORCA, DANILO AUGUSTO; DOS SANTOS, LUCAS BORGES; et al. The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns. FRONTIERS IN PLANT SCIENCE, v. 12, JUL 7 2021. (14/11482-9, 18/18588-8, 19/03232-6, 15/22993-7, 15/16399-5, 08/52197-4, 19/21682-9, 05/55258-6, 19/19340-2)

ALVES MARGARIDO, GABRIEL RODRIGUES; CORRER, FERNANDO HENRIQUE; FURTADO, AGNELO; BOTHA, FREDERIK C.; HENRY, ROBERT JAMES. imited allele-specific gene expression in highly polyploid sugarcan. Genome Research, v. 32, n. 2, p. 297-308, FEB 2022. (15/22993-7)

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. (15/22993-7, 15/17935-8)

HOSAKA, GUILHERME KENICHI; CORRER, FERNANDO HENRIQUE; DA SILVA, CARLA CRISTINA; SFORCA, DANILO AUGUSTO; BARRETO, FERNANDA ZATTI; BALSALOBRE, THIAGO WILLIAN ALMEIDA; PASHA, ASHER; DE SOUZA, ANETE PEREIRA; PROVART, NICHOLAS JAMES; CARNEIRO, MONALISA SAMPAIO; et al. Temporal Gene Expression in Apical Culms Shows Early Changes in Cell Wall Biosynthesis Genes in Sugarcane. FRONTIERS IN PLANT SCIENCE, v. 12, DEC 13 2021. (15/22993-7)

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. (15/22993-7, 13/25132-7)

CORRER, FERNANDO HENRIQUE; HOSAKA, GUILHERME KENICHI; BARRETO, FERNANDA ZATTI; VALADAO, ISABELLA BARROS; ALMEIDA BALSALOBRE, THIAGO WILLIAN; FURTADO, AGNELO; HENRY, ROBERT JAMES; CARNEIRO, MONALISA SAMPAIO; ALVES MARGARIDO, GABRIEL RODRIGUES. Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning. BMC Genomics, v. 21, n. 1, SEP 29 2020. (15/22993-7)

VICTOR HUGO MELLO; ANA LETYCIA BASSO GARCIA; FERNANDO HENRIQUE CORRER; GUILHERME KENICHI HOSAKA; MONALISA SAMPAIO CARNEIRO; GABRIEL RODRIGUES ALVES MARGARIDO. Sampling strategies for sugarcane using either clonal replicates or diverse genotypes can bias the conclusions of RNA-Seq studies. GENETICS AND MOLECULAR BIOLOGY, v. 46, n. 1, 2023-04-03. (18/21345-0, 15/22993-7)

CORRER, FERNANDO HENRIQUE; FURTADO, AGNELO; FRANCO GARCIA, ANTONIO AUGUSTO; HENRY, ROBERT JAMES; RODRIGUES ALVES MARGARIDO, GABRIEL. Allele expression biases in mixed-ploid sugarcane accessions. SCIENTIFIC REPORTS, v. 12, n. 1, p. 10-pg., 2022-05-24. (15/22993-7)

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., 2019-12-01. (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)