Comparison of sampling strategies in differential gene expression studies

• Grant number: 18/21345-0
• Support Opportunities: Scholarships in Brazil - Master
• Start date: November 01, 2018
• End date: February 29, 2020
• Field of knowledge: Agronomical Sciences - Agronomy - Crop Science
• Principal Investigator: Gabriel Rodrigues Alves Margarido
• Grantee: Victor Hugo de Mello Pessoa
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated research grant: 15/22993-7 - Transcriptomics for the identification of commercially important genes in sugarcane, AP.BIOEN.JP

Abstract

Performing differential gene expression studies requires biological replicates from contrasting groups, in order to estimate the residual variability between samples from the same treatment. Because it is possible to perform vegetative propagation in many plant species, these differential gene expression studies often use clonal replicates of a one or a few distinct genotypes, such that conclusions are restricted to only a limited number of genotypes. Alternative strategies can be devised to provide residual variance estimates in two levels: among samples from different genotypes representing the same experimental group, or among samples from the same genotype. Due to the high cost of sequencing technologies, it is usually not viable to jointly leverage both approaches, justifying efforts to determine a more proper experimental design. In particular for sugarcane, the genetic variability employed in Brazilian breeding programs, a substantial part of which is represented in the Brazilian Panel of Sugarcane Genotypes (BPSG), is still largely unexplored regarding its genomic structure and gene expression differences. This activity plan aims to characterize the transcriptional profiles of distinct genotypes of the BPSG, with contrasting levels of sugar accumulation, according to two distinct sampling strategies. To that end, sequencing data from this research will be integrated with those obtained in a CNPq Universal project also under the responsibility of this coordinator. (AU)

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)

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)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

PESSOA, Victor Hugo de Mello. Dissecting expression patterns in the transcriptome of immature sugarcane culms: from methodology to biology. 2020. Master's Dissertation - Universidade de São Paulo (USP). Escola Superior de Agricultura Luiz de Queiroz (ESALA/BC) Piracicaba.