| Full text | |
| Author(s): |
Victor Hugo Mello
[1]
;
Ana Letycia Basso Garcia
[2]
;
Fernando Henrique Correr
[3]
;
Guilherme Kenichi Hosaka
[4]
;
Monalisa Sampaio Carneiro
[5]
;
Gabriel Rodrigues Alves Margarido
[6]
Total Authors: 6
|
| Affiliation: | [1] Universidade de São Paulo. Escola Superior de Agricultura Luiz de Queiroz. Departamento de Genética - Brasil
[2] Universidade de São Paulo. Escola Superior de Agricultura Luiz de Queiroz. Departamento de Genética - Brasil
[3] Universidade de São Paulo. Escola Superior de Agricultura Luiz de Queiroz. Departamento de Genética - Brasil
[4] Universidade de São Paulo. Escola Superior de Agricultura Luiz de Queiroz. Departamento de Genética - Brasil
[5] Universidade Federal de São Carlos. Centro de Ciências Agrárias. Departamento de Biotecnologia e Produção Vegetal e Animal - Brasil
[6] Universidade de São Paulo. Escola Superior de Agricultura Luiz de Queiroz. Departamento de Genética - Brasil
Total Affiliations: 6
|
| Document type: | Journal article |
| Source: | GENETICS AND MOLECULAR BIOLOGY; v. 46, n. 1 2023-04-03. |
| Abstract | |
Abstract A key procedure for ensuring statistical confidence in differential gene expression analyses is to use biological replicates to compare distinct groups. Biological replicates allow the estimation of the residual variation in the gene expression levels among samples of a given experimental condition. In sugarcane, it is possible to obtain an estimate of residual variability at two levels: among samples of distinct genotypes of the same experimental treatment, or clonal replicates of the same genotype. The sequencing costs are often a limitation to leveraging both these levels in the same study, stressing the relevance of efforts to determine an appropriate experimental design. We aim to investigate this question by comparing the transcriptional profiles of young sugarcane culms with different sucrose levels using both sampling strategies. Our results show that clonal replicates provided enough statistical power to identify nearly three times more deferentially expressed genes than the more diverse strategy. However, it resulted in potentially less meaningful biological results, because many of the significant genes were likely related to the particular genotype of choice, rather than representing a common expression profile for the compared groups. This study supports the development of sound experimental designs in new studies regarding differential expression for sugarcane. (AU) | |
| FAPESP's process: | 18/21345-0 - Comparison of sampling strategies in differential gene expression studies |
| Grantee: | Victor Hugo de Mello Pessoa |
| Support Opportunities: | Scholarships in Brazil - Master |
| FAPESP's process: | 15/22993-7 - Transcriptomics for the identification of commercially important genes in sugarcane |
| Grantee: | Gabriel Rodrigues Alves Margarido |
| Support Opportunities: | Program for Research on Bioenergy (BIOEN) - Young Investigators Grants |