Sampling strategies for sugarcane using either clonal replicates or diverse genotypes can bias the conclusions of RNA-Seq studies



Título del documento: Sampling strategies for sugarcane using either clonal replicates or diverse genotypes can bias the conclusions of RNA-Seq studies
Revista: Genetics and molecular biology
Base de datos: PERIÓDICA
Número de sistema: 000459156
ISSN: 1415-4757
Autores: 1
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1
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2
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Instituciones: 1Universidade de Sao Paulo, Escola Superior de Agricultura "Luiz de Queiroz", Piracicaba, Sao Paulo. Brasil
2Universidade Federal de Sao Carlos, Centro de Ciencias Agrarias, Araras, Sao Paulo. Brasil
Año:
Volumen: 46
Número: 1
País: Brasil
Idioma: Inglés
Tipo de documento: Artículo
Enfoque: Experimental, analítico
Resumen en inglés 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
Disciplinas: Biología
Palabras clave: Angiospermas,
Genética,
Caña de azúcar,
Muestreo,
Clones,
RNA-Seq
Keyword: Angiosperms,
Genetics,
Sugar cane,
Clones,
Sampling,
RNA-Seq
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