PUBLICATION
RNA Sequencing to Study Gene Expression and SNP Variations Associated with Growth in Zebrafish Fed a Plant Protein-Based Diet
- Authors
- Ulloa, P.E., Rincón, G., Islas-Trejo, A., Araneda, C., Iturra, P., Neira, R., Medrano, J.F.
- ID
- ZDB-PUB-150224-12
- Date
- 2015
- Source
- Marine biotechnology (New York, N.Y.) 17(3): 353-63 (Journal)
- Registered Authors
- Keywords
- none
- MeSH Terms
-
- Animals
- Gene Expression Profiling
- Gene Expression Regulation, Developmental*
- Gene Library
- Gene Ontology
- Genotype
- Male
- Molecular Sequence Annotation
- Muscle, Skeletal/growth & development
- Muscle, Skeletal/metabolism*
- Phenotype
- Plant Proteins, Dietary/chemistry*
- Polymorphism, Single Nucleotide*
- Sequence Analysis, RNA
- Software
- Transcriptome
- Weight Gain/genetics*
- Zebrafish/genetics*
- Zebrafish/growth & development
- PubMed
- 25702041 Full text @ Mar. Biotechnol.
Citation
Ulloa, P.E., Rincón, G., Islas-Trejo, A., Araneda, C., Iturra, P., Neira, R., Medrano, J.F. (2015) RNA Sequencing to Study Gene Expression and SNP Variations Associated with Growth in Zebrafish Fed a Plant Protein-Based Diet. Marine biotechnology (New York, N.Y.). 17(3):353-63.
Abstract
The objectives of this study were to measure gene expression in zebrafish and then identify SNP to be used as potential markers in a growth association study. We developed an approach where muscle samples collected from low- and high-growth fish were analyzed using RNA-Sequencing (RNA-seq), and SNP were chosen from the genes that were differentially expressed between the low and high groups. A population of 24 families was fed a plant protein-based diet from the larval to adult stages. From a total of 440 males, 5 % of the fish from both tails of the weight gain distribution were selected. Total RNA was extracted from individual muscle of 8 low-growth and 8 high-growth fish. Two pooled RNA-Seq libraries were prepared for each phenotype using 4 fish per library. Libraries were sequenced using the Illumina GAII Sequencer and analyzed using the CLCBio genomic workbench software. One hundred and twenty-four genes were differentially expressed between phenotypes (p value < 0.05 and FDR < 0.2). From these genes, 164 SNP were selected and genotyped in 240 fish samples. Marker-trait analysis revealed 5 SNP associated with growth in key genes (Nars, Lmod2b, Cuzd1, Acta1b, and Plac8l1). These genes are good candidates for further growth studies in fish and to consider for identification of potential SNPs associated with different growth rates in response to a plant protein-based diet.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping