Marine Biotechnology

, Volume 17, Issue 3, pp 353–363

RNA Sequencing to Study Gene Expression and SNP Variations Associated with Growth in Zebrafish Fed a Plant Protein-Based Diet

  • Pilar E. Ulloa
  • Gonzalo Rincón
  • Alma Islas-Trejo
  • Cristian Araneda
  • Patricia Iturra
  • Roberto Neira
  • Juan F. Medrano
Original Article

DOI: 10.1007/s10126-015-9624-1

Cite this article as:
Ulloa, P.E., Rincón, G., Islas-Trejo, A. et al. Mar Biotechnol (2015) 17: 353. doi:10.1007/s10126-015-9624-1

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.

Keywords

Zebrafish Gene expression Single nucleotide polymorphism Dietary plant proteins Growth association analysis 

Supplementary material

10126_2015_9624_MOESM1_ESM.docx (22 kb)
Supplementary file 1(DOCX 22 kb)
10126_2015_9624_MOESM2_ESM.docx (27 kb)
Supplementary file 2(DOCX 26 kb)
10126_2015_9624_MOESM3_ESM.docx (23 kb)
Supplementary file 3(DOCX 22 kb)
10126_2015_9624_MOESM4_ESM.docx (23 kb)
Supplementary file 4(DOCX 23 kb)

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Pilar E. Ulloa
    • 1
    • 2
    • 6
  • Gonzalo Rincón
    • 5
    • 7
  • Alma Islas-Trejo
    • 5
  • Cristian Araneda
    • 2
  • Patricia Iturra
    • 3
  • Roberto Neira
    • 2
    • 4
  • Juan F. Medrano
    • 5
  1. 1.Programa de Doctorado en Ciencias de Recursos NaturalesUniversidad de La FronteraTemucoChile
  2. 2.Departamento de Producción Animal, Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
  3. 3.Programa de Genética Humana, ICBM, Facultad de MedicinaUniversidad de ChileSantiagoChile
  4. 4.AQUAINNOVO S.A.Puerto MonttChile
  5. 5.Department of Animal ScienceUniversity of California-DavisDavisUSA
  6. 6.Departamento de Ciencias Biológicas, Facultad de Ciencias BiológicasUniversidad Andrés BelloSantiagoChile
  7. 7.Zoetis, VMRD Genetics R&DKalamazooUSA