Marine Biotechnology

, Volume 17, Issue 3, pp 353–363 | Cite as

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


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.


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



PEU wishes to thank the Animal Genomic Laboratory research group at the University of California-Davis where the RNA-Seq experiments were performed and the UC-Davis Genome Center for excellent technical expertise in performing the Illumina GAII sequencing. PEU received a doctoral fellowship from the Consorcio Empresarial de Genética y Desarrollo Biotecnológico para la Industria Salmonera (Aquainnovo S.A.), and Apoyo a la Realización de Tesis Doctoral Fellowship from Conicyt AT-24091052, and Becas Chile Scholarship 75110126. PEU wishes to thank the Programa Convenio Desempeño EVOLUCIONA de la Universidad de la Frontera and its Programa de Doctorado en Ciencias de Recursos Naturales.

A special thanks goes to Kamila Solis for helping in the improve the quality of the Fig. 3.

Conflict of Interest

The authors declare that they have no competing interests.

Supplementary material

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Supplementary file 1 (DOCX 22 kb)
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Supplementary file 2 (DOCX 26 kb)
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Supplementary file 3 (DOCX 22 kb)
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Supplementary file 4 (DOCX 23 kb)


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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

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