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Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (Oncorhynchus mykiss)

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Abstract

Growth is one of the most important traits from both a physiological and economic perspective in aquaculture species. Thus, identifying the genomic regions and genes underpinning genetic variation for this trait is of particular interest in several fish species, including rainbow trout. In this work, we perform a genome-wide association study (GWAS) to identify the genomic regions associated with body weight at tagging (BWT) and at 18 months (BW18M) using a dense SNP panel (57 k) and 4596 genotyped rainbow trout from 105 full-sib families belonging to a Chilean breeding population. Analysis was performed by means of single-step GBLUP approach. Genetic variance explained by 20 adjacent SNP windows across the whole genome is reported. To further explore candidate genes, we focused on windows that explained the highest proportion of genetic variance in the top 10 chromosomes for each trait. The main window from the top 10 chromosomes was explored by BLAST using the first and last SNP position of each window to determine the target nucleotide sequence. As expected, the percentage of genetic variance explained by windows was relatively low, due to the polygenic nature of body weight. The most important genomic region for BWT and BW18M were located on chromosomes 15 and 24 and they explained 2.14% and 3.02% of the genetic variance for each trait, respectively. Candidate genes including several growth factors, genes involved in development of skeletal muscle and bone tissue and nutrient metabolism were identified within the associated regions for both traits BWT and BW18M. These results indicate that body weight is polygenic in nature in rainbow trout, with the most important loci explaining as much as 3% of the genetic variance for the trait. The genes identified here represent good candidates for further functional validation to uncover biological mechanisms underlying variation for growth in rainbow trout.

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Acknowledgements

We thank Aguas Claras SA. For providing the fish used in this study.

Funding

This study was funded by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP processes numbers 2017/00123-6) and FONDECYT REGULAR N° 1171720. JMY is supported by Nucleo Milenio INVASAL funded by Chile’s government program, Iniciativa Cientifica Milenio from Ministerio de Economia, Fomento y Turismo.

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Authors and Affiliations

  1. Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santa Rosa 11735, La Pintana, Santiago, Chile

    Rafael Vilhena Reis Neto, Grazyella Massako Yoshida & José Manuel Yáñez

  2. Departamento de Engenharia de Pesca, Campus Experimental de Registro, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Av. Nelso Briho Badur 430, Registro, SP, 11900-000, Brazil

    Rafael Vilhena Reis Neto

  3. School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, Jaboticabal, 14884-900, Brazil

    Grazyella Massako Yoshida

  4. Benchmark Genetics Chile S.A., Puerto Montt, Chile

    Jean Paul Lhorente & José Manuel Yáñez

  5. Núcleo Milenio INVASAL, Concepción, Chile

    José Manuel Yáñez

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  1. Rafael Vilhena Reis Neto
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  2. Grazyella Massako Yoshida
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  3. Jean Paul Lhorente
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  4. José Manuel Yáñez
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Correspondence to José Manuel Yáñez.

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Rafael Vilhena Reis Neto declares that he has no conflict of interest. Grazyella Massako Yoshida declares that he has no conflict of interest. Jean Paul Lhorente was hired by Aquainnovo S.A. during the course of the study. José Manuel Yáñez declares that he has no conflict of interest.

Ethical approval

All applicable institutional guidelines for the care and use of animals were followed. All the experimental and sampling procedures were approved by the Comité de Bioética Animal from the Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile (Certificate N 17,041-VET-UCH).

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Reis Neto, R.V., Yoshida, G.M., Lhorente, J.P. et al. Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (Oncorhynchus mykiss). Mol Genet Genomics 294, 563–571 (2019). https://doi.org/10.1007/s00438-018-1518-2

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