Single-step genomic evaluation improves accuracy of breeding value predictions for resistance to infectious pancreatic necrosis virus in rainbow trout

Grazyella M Yoshida; Roberto Carvalheiro; Francisco H Rodríguez; Jean P Lhorente; José M Yáñez

doi:10.1016/j.ygeno.2018.01.008

Single-step genomic evaluation improves accuracy of breeding value predictions for resistance to infectious pancreatic necrosis virus in rainbow trout

Genomics. 2019 Mar;111(2):127-132. doi: 10.1016/j.ygeno.2018.01.008. Epub 2018 Jan 31.

Authors

Grazyella M Yoshida¹, Roberto Carvalheiro², Francisco H Rodríguez³, Jean P Lhorente⁴, José M Yáñez⁵

Affiliations

¹ Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av Santa Rosa 11735, La Pintana, Santiago 8820808, Chile; Animal Science Department, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Faculdade de Ciências Agrárias e Veterinárias (FCAV), Campus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, 14884-900 Jaboticabal, Brazil.
² Animal Science Department, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Faculdade de Ciências Agrárias e Veterinárias (FCAV), Campus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, 14884-900 Jaboticabal, Brazil.
³ Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av Santa Rosa 11735, La Pintana, Santiago 8820808, Chile; Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional del Altiplano, Av. Floral 1153, Puno, Perú.
⁴ Aquainnovo, Cardonal S/N, Puerto Montt, Chile.
⁵ Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av Santa Rosa 11735, La Pintana, Santiago 8820808, Chile; Aquainnovo, Cardonal S/N, Puerto Montt, Chile; Núcleo Milenio INVASAL, Concepción, Chile. Electronic address: jmayanez@uchile.cl.

PMID: 29357303
DOI: 10.1016/j.ygeno.2018.01.008

Abstract

The aim of this study was to compare the accuracy of breeding values (EBVs) predicted using the traditional pedigree based Best Linear Unbiased Prediction (PBLUP) and the single-step genomic Best Linear Unbiased Prediction (ssGBLUP) for resistance against infectious pancreatic necrosis virus (IPNV) in rainbow trout. A total of 2278 animals were challenged against IPNV and 768 individuals were genotyped using a 57 K single nucleotide polymorphism array for rainbow trout. Accuracies for both methods were assessed using five-fold cross-validation. The heritabilities were higher for PBLUP compared to ssGBLUP. The ssGBLUP accuracies outperformed PBLUP in 7 and 11% for days to death and binary survival, respectively. The ssGBLUP could be an alternative approach to improve the accuracy of breeding values for resistance against infectious pancreatic necrosis virus in rainbow trout, using information from genotyped and non-genotyped animals.

Keywords: Bias; Heritability; Oncorhynchus mykiss; Pearson's correlation.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Birnaviridae Infections / genetics*
Birnaviridae Infections / immunology
Disease Resistance*
Fish Diseases / genetics*
Fish Diseases / immunology
Genome-Wide Association Study / methods*
Genome-Wide Association Study / standards
Infectious pancreatic necrosis virus / pathogenicity
Selective Breeding*
Trout / genetics*
Trout / virology