Empirical Determination of Breed-of-origin of Alleles in Three-breed Cross Pigs

Overview

Journal Genet Sel Evol

Publisher Biomed Central

Specialties Biology
Genetics

Date 2016 Aug 6

PMID 27491547

Citations 20

Authors

Claudia A Sevillano

Jeremie Vandenplas

John W M Bastiaansen

Mario P L Calus

Affiliations

Soon will be listed here.

Abstract

Background: Although breeding programs for pigs and poultry aim at improving crossbred performance, they mainly use training populations that consist of purebred animals. For some traits, e.g. residual feed intake, the genetic correlation between purebred and crossbred performance is low and thus including crossbred animals in the training population is required. With crossbred animals, the effects of single nucleotide polymorphisms (SNPs) may be breed-specific because linkage disequilibrium patterns between a SNP and a quantitative trait locus (QTL), and allele frequencies and allele substitution effects of a QTL may differ between breeds. To estimate the breed-specific effects of alleles in a crossbred population, the breed-of-origin of alleles in crossbred animals must be known. This study was aimed at investigating the performance of an approach that assigns breed-of-origin of alleles in real data of three-breed cross pigs. Genotypic data were available for 14,187 purebred, 1354 F1, and 1723 three-breed cross pigs.

Results: On average, 93.0 % of the alleles of three-breed cross pigs were assigned a breed-of-origin without using pedigree information and 94.6 % with using pedigree information. The assignment percentage could be improved by allowing a percentage (fr) of the copies of a haplotype to be observed in a purebred population different from the assigned breed-of-origin. Changing fr from 0 to 20 %, increased assignment of breed-of-origin by 0.6 and 0.7 % when pedigree information was and was not used, respectively, which indicates the benefit of setting fr to 20 %.

Conclusions: Breed-of-origin of alleles of three-breed cross pigs can be derived empirically without the need for pedigree information, with 93.7 % of the alleles assigned a breed-of-origin. Pedigree information is useful to reduce computation time and can slightly increase the percentage of assignments. Knowledge on the breed-of-origin of alleles allows the use of models that implement breed-specific effects of SNP alleles in genomic prediction, with the aim of improving selection of purebred animals for crossbred offspring performance.

Citing Articles

Classification of breed combinations for slaughter pigs based on genotypes-modeling DNA samples of crossbreeds as fuzzy sets from purebred founders.

Vinje H, Brustad H, Heggli A, Sevillano C, Van Son M, Gangsei L Front Genet. 2023; 14:1289130.

PMID: 38116292 PMC: 10729766. DOI: 10.3389/fgene.2023.1289130.

Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available.

Hayes B, Copley J, Dodd E, Ross E, Speight S, Fordyce G Genet Sel Evol. 2023; 55(1):71.

PMID: 37845626 PMC: 10578004. DOI: 10.1186/s12711-023-00847-6.

Estimation of dam line composition of 3-way crossbred animals using genomic information.

Calus M, Henshall J, Hawken R, Vandenplas J Genet Sel Evol. 2022; 54(1):44.

PMID: 35705918 PMC: 9199202. DOI: 10.1186/s12711-022-00728-4.

Genomic Prediction Methods Accounting for Nonadditive Genetic Effects.

Varona L, Legarra A, Toro M, Vitezica Z Methods Mol Biol. 2022; 2467:219-243.

PMID: 35451778 DOI: 10.1007/978-1-0716-2205-6_8.

Editorial: Advances in Genomics of Crossbred Farm Animals.

Wu X, Zhao S Front Genet. 2021; 12:709483.

PMID: 34422012 PMC: 8375302. DOI: 10.3389/fgene.2021.709483.

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