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BMC Genetics

, 18:6

Animal population genetics

Abstract

BackgroundKnowledge on the levels of linkage disequilibrium LD across the genome, persistence of gametic phase between breed pairs, genetic diversity and population structure are important parameters for the successful implementation of genomic selection. Therefore, the objectives of this study were to investigate these parameters in order to assess the feasibility of a multi-herd and multi-breed training population for genomic selection in important purebred and crossbred pig populations in Canada. A total of 3,057 animals, representative of the national populations, were genotyped with the Illumina Porcine SNP60 BeadChip 62,163 markers.

ResultsThe overall LD r between adjacent SNPs was 0.49, 0.38, 0.40 and 0.31 for Duroc, Landrace, Yorkshire and Crossbred Landrace x Yorkshire populations, respectively. The highest correlation of phase r across breeds was observed between Crossbred animals and either Landrace or Yorkshire breeds, in which r was approximately 0.80 at 1 Mbp of distance. Landrace and Yorkshire breeds presented r ≥ 0.80 in distances up to 0.1 Mbp, while Duroc breed showed r ≥ 0.80 for distances up to 0.03 Mbp with all other populations. The persistence of phase across herds were strong for all breeds, with r ≥ 0.80 up to 1.81 Mbp for Yorkshire, 1.20 Mbp for Duroc, and 0.70 Mbp for Landrace. The first two principal components clearly discriminate all the breeds. Similar levels of genetic diversity were observed among all breed groups. The current effective population size was equal to 75 for Duroc and 92 for both Landrace and Yorkshire.

ConclusionsAn overview of population structure, LD decay, demographic history and inbreeding of important pig breeds in Canada was presented. The rate of LD decay for the three Canadian pig breeds indicates that genomic selection can be successfully implemented within breeds with the current 60 K SNP panel. The use of a multi-breed training population involving Landrace and Yorkshire to estimate the genomic breeding values of crossbred animals Landrace × Yorkshire should be further evaluated. The lower correlation of phase at short distances between Duroc and the other breeds indicates that a denser panel may be required for the use of a multi-breed training population including Duroc.

KeywordsEffective population size Linkage disequilibrium Pig breeds Population structure Runs of homozygosity AbbreviationsCRCall rate

DUDuroc

F1Crossbred, Landrace × Yorkshire

GEBVGenomic estimated breeding value

GSGenomic selection

HWEHardy-Weinberg equilibrium

LALandrace

LDLinkage disequilibrium

MAFMinor allele frequency

MbpMega base pairs

NeEffective population size

QTLQuantitative trait locus

RCorrelation of gametic phase

rLinkage disequilibrium

SNPSingle nucleotide polymorphism

YOYorkshire

Electronic supplementary materialThe online version of this article doi:10.1186-s12863-017-0473-y contains supplementary material, which is available to authorized users.

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Autor: Daniela A. Grossi - Mohsen Jafarikia - Luiz F. Brito - Marcos E. Buzanskas - Mehdi Sargolzaei - Flávio S. Schenkel

Fuente: https://link.springer.com/



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