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Open Access Research article

Improved estimation of inbreeding and kinship in pigs using optimized SNP panels

Marcos S Lopes1*, Fabyano F Silva2, Barbara Harlizius1, Naomi Duijvesteijn1, Paulo S Lopes2, Simone EF Guimarães2 and Egbert F Knol1

Author Affiliations

1 TOPIGS Research Center IPG B.V., P.O. Box 43, 6640 AA, Beuningen, the Netherlands

2 Departamento de Zootecnia, Universidade Federal de Viçosa, 36571-000, Viçosa, MG, Brazil

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BMC Genetics 2013, 14:92  doi:10.1186/1471-2156-14-92

Published: 25 September 2013

Abstract

Background

Traditional breeding programs consider an average pairwise kinship between sibs. Based on pedigree information, the relationship matrix is used for genetic evaluations disregarding variation due to Mendelian sampling. Therefore, inbreeding and kinship coefficients are either over or underestimated resulting in reduction of accuracy of genetic evaluations and genetic progress. Single nucleotide polymorphism (SNPs) can be used to estimate pairwise kinship and individual inbreeding more accurately. The aim of this study was to optimize the selection of markers and determine the required number of SNPs for estimation of kinship and inbreeding.

Results

A total of 1,565 animals from three commercial pig populations were analyzed for 28,740 SNPs from the PorcineSNP60 Beadchip. Mean genomic inbreeding was higher than pedigree-based estimates in lines 2 and 3, but lower in line 1. As expected, a larger variation of genomic kinship estimates was observed for half and full sibs than for pedigree-based kinship reflecting Mendelian sampling. Genomic kinship between father-offspring pairs was lower (0.23) than the estimate based on pedigree (0.26). Bootstrap analyses using six reduced SNP panels (n = 500, 1000, 1500, 2000, 2500 and 3000) showed that 2,000 SNPs were able to reproduce the results very close to those obtained using the full set of unlinked markers (n = 7,984-10,235) with high correlations (inbreeding r > 0.82 and kinship r > 0.96) and low variation between different sets with the same number of SNPs.

Conclusions

Variation of kinship between sibs due to Mendelian sampling is better captured using genomic information than the pedigree-based method. Therefore, the reduced sets of SNPs could generate more accurate kinship coefficients between sibs than the pedigree-based method. Variation of genomic kinship of father-offspring pairs is recommended as a parameter to determine accuracy of the method rather than correlation with pedigree-based estimates. Inbreeding and kinship coefficients can be estimated with high accuracy using ≥2,000 unlinked SNPs within all three commercial pig lines evaluated. However, a larger number of SNPs might be necessary in other populations or across lines.

Keywords:
Linkage equilibrium; Bootstrap; Pedigree; Genomic selection; Relationship