A comparison of approaches to estimate the inbreeding coefficient and pairwise relatedness using genomic and pedigree data in a sheep population

Abstract

Genome-wide SNP data provide a powerful tool to estimate pairwise relatedness among individuals and individual inbreeding coefficient. The aim of this study was to compare methods for estimating the two parameters in a Finnsheep population based on genome-wide SNPs and genealogies, separately. This study included ninety-nine Finnsheep in Finland that differed in coat colours (white, black, brown, grey, and black/white spotted) and were from a large pedigree comprising 319 119 animals. All the individuals were genotyped with the Illumina Ovine SNP50K BeadChip by the International Sheep Genomics Consortium. We identified three genetic subpopulations that corresponded approximately with the coat colours (grey, white, and black and brown) of the sheep. We detected a significant subdivision among the colour types (F ST=5.4%,P<0.05).We applied robust algorithms for the genomic estimation of individual inbreeding (F SNP) and pairwise relatedness (Φ SNP) as implemented in the programs KING and PLINK, respectively. Estimates of the two parameters from pedigrees (F PED and Φ PED) were computed using the RelaX2 program. Values of the two parameters estimated from genomic and genealogical data were mostly consistent, in particular for the highly inbred animals (e.g. inbreeding coefficient F>0.0625) and pairs of closely related animals (e.g. the full- or half-sibs). Nevertheless, we also detected differences in the two parameters between the approaches, particularly with respect to the grey Finnsheep. This could be due to the smaller sample size and relative incompleteness of the pedigree for them. We conclude that the genome-wide genomic data will provide useful information on a per sample or pairwise-samples basis in cases of complex genealogies or in the absence of genealogical data. © 2011 Li et al.