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Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP ‐derived metrics
Author(s) -
Silió L.,
Rodríguez M.C.,
Fernández A.,
Barragán C.,
Benítez R.,
Óvilo C.,
Fernández A.I.
Publication year - 2013
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12031
Subject(s) - inbreeding , inbreeding depression , runs of homozygosity , biology , genetics , single nucleotide polymorphism , genotyping , population , genotype , demography , gene , sociology
Summary Multilocus homozygosity, measured as the proportion of the autosomal genome in homozygous genotypes or in runs of homozygosity, was compared with the respective pedigree inbreeding coefficients in 64 Iberian pigs genotyped using the Porcine SNP 60 Beadchip. Pigs were sampled from a set of experimental animals with a large inbreeding variation born in a closed strain with a completely recorded multi‐generation genealogy. Individual inbreeding coefficients calculated from pedigree were strongly correlated with the different SNP ‐derived metrics of homozygosity ( r = 0.814–0.919). However, unequal correlations between molecular and pedigree inbreeding were observed at chromosomal level being mainly dependent on the number of SNP s and on the correlation between heterozygosities measured across different loci. A panel of 192 SNP s of intermediate frequencies was selected for genotyping 322 piglets to test inbreeding depression on postweaning growth performance (daily gain and weight at 90 days). The negative effects on these traits of homozygosities calculated from the genotypes of 168 quality‐checked SNP s were similar to those of inbreeding coefficients. The results support that few hundreds of SNP s may be useful for measuring inbreeding and inbreeding depression, when the population structure or the mating system causes a large variance of inbreeding.