Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics

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 SNP60 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 SNPs and on the correlation between heterozygosities measured across different loci. A panel of 192 SNPs 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 SNPs were similar to those of inbreeding coefficients. The results support that few hundreds of SNPs may be useful for measuring inbreeding and inbreeding depression, when the population structure or the mating system causes a large variance of inbreeding. © 2013 Blackwell Verlag GmbH.

Bibliographic Details

Main Authors:	Silió, L., Rodríguez, M. C., Fernández, A., Barragán, C., Benítez Yáñez, Rita María, Óvilo Martín, Cristina, Fernández, A. I.
Format:	artículo biblioteca
Language:	English
Published:	Wiley 2013
Subjects:	Iberian pig, Inbreeding depression, Pedigree, Runs of homozygosity, SNP,
Online Access:	http://hdl.handle.net/20.500.12792/4322 http://hdl.handle.net/10261/291895
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