engleski

Genomic metrics of individual autozygosity, applied to a cattle population

High throughput genotyping technology provides information about a large number of genetic markers roughly evenly spread across the genome. Levels of individual homozygosity and homozygous segments (runs of homozygosity) provide information about levels of inbreeding of animals. We computed several indicators of autozygosity for a population of 1851 Simmental/Fleckvieh bulls genotyped with the Illumina Bovine SNP50 Beadchip and compared them to inbreeding coefficients calculated from pedigrees with a completeness of >6 complete generation equivalents. The genomic metrics of autozygosity, applied to all autosomal loci and pseudo-autosomal loci on the X chromosomes were: 1) Level of homozygosity: number of homozygous loci/number of all loci. 2) Runs of homozygosity: overall length of homozygous segments >3 (>1, >5) MB. 3) Diagonal element of the genomic relationship matrix as implemented in genomic selection procedures, considering average and base population allele frequencies. 4) Inbreeding coefficient (F), as calculated by FEstim software, after applying MASEL software for selecting unlinked markers 5) Inbreeding coefficient (F), as calculated by PLINK software, with and without pruning to include loci in approximate linkage disequilibrium. Results indicate that level of homozygosity seems to be more closely correlated with pedigree inbreeding coefficients than other, more sophisticated metrics of autozygosity. Among the metrics compared, the approach as implemented in the diagonal elements of the genomic relationship matrix had the lowest correlation with pedigree inbreeding.

Genotyping; Runs of homozygosity; Autozygosity; Cattle

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