engleski

The impact of high density SNP chip on the estimation of genomic inbreeding in cattle

Runs of homozygosity (ROH) were recently proposed as genomic estimate of inbreeding that accounts for stochastic variation. In addition ROHs provide inference of more remote inbreeding than estimates obtained from pedigree. We analyzed impact of SNP chip density [Illumina Bovine 50k SNP chip (ld) versus Illumina Bovine HD 770k SNP chip (hd)] on the inbreeding estimates calculated for 115 Tyrolean Grey bulls. Inbreeding was calculated for whole pedigree (FpedT), for five generation pedigree (Fped5), and from five ROH lengths (k>1Mb, k>2Mb, k>4Mb, k>8Mb, k>16Mb) for both SNP chips (FldROHk & FhdROHk ). We found low FpedT and Fped5 (means of 2.2% and 1.4%) while FldROH1 and FhdROH1 gave identical value of 8.1% indicating ancient inbreeding which we were not able to detect using pedigree. For other segment lengths FhdROHk gives higher mean levels of inbreeding than FldROHk with similar variances.

inbreeding; genomic data; ROH; SNP chip density

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