Pedigree- and marker-based methods in the estimation of genetic diversity in small groups of Holstein cattle

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Genetic diversity is often evaluated using pedigree information. Currently, diversity can be evaluated in more detail over the genome based on large numbers of SNP markers. Pedigree- and SNP-based diversity were compared for two small related groups of Holstein animals genotyped with the 50 k SNP chip, genome-wide, per chromosome and for part of the genome examined. Diversity was estimated with coefficient of kinship (pedigree) and expected heterozygosity (SNP). SNP-based diversity at chromosome regions was determined using 5-Mb sliding windows, and significance of difference between groups was determined by bootstrapping. Both pedigree- and SNP-based diversity indicated more diversity in one of the groups; 26 of the 30 chromosomes showed significantly more diversity for the same group, as did 25.9% of the chromosome regions. Even in small populations that are genetically close, differences in diversity can be detected. Pedigree- and SNP-based diversity give comparable differences, but SNP-based diversity shows on which chromosome regions these differences are based. For maintaining diversity in a gene bank, SNP-based diversity gives a more detailed picture than pedigree-based diversity.
Original languageEnglish
Pages (from-to)195-205
JournalJournal of Animal Breeding and Genetics
Issue number3
Publication statusPublished - 2012


  • effective population-size
  • genome-wide association
  • linkage disequilibrium
  • dairy-cattle
  • inbreeding coefficients
  • finnish ayrshire
  • fertility traits
  • selection
  • breeds
  • conservation

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