The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle
Controlling inbreeding in livestock populations is of great importance because excess relatedness among animals leads to a rapid loss of genetic variation and to adverse phenotypical effects associated with an inbreeding depression. Recent advances in genotyping technology have made it possible to study inbreeding at a molecular level by the analysis of genome-wide single nucleotide polymorphism panels. In this study, we used BovineSNP50 assay (Illumina) to estimate genomic inbreeding coefficient in 298 Holstein cattle by the analysis of the genome portion in runs of homozygosity (FROH) or using genomic relationship matrix (FGRM), and compared this data with conventional pedigree-based inbreeding coefficients (FPED). Weak or moderate Spearman’s rank correlations were observed between FROH and FPED which depended on the ROH length categories used for calculations and inclusion of animals with different number of complete generations registered in pedigrees. The highest correlations were observed when using ROH with lengths over 8 Mb (0.334). The correlations tended to increase as pedigree depth increased, and were the highest for animals with seven complete generations of pedigree data. FGRM correlated poorly with pedigree-based estimates, which suggests that ROH-based inbreeding coefficients better reflect recent relatedness among animals.
KeywordsInbreeding ROH Holstein
- Boichard D (2007) PEDIG: a Fortran package for pedigree analysis suited for large populations. Manual — Updated Version 2007Google Scholar
- Ferencakovic M, Hamzic E, Gredler B, Curik I, Solkner J (2011) Runs of homozygosity reveal genome-wide autozygosity in the Austrian Fleckvieh cattle. ACS 76:325–328Google Scholar
- Hamzić E (2011) Levels of inbreeding derived from runs of homozygosity: a comparison of Austrian and Norwegian cattle breeds. Master of Science thesis. University of Natural Resources and Life Sciences, ViennaGoogle Scholar
- Malécot G (1948) Les mathématiques de l’hérédité. Masson & Cie, Paris, pp 1–64Google Scholar
- McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, Macleod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF (2008) Runs of homozygosity in European populations. Am J Hum Genet 83:359–372CrossRefPubMedPubMedCentralGoogle Scholar