Abstract
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.
This is a preview of subscription content, log in via an institution to check access.
References
Bjelland D, Weigel K, Vukasinovic N, Nkrumah J (2013) Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. J Dairy Sci 96:4697–4706
Boichard D (2007) PEDIG: a Fortran package for pedigree analysis suited for large populations. Manual — Updated Version 2007
Broman KW, Weber JL (1999) Long homozygous chromosomal segments in reference families from the Centre d’Etude du Polymorphisme Humain. Am J Hum Genet 65:1493–1500
Carothers AD, Rudan I, Kolcic I, Polasek O, Hayward C, Wright AF, Campbell H, Teague P, Hastie ND, Weber JL (2006) Estimating human inbreeding coefficients: comparison of genealogical and marker heterozygosity approaches. Ann Hum Genet 70:666–676
Charlesworth D, Willis JH (2009) Fundamental concepts in genetics. The genetics of inbreeding depression. Nat Rev Genet 10:783–796
Ferencakovic M, Hamzic E, Gredler B, Curik I, Solkner J (2011) Runs of homozygosity reveal genome-wide autozygosity in the Austrian Fleckvieh cattle. ACS 76:325–328
Ferenčaković M, Hamzić E, Gredler B, Solberg TR, Klemetsdal G, Curik I, Sölkner J (2013a) Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations. J Anim Breed Genet 130:286–293
Ferenčaković M, Sölkner J, Curik I (2013b) Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors. GSE 45:42
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, Vienna
Malécot G (1948) Les mathématiques de l’hérédité. Masson & Cie, Paris, pp 1–64
Marras G, Gaspa G, Sorbolini S, Dimauro C, Ajmone-Marsan P, Valentini A, Williams JL, Macciotta NPP (2014) Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Anim Genet 46:110–121
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 83:359–372
Purfield DC, Berry DP, McParland S, Bradley DG (2012) Runs of homozygosity and population history in cattle. BMC Genet 13:70
Ron M, Blanc Y, Band M, Ezra E, Weller JI (1996) Misidentification rate in the Israeli dairy cattle population and its implications for genetic improvement. J Dairy Sci 79:676–681
VanRaden P (1992) Accounting for inbreeding and crossbreeding in genetic evaluation for large populations. J Dairy Sci 75:3136–3144
VanRaden PM (2008) Efficient methods to compute genomic predictions. J Dairy Sci 91:4414–4423
Westell RA, Quaas RL, Van Vleck LD (1988) Genetic groups in an animal model. J Dairy Sci 71:1310–1318
Yang J, Lee SH, Goddard ME, Visscher PM (2011) GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 88:76–82
Zhang L, Orloff MS, Reber S, Li S, Zhao Y et al (2013) cgaTOH: extended approach for identifying tracts of homozygosity. PLoS One 8:e57772
Zhang Q, Calus MP, Guldbrandtsen B, Lund MS, Sahana G (2015) Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds. BMC Genet 16:88
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by: Maciej Szydlowski
Rights and permissions
About this article
Cite this article
Gurgul, A., Szmatoła, T., Topolski, P. et al. The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle. J Appl Genetics 57, 527–530 (2016). https://doi.org/10.1007/s13353-016-0337-6
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13353-016-0337-6