Discipline: genomic assessment; Keywords: homozygosity, pedigree-based inbreeding, dairy breeds, Dairy Genomics Program.

Small effective population sizes and inbreeding are major challenges faced by dairy cattle populations worldwide. Estimates of pedigree-based inbreeding (FPED) are unreliable due to a lack of pedigree data and pedigree errors and that may lead to an underestimation of inbreeding rates. Thus, inbreeding based on runs of homozygosity (FROH) has become the preferred method of estimating inbreeding as it is able to accurately predict the amount of autozygosity within the genome. No genomic estimates for inbreeding in SA dairy breeds are currently available, and therefore the aim of the study of the authors cited below was to estimate genomic inbreeding and effective population sizes for these breeds.

In this study 1002 dairy cattle, representing four dairy breeds (Ayrshire, Holstein, Jersey and SA Dairy Swiss) were genotyped at the ARC-Biotechnology Platform with the so-called bovine 50K Ilumina SNP bead chip. The genotypes originated from the Dairy Genomics Program (DGP) of the industry. The PLINK v1.90 program was used to perform animal and marker-based quality control, as well as to investigate levels of inbreeding based on runs of homozygosity. These were calculated according to the following parameters: no more than one possible heterozygous genotype was allowed and no more than two missing genotypes were allowed per window. The minimum SNP density was set to one SNP every 120 kb with no restriction placed on the minimum number of SNPs in a run of homozygosity. The maximum gap length allowed between two consecutive SNPs was no more 1000 kb. Pedigree-based inbreeding estimates were received from SA Stud Book for the Ayrshire, Holstein and Jersey and compared with the genomic inbreeding estimates.

FROH estimates for the four South African dairy populations indicated an increase in inbreeding across the last ten generations. The inbreeding coefficients estimated from FPED were lower than inbreeding estimated calculated for FROH. This difference may be due to FPED only capturing inbreeding based on recorded pedigrees that may only extend to a few generations back, whereas FROH is able to capture both ancient and recent inbreeding. The effective population size (Ne) can be used to assess inbreeding rates and thus genetic diversity within populations. The Ne for the four populations included in the study has decreased to 117, 133, 120 and 112 for the Ayrshire, Holstein, Jersey and SA Dairy Swiss, respectively as estimated approximately 13 generations ago. Strong selection pressure practiced on dairy breeds over the past few decades has resulted in high rates of genetic gain along with increases in inbreeding and thus decreases in the effective population size.  

The results indicate that inbreeding has been increasing in South African dairy populations, possibly due to the increased use of artificial insemination. Therefore, the monitoring and control of inbreeding using effective population size as a parameter, is essential for implementation of genetic improvement programs based on genomic information. 


J. Limper, C. Visser & E. van Marle-Köster, 2019. Assessment of inbreeding in SA dairy breeds on genomic parameters. In Proc. of the 51st Annual SASAS Congress, Bloemfontein, 10-12 June 2019, Abstract 77.