- Population structure and pedigree analysis of the Grootfontein and Cradock Merino studs
POPULATION STRUCTURE AND PEDIGREE ANALYSIS OF THE GROOTFONTEIN AND CRADOCK MERINO STUDS
M.A. Snyman# & W.J. Olivier
Grootfontein Agricultural Development Institute, Private bag X529, Middelburg EC, 5900, South Africa
#Corresponding author: Gretha Snyman
Background: The Grootfontein Merino stud (GMS) and Cradock fine wool Merino stud (CFM) were founded in 1968 and 1988 respectively. While planning to establish a reference population for Merino sheep with the ultimate aim of implementing genomic selection in South Africa, it was decided to include several existing research flocks in the reference population. Several factors affect the efficiency of a reference population. The average genetic relationship among animals and the effective population size are two factors playing a role in setting up an effective reference population.
Aim: The suitability of the GMS and CFM to be part of the reference population for South African Merino sheep was investigated through analysis of the respective population structures and pedigrees.
Methodologies: Pedigree data of the studs were analysed with the POPREP software system via the website http://popreport.tzv.fal.de, provided by the Institute of Farm Animal Genetics (FLI) in Germany. The uploaded pedigree files included identification numbers for 16970 (GMS) and 10488 (CFM) animals, as well as the sire and dam, the birth date and gender of each animal. Information on pedigree completeness, generation interval, inbreeding coefficients, additive genetic relationships and effective population size was obtained from the POPREP output and data files provided.
Results: The average pedigree completeness for animals born over the past 10 years in the GMS were 99.9%, 81.5%, 68.7%, 60.1, 54.0% and 49.4% for one to six generations deep, respectively. Corresponding values in the CFM were 99.9%, 99.8%, 99.6%, 99.2%, 98.4% and 96.6% respectively. The average rate of change of the additive genetic relationships (Δf) for the GMS was 0.00028 per year, which results in a Δf per generation of 0.00087. The rate of change of the average inbreeding coefficients (ΔF) was 0.00026, which represents a ΔF per generation of 0.00078. The average inbreeding coefficient of the 2014-born lambs was 1.05%, while the respective values for the sires and dams used in 2014 were 0.51% and 1.19%. The effective population sizes for the GMS, based on Δf and ΔF were 576 and 638, respectively. For the CFM, Δf was 0.00294 per year, which results in a Δf per generation of 0.00936. The annual ΔF was 0.00284, which represents a ΔF per generation of 0.00909. The average inbreeding coefficient of the 2014-born lambs was 7.92%, while the respective values for the sires and dams used in 2014 were 6.90% and 5.84%. The effective population sizes for the CFM, based on Δf and ΔF, were 53 and 55 respectively.
Discussion: The difference in Δf and ΔF between the flocks could largely be ascribed to the degree of pedigree completeness. The lower values for the GMS are due to sires brought into the flock from outside sources during the past few years. As the effective population sizes are still above 50, the studs are currently not in danger of losing genetic diversity. However, measurements should be employed to reduce the level of inbreeding in the CFM.
Conclusions: The GMS and CFM are suitable to be part of the reference population for South African Merino sheep A combined analysis, including the industry and other participating flocks, will also be done to include the effect of genetic ties between the studs.
Proceedings 49th SASAS congress, Stellenbosch