- Population structure and pedigree analysis of the Carnarvon Afrino flock
POPULATION STRUCTURE AND PEDIGREE ANALYSIS OF THE CARNARVON AFRINO FLOCK
M.A. Snyman# & W.J. Olivier
Grootfontein Agricultural Development Institute, Private bag X529, Middelburg EC, 5900, South Africa
#Corresponding author: Gretha Snyman
Background: The Carnarvon Afrino flock was founded in 1969, when breed development of a white wool breed for the extensive sheep grazing areas started at the Carnarvon Experimental Station. Since 1980, the flock annually comprise around 180 to 200 breeding ewes and only two rams were introduced into the flock from an outside source. This flock has formed part of the biological bank of the Grootfontein Agricultural Development Institute (GADI-Biobank) since 2006. Resources from the GADI-Biobank are being used for various genomic studies by researchers throughout South Africa. Genomic studies are expensive and it is important that the correct animals are sampled for the specific studies, otherwise the results will be meaningless and a lot of money will be wasted. During 2014, role players in the sheep industry discussed the possibilities of implementing genomic selection in South Africa. However, before genomic selection can be implemented in any breed, a reference population should be established. 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 Carnarvon Afrino flock to become part of a reference population for South African woolled sheep was investigated through analysis of its population structure and pedigree.
Methodologies: Pedigree data of the flock 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 file included identification numbers for 10836 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 flock were 99.8%, 99.8%, 99.8%, 99.8, 99.7% and 99.5% for one to six generations deep, respectively. The average generation intervals for males and females were 2.4 and 3.7 years respectively, amounting to an average generation interval of 3.1 years. The average rate of change of the additive genetic relationships (Δf) for the flock was 0.00195 per year, which results in a Δf per generation of 0.00640. The rate of change of the average inbreeding coefficients (ΔF) was 0.00185, which represents a ΔF per generation of 0.00627. The average inbreeding coefficient of the 2015-born lambs was 12.21%, while the respective values for the sires and dams used in 2015 were 11.93% and 11.43%. The effective population sizes for the flock, based on Δf and ΔF were 78 and 80, respectively.
Discussion: The high degree of completeness of the pedigree of the flock will contribute to the estimation of more accurate inbreeding coefficients, effective population size and breeding values. Although both Δf and ΔF are still low, the relatively high inbreeding coefficients of the animals currently in the flock is a cause for concern. As the effective population size is above 50, the flock is currently not in danger of losing genetic diversity.
Conclusions: The Carnarvon Afrino flock is suitable for inclusion in a reference population for South African woolled sheep. However, management of the population should employ measurements to reduce the level of inbreeding in the flock.
Proceedings 49th SASAS congress, Stellenbosch