Title: Pedigree Analysis Of Five U.S. Swine Breeds And The Implications For Genetic Conservation Authors
Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 19, 2010
Publication Date: April 1, 2010
Citation: Welsh, C.S., Stewart, T.S., Schwab, C., Blackburn, H.D. 2010. Pedigree Analysis Of Five U.S. Swine Breeds And The Implications For Genetic Conservation. Journal of Animal Science. 88:1610–1618. Interpretive Summary: Interpretive Summary Assessments of inbreeding levels and the rate of increase in inbreeding have not been performed for commercially important swine breeds. Such measures provide insight into the levels of genetic diversity at the breed level and can help breeders and their organizations determine appropriate steps to maintain genetic diversity. In this study inbreeding was evaluated for the Hampshire, Duroc, Yorkshire, Landrace, and Berkshire pig breeds. Inbreeding levels and rates of change were determined by using the pedigrees of all animals registered from approximately 1980 to the present. Across all breeds the total number of animals included in the analysis was approximately 2.5 million head. It was found that the rate of inbreeding was increasing across all breeds and the range of this rate was from 0.4% to 0.7% per generation. These values are below the 1% per generation level recommended by FAO. From the inbreeding rate effective population sizes were calculated and ranged from 74 head to 113 head were found. For the five breeds the Berkshire and Landrace were shown to have the highest inbreeding rate and the lowest effective population size. As a result breeders and associations may wish to monitor the changes in inbreeding more closely in those breeds. Breed associations may wish to take additional steps by incorporating computational routines in their genetic progress programs that will minimize the amount of inbreeding that occurs.
Technical Abstract: Technical Abstract Globally, genetic diversity of livestock populations is contracting. Knowing the true extent of the contraction is needed to develop effective conservation strategies. While contractions of genetic diversity have been documented at the breed level, little within breed documentation has occurred. This situation is no different for U.S. swine breeds. Therefore, the objective of this study was to establish an inbreeding baseline for five pig breeds via pedigree records extracted from purebred registrations to each breed association for: Berkshire (n = 116,758), Duroc (n = 878,480), Hampshire (n = 744,270), Landrace (n = 126,566), and Yorkshire (n = 727,268). Number of registrations peaked in 1990, except for Berkshire (2000), and declined since that time. The breeder structure was analyzed for Berkshire and Duroc; the average breeder registered pigs for 4.0 years for both breeds. Breeders were grouped by longevity and herd size and the inbreeding levels for the current population (pigs born 2006 and later) were evaluated. Presently, more than 99% of all pigs are inbred with the majority having inbreeding less than 10%. The range for percent of animals that are more than 25% inbred ranged from 1.16% for Yorkshire to 6.09% for Berkshire. The highest inbreeding for all animals within a breed ranged from 51% for Landrace and 65% for Yorkshire. Sires were grouped into ten percentiles based on number of great-grandprogeny (GGP) produced; for all breeds, the top ten percentile accounted for more than 75% of all GGP. Sixty percent of all sires produced less than 1% of all GGP, indicating few males are contributing to future generations. Generations ranged from 17 to 19 per breed with a generation interval ranging from 1.65 yr for Berkshire to 2.21 yr for Yorkshire. Mean inbreeding (%) at generation 17 (the most generations computed across breeds), rate of inbreeding per generation, and effective population size were 12.3, 0.0065, and 77 for Berkshire, 11.8, 0.0044, and 113 for Duroc, 6.8, 0.0046, and 109 for Hampshire, 17.9, 0.0067, and 74 for Landrace, and 8.0, 0.0044, and 113 for Yorkshire, respectively. The two breeds with fewest registrations, Berkshire and Landrace, had higher inbreeding rates and lower effective population sizes, suggesting a need for more immediate conservation efforts. This analysis provides a basis for future monitoring of the genetic diversity of pig breeds and serves as a basis for planning conservation activities.