Pedigree analysis of 5 swine breeds in the United States and the implications for genetic conservation

Abstract

Globally, genetic diversity of livestock populations is contracting. Knowing the true extent of the contraction is needed to develop effective conservation strategies. Although contractions of genetic diversity have been documented at the breed level, little within breed documentation has occurred. This situation is no different for US swine breeds. Therefore, the objective of this study was to establish an inbreeding baseline for 5 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). For all breeds the number of registrations peaked after 1990 and declined since that time. The breeder structure was analyzed for Berkshire and Duroc; the average breeder registered pigs for 4.0 yr 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 percentage of animals that are more than 25% inbred ranged from 1.16% for Yorkshire to 6.09% for Berkshire. The greatest inbreeding for all animals within a breed ranged from 51% for Landrace and 65% for Yorkshire. Sires were grouped into 10 percentiles based on number of great-grandprogeny (GGP) produced; for all breeds, the top 10 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 2 breeds with fewest registrations, Berkshire and Landrace, had greater inbreeding rates and smaller 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.