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.

In the United States, poultry genetic resources have consolidated because of economic pressures. Such consolidations can potentially jeopardize the poultry industry and the ability of research communities to respond to future challenges. To address the loss of genetic resources for all livestock and aquatic species, USDA established the National Animal Germplasm Program (NAGP) in 1999. Since the initiation of NAGP, population surveys have been conducted on nonindustrial chicken and turkey breeds. These surveys not only provide insight into breed status, but also serve as a benchmark for future comparisons. The survey results revealed that 20 chicken breeds and 9 turkey breeds were in various stages of being lost. The NAGP has initiated an ex situ repository for cryopreserved germplasm and tissue that already contains 59 chicken lines and 2,915 tissue samples. As the NAGP, along with its industry and university partners, continues developing the ex situ collection, there are research opportunities in cryopreserved tissue utilization and studies of genetic diversity. For cryopreserved tissues, several key research areas include improving the cryopreservation protocols for rooster and tom semen by using cryoprotectants other than glycerol and utilizing embryonic cells. Although surveys have been conducted on public research lines and rare breeds, there is a void in understanding the level of genetic diversity present in U.S. poultry populations. Therefore, an opportunity exists to perform a series of genetic diversity studies using molecular- based approaches. Such an evaluation can help clarify population differences between research lines and rare breeds and, thereby, facilitate conservation strategies. There appears to be growing consumer interest in poultry products derived from heritage breeds and/or poultry raised in nonindustrial production systems. Although the depth of such market trends is unknown, such an interest may provide an important niche for rare poultry breeds and, thereby, strengthen the genetic base.

Holstein-Friesian (HF) gene bank collections were established in France, the Netherlands, and the United States to conserve genetic diversity for this breed. Genetic diversity of HF collections within and between countries was assessed and compared with active male HF populations in each country by using pedigree data. Measures of genetic diversity such as probability of gene origin inbreeding and kinship were calculated. The cryobanks have captured substantial amounts of genetic diversity for the HF compared with the current populations. A substantial part of the US, French, and Dutch collections seems to be genetically similar. On the other hand, the US collection in particular represents an interesting reservoir of HF genes of the past. Gene banks can play an important role in conserving genetic diversity within livestock breeds over time, and may support industry in the future when needed.

Genetic diversity in the U.S. Hereford population was characterized by examining the level and rate of inbreeding and effective population size. Pedigree records for 20,624,418 animals were obtained from the American Hereford Association, of which 96.1% had both parents identified. Inbreeding coefficients were computed and mean inbreeding (Fx) calculated by year from 1900 to 2001. Inbreeding increased rapidly between 1900 and 1945. From 1946, inbreeding increased linearly to a maximum of 11.5% in 1966. Throughout the 1970s and 1980s, mean inbreeding decreased to mid-century levels. Several alternatives were investigated to explain this decline. The average relationship between prominent sires fell from 20 to 12% during the time that the level of inbreeding decreased, which reflects an increase in the popularity of certain less fashionable sire lines that would have temporarily decreased inbreeding. Pedigrees were constructed for animals born after 1990. This subsample of animals with no missing ancestors in at least 12 generations did not exhibit a decrease in inbreeding. Missing ancestral information therefore contributed to the apparent decline. One cause of missing ancestry results from outcrossing to imported animals. The effect of missing ancestry was investigated by simulating the missing ancestors. In 2001, Fx was 9.8%, and approximately 95% of individuals were inbred. The maximal inbreeding coefficient was 76%. The annual change in mean inbreeding (DeltaFx) was estimated for Herefords born during five time periods from 1946 to 2001, where inbreeding was changing at different linear rates. The DeltaFx for the most recent generation (1990 to 2001) was 0.12%/yr. Assuming a generation interval of 4.88 yr, the estimated effective population size was 85. This study provides a benchmark of current genetic diversity in the Hereford population. Results indicate that inbreeding is accumulating linearly and below critical levels. Increases in the adoption of reproductive technologies could decrease genetic diversity, and in the future, we may need to consider strategies to minimize inbreeding.

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