Pedigree analysis of 5 swine breeds in the United States and the implications for genetic conservation1

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.

Genealogical analysis of the Gochu Asturcelta pig breed: insights for conservation

“…In any case, the general scenario of the Gochu Asturcelta pig breed can hardly be compared with others in the literature. Indeed, pedigree depth is substantially lower than the depths reported for the well-established commercial pig breeds of Canada and the United States (Melka and Schenkel 2010;Welsh et al 2010) which included, in general, more than 11 complete generation equivalents. Nevertheless, the mean inbreeding in the breed is up to seven-fold higher than that reported for these American pig populations, ranging from 0.032 to 0.078.…”

“…Average generation interval computed for Gochu Asturcelta (1.8 years) is consistently the same as the others previously reported in the literature for non-endangered pig breeds. Melka and Schenkel (2010) reported generation intervals of 1.6 and 1.7 years for Canadian Duroc and Landrace, respectively; Welsh et al (2010), analyzing the pedigree of five United States pig breeds, reported generations intervals ranging from 1.7 (Berkshire) to 2.2 (Yorkshire) years; Tang et al (2013), in three cosmopolitan pig breeds imported into China, reported generation intervals ranging between 1.8 and 1.9 years.…”

“…Nevertheless, the mean inbreeding in the breed is up to seven-fold higher than that reported for these American pig populations, ranging from 0.032 to 0.078. Furthermore, most estimates of effective population sizes available in the literature (usually ranging from N e = 72 to N e = 125) have been obtained in pig breeds with founder populations including hundreds or thousands individuals and rates of inbreeding per generation lower than 1% (Melka and Schenkel 2010;Welsh et al 2010;Tang et al 2013). Melka and Schenkel (2010) reported N e = 14 for the Canadian Hampshire pig which had a founder population size of 257 individuals and a rate of inbreeding of 0.036.…”

“…Reports analyzing pedigree data in pig are scant Melka and Schenkel 2010;Welsh et al 2010;Tang et al 2013). Despite the local origin and development of the breed, the analysis of the very particular genetic scenario of the Gochu Asturcelta pig breed will give insights of general interest for breeders and conservationists.…”

Evaluation of conservation program for the Pantaneiro horse in Brazil

“…Ideal inbreeding rates vary between 0.05 (Nicholas, 1989) and 0.01 (FAO, 1998) per generation. This would indicate that current levels are favorable for the Pantaneiro horse but it should be remembered that registration is on the increase and Welsh et al (2010) also showed low initial inbreeding for commercial pig breeds in the US, but in later generations it increased to high levels. The predicted curve in the present study (Figure 3) shows that inbreeding cannot be ignored if conservation issues are to be met, especially with closure of the herd book.…”