Farm‐by‐farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed

Abstract

The Chato Murciano (CM), a pig breed from the Murcia region in the southeastern region of Spain, is a good model for endangered livestock populations. The remaining populations are bred on approximately 15 small farms, and no herdbook exists. To assess the genetic threats to the integrity and survival of the CM breed, and to aid in designing a conservation program, three genetic marker systems - microsatellites, SNPs and mtDNA - were applied across the majority of the total breeding stock. In addition, mtDNA and SNPs were genotyped in breeds that likely contributed genetically to the current CM gene pool. The analyses revealed the levels of genetic diversity within the range of other European local breeds (H(e) = 0.53). However, when the eight farms that rear at least 10 CM pigs were independently analyzed, high levels of inbreeding were found in some. Despite the evidence for recent crossbreeding with commercial breeds on a few farms, the entire breeding stock remains readily identifiable as CM, facilitating the design of traceability assays. The genetic management of the breed is consistent with farm size, farm owner and presence of other pig breeds on the farm, demonstrating the highly ad hoc nature of current CM breeding. The results of genetic diversity and substructure of the entire breed, as well as admixture and crossbreeding obtained in the present study, provide a benchmark to develop future conservation strategies. Furthermore, this study demonstrates that identifying farm-based practices and farm-based breeding stocks can aid in the design of a sustainable breeding program for minority breeds.

Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

“…Population structure analysis, based on differences in allele frequencies, has been a proven method to assess relationships between populations [23,37]. We combined this widely used approach with the estimates of persistence of phase as a measure of relationship between populations [24].…”

“…A genome-wide SNP assay, combined with a detailed recombination map for the species [20] can therefore aid in giving insight into the conservation management of pig populations. Despite the fact that SNP assays are gaining interest for traceability purposes [21,22], only few studies have used a high-density SNP assays for conservation purposes [1,12,23-25]. …”

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

“…These characteristics of local breeds are very relevant for humans living in developing countries where local domestic animals are an important source of protein. Local breeds are also appreciated in developed countries for their cultural heritage value, and as producers of traditional and high quality meat products [4, 5]. Increasingly, local heritage breeds are recognized for their potential in sustainable or organic food production systems.…”

“…Inbreeding is particularly relevant in local breeds that have low population numbers [5, 8]. The loss of genetic diversity within a breed due to drift and inbreeding can have direct consequences for reduction of survival, reproduction efficiency and capacity of adaptation to environmental changes [10].…”

Genetic admixture analysis in Prestice Black-Pied pigs

“…The most detailed information is available about the Spanish Iberian pig breed (Martínez et al, 2000;Toro et al, 2002;Fabuel et al, 2004;Alves et al, 2006;Rodrigáñez et al, 2008;Herrero-Medrano et al, 2013). All authors used data on microsatellite markers in order to describe the genetic variability of Iberian pigs.…”