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

The C hato M urciano ( CM ), a pig breed from the M urcia region in the southeastern region of S pain, 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, SNP s and mt DNA – were applied across the majority of the total breeding stock. In addition, mt DNA and SNP s 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 E uropean 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.