Variability in genes affecting morphological traits in the Greek black pig breed and conservation of this genetic resource

Autochthonous pig breeds of Mediterranean regions are genetic resources that are well adapted to the harsh and hot environmental conditions of this area. These breeds might represent important reservoirs of genetic variability that could be exploited in the context of climate change. The Greek black pig is a local breed mainly raised in Thessaly and Macedonia regions whose origin goes back to the ancient times. The desertification of Greek countryside occurred between 1955 and 1960 and the migration of the inhabitants to large urban centers caused a harsh extinction of this breed and the import of well-known foreign pigs. About 20 years ago, a conservation program for this breed started from only ~100 animals found in the whole country. Pigs of this breed are characterized by a solid black coat colour phenotype. The current population is constituted by a few small nuclei of pigs bred in extensive or semi extensive production systems where genetic hybridization with wild boars could frequently occur. This breed has not been characterized at the molecular genetic level yet. In this study, we analysed polymorphisms in five genes affecting coat colour and colour patterns (MC1R and KIT), growth rate and lean meat/fat deposition (IGF2) and vertebral and teat number (NR6A1 and VRTN) in a total of 59 Greek black pigs (7 boars and 52 sows). At the MC1R gene, the most frequent allele was the European dominant black ED2 (0.70). Other alleles at this gene were identified but always in heterozygous state with the dominant allele that might confer the characteristic black coat colour of the analysed animals. A new ED2 variant was also identified in three pigs. We also detected the presence of the KIT gene polymorphism associated with the belted phenotype in two animals and the KIT gene duplication in one pig. At the IGF2 gene, allele g.3072A had a frequency of 0.86. The domestic allele g.265347265T of the NR6A1 gene was the most frequent (0.84). The wild type C allele at this polymorphic site was detected in 11 pigs. Finally, the SINE insertion of 291 bp in the VRTN gene, associated with an increased number of vertebrae and teats, had a frequency equal to 0.45. The genetic variability detected in the five investigated genes can confirm, to some extent, the occurrence of introgression events with both wild boars and other pig populations, further strengthening the need to develop appropriate conservation programs of this autochthonous Greek pig breed.