Abstract
The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population’s structure and relationships.
Highlights
Modern pig production is mostly based on highly-selected genotypes from lean breeds, farmed in intensive production systems for provisioning the market with fresh pork
The most representative local pig breed is the Iberian raised in the southwest of the Iberian Peninsula, but there are many other breeds reared in European countries
These breeds are in general characterized by a good adaptation to specific environments, high potential for fat deposition and characteristic meat quality, mostly related to high intramuscular or intermuscular fat content, which are associated with high quality pork productions
Summary
Modern pig production is mostly based on highly-selected genotypes from lean breeds, farmed in intensive production systems for provisioning the market with fresh pork. The most representative local pig breed is the Iberian raised in the southwest of the Iberian Peninsula, but there are many other breeds reared in European countries. These breeds are in general characterized by a good adaptation to specific environments, high potential for fat deposition and characteristic meat quality, mostly related to high intramuscular or intermuscular fat content, which are associated with high quality pork productions. Conservation of animal genetic resources depends on current and future economic relevance of autochthonous breeds and on scientific importance, the cultural and historical value, adaptation to environment and contribution to the development of local communities and marginal areas. In order to help breed promotion and sustainability, a deep phenotypic and genetic characterization is needed
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