Diversity across major and candidate genes in European local pig breeds

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.

Comparative Transcriptomic Analysis of Subcutaneous Adipose Tissue from Local Pig Breeds

“…An intronic mutation in IGF2 (g.3072G > A) is strongly related to fat depot and muscle development when the G allele is present [81]. In AL pigs the G allele is fixed while in BI the A allele is residual (0.01) [6]. IGF2 was found significantly overexpressed in BI (log2 FC = −0.884, p < 0.05) despite their leaner phenotype which indicates that fat deposition is regulated at other levels.…”

“…In pigs, taste perception can influence feeding patterns which can consequently determine production traits and TAS2R39 in particular has been previously associated with increased lipid deposition [54]. A recent study that investigated the allele frequency of known polymorphisms with associated meat quality traits in European local pig breeds [6], including AL and BI, found that the missense mutation p.Leu37Ser in TAS2R39 associated with higher backfat deposition is practically absent in AL (0.01), while in BI is present in 13% of individuals. This contradicts phenotypic data and suggests that regulation of lipid content may occur at different levels and differ in pathways from AL pigs.…”

“…Increased signalling of CD40 together with the predicted activation of INSIG1 and INSIG2 in BI suggests that this breed is more sensitive to insulin whereas the AL is less sensitive like the Iberian breed.Genes 2020, 11, 422 2 of 20 inherent genetic value for biodiversity, local breeds are used to produce high quality dry-cured meat products, representing an important role in local economies, culture and landscape as the basics of sustainable local pork chains [2,4].Alentejano (AL) and Bísaro (BI) are the two main Portuguese pig breeds. AL evolved from the primitive Sus scrofa mediterraneus, belongs to the Mediterranean group of breeds [5] and is genetically similar to the Iberian (IB) pig [6]. This breed is commonly raised in the south of Portugal and generally characterized by its light bone structure, black color, short and slim extremities and energetic nature [7].…”

“…Leptin is secreted by the adipocytes as an attempt to control appetite and food intake [24], however humans and animals naturally propense to become obese, such as the IB pig, are found to display a pattern of resistance to leptin [25]. In IB pigs, leptin-resistance is at least partially justified by the presence of a fixed functional polymorphism in the leptin receptor gene [26,27] which was recently found as almost fixed in the AL (0.98) and at a much lower frequency in the BI breed (0.26) [6]. Obese animals also secrete more insulin in order to control circulating glucose levels by inducing glucose uptake and storage as glycogen, while triggering lipogenesis and preadipocyte differentiation [28,29].…”

“…Alentejano (AL) and Bísaro (BI) are the two main Portuguese pig breeds. AL evolved from the primitive Sus scrofa mediterraneus, belongs to the Mediterranean group of breeds [5] and is genetically similar to the Iberian (IB) pig [6]. This breed is commonly raised in the south of Portugal and generally characterized by its light bone structure, black color, short and slim extremities and energetic nature [7].…”