Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on F_SToutlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.

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.

Background: Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (H _P ) and fixation index (F _ST )] and group-based F _ST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results: We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Conclusions: Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.

The objective of this study was to determine species-associated differences in the seed proximate and fatty acid composition of three traditional oil crop species, hemp (Cannabis sativa), flax (Linum usitatissimum), and camelina (Camelina sativa), and the sowing season of camelina harvested under Lithuanian farming conditions for food use. Camelina seeds had the highest (p < 0.001) content of protein, oil, and sugar contents compared to both dehulled hemp and flax seeds. The amounts of protein and oil in camelina seeds were considerably increased by their summer cultivar, which showed higher (p < 0.001) contents of protein and oil than winter cultivars. However, the highest and lowest (p < 0.001) fiber content was found in flax seeds and camelina seeds, respectively. Camelina seeds showed considerably higher and lower (p < 0.001) proportions of total monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acids, respectively, compared with hemp and flax. The summer cultivar of camelina had higher (p < 0.001) proportions of saturated (SFA) and MUFA and lower proportions of PUFA compared with winter cultivars. Hemp seeds had the highest and lowest (p < 0.001) proportions of PUFA and MUFA, respectively. The n-6/n-3 PUFA ratio in hemp seeds is optimal (3.79), whereas the use of flax and camelina seeds with their n-6/n-3 ratios of 0.28 and 0.48, respectively, can significantly improve this ratio in the overall diet. The properties of oil crop seeds showed that whole seeds of hemp, flax, and camelina are potentially highly beneficial to human health.

The objective of the study was to characterize tissue-associated differences in the fatty acid composition of fat in skeletal muscles M. longissimus dorsi (loin), M. biceps femoris (hind quarter), and M. triceps brachii (shoulder), and internal organs (i.e., liver, heart, and kidney) from free-living red deer (Cervus elaphus) females (n = 11) hunted in Lithuania. Skeletal muscles were characterized by lower content of free fat compared with the offal. The highest percentage of saturated fatty acids was found in the liver fat, whereas the lowest percentage was in the heart. Red deer offal showed significantly lower and higher proportions of monounsaturated and polyunsaturated fatty acids compared to meat, respectively. Higher proportions of oleic fatty acid in the shoulder and hind quarter compared to the loin were the only significant differences between skeletal muscles. The lowest and the highest n-6 polyunsaturated/n-3 polyunsaturated fatty acids (n-6/n-3PUFA) ratio were found in the liver and heart, respectively. More favorable lower atherogenic index and higher hypocholesterolemic/hypercholesterolemic ratio found in the offal showed their high nutritional value, however, higher peroxidizability index indicated higher susceptibility to lipid peroxidation compared to skeletal muscles.