Effects of Genotype on Pig Carcass, Meat Quality and Consumer Sensory Evaluation of Loins and Bellies.

The objective of the study was to compare carcass and meat quality among Lithuanian White, Lithuanian Indigenous Wattle and conventional hybrids as well as consumer sensory evaluations. The pigs were slaughtered at a live weight of approximately 95-100 kg. After 24 h of slaughter, carcasses were evaluated and sampled for the analysis of meat quality traits of loins and consumer evaluation of cooked loins and baked bellies. The pigs of both Lithuanian breeds had higher backfat thickness and depth of underbelly but lower loin area compared with hybrids. However, more fatty local breeds had higher intramuscular fat content but lower cholesterol content than hybrids. The loins from local pigs displayed higher pH and colour with lower lightness and yellowness but higher redness and also lower cooking loss, shear force and hardness than conventional hybrids. Pork from lean hybrids had a higher proportion of polyunsaturated fatty acids and more favourable lipid quality indices such as atherogenic (AI) and thrombogenic (TI) indices and the hypocholesterolemic/hypercholesterolemic (h/H) ratio; however, the peroxidisability index (PI) and iodine value (IV) were less favourable compared with local pigs. Consumers evaluated cooked loins and baked bellies. The loins from local breeds scored higher in juiciness, taste and overall acceptability compared with conventional hybrids. However, a higher overall acceptability was observed for the lean bellies of hybrids. The results can be used to increase pork consumption choices.

A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits.

BACKGROUND: Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments. RESULTS: Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene. CONCLUSIONS: In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.

Genetic Variability and Conservation Challenges in Lithuanian Dairy Cattle Populations.

The purpose of the study was to investigate the genetic variability of open Lithuanian Red and Red-and-White (LRWP) and Lithuanian Black-and-White (LBWP) dairy cattle populations and indicate the differences from the old genotypes of Lithuanian Black-and-White (LBW) and Lithuanian Red cattle (LR), which are currently under a conservation program. In order to gain a better understanding of the populations under conservation and to minimize the potential influence of other breeds, a distinct subgroup was formed that comprised animals whose father and mother belonged to the same breed (LR_pure and LBW_pure). The genetic variability was estimated using the number of founders, pedigree completeness, number of males and females in reproduction and age distribution, generation interval (GI), inbreeding coefficient (F) and effective population size (Ne). The highest average pedigree completeness values in the second generations of the old genotype LR and LBW were 100%. Higher ages of females in the populations under conservation were related to a higher GI and their longer life expectancy. In 2021, the reproductive age of bulls used for insemination within these populations ranged from 5.1 to 27.8 years. The proportions of males producing offspring in their older age indicate that the semen was used from the national gene bank of commercial artificial insemination companies. The GI (>5) in LR and LBW females was higher than that in LRWP and LBWP. The analysis of the data over the 15-year period showed that the GI of males in LRWP and LBWP decreased equally by 38%, while in LR_pure population, it increased by 80%. A high (9.24%) average inbreeding coefficient (F) was found in inbred animals of LR_pure population, while in LBW_pure, it was 5.35% in 2021. The coefficient of inbreeding varied within the different cattle populations. In the open LR population, it ranged from 1.48% to 2.7%, while in the LRWP population, it fell between 2.12% and 3.72%. The lowest effective population size (Ne) concerning the rate of inbreeding was observed in LBW_pure (23) and LR_pure (59), with the highest Ne identified in the LBWP population (462). When considering Ne based on the number of parents, LR_pure displayed the lowest Ne (42), while the highest Ne was found in LBWP (4449). An analysis of local cattle populations reveals that LR faces the most critical situation. This particular population has been steadily declining for a number of years, necessitating additional measures and efforts to safeguard the LR's ancestral genetic makeup. The results of the LBWP analysis also highlight a concerning trend. Even in very large populations with open breeding programs, the effective population size per generation can experience a significant decrease.

Effects of Sex and Hunting Season on Carcass and Meat Quality Characteristics of the Brown Hare (Lepus europaeus).

The objective of the study was to determine the effects of sex and hunting season on the carcass, meat and fat quality of hunted brown hares (Lepus europaeus). Twenty-two hares of both sexes hunted in winter (December) during two hunting seasons in accordance with the law on hunting in Lithuania were evaluated using reference methods The data were subjected to two-factor analysis of variance in the general linear (GLM) procedure. No significant differences in carcass measurements and muscularity or internal organs between the sexes of brown hares were found; however, the hunting season appeared to affect the size of hares. The biceps femoris (BF) thigh muscle of males had lower (p < 0.05) dry matter content and higher (p < 0.05) drip loss compared with females. The hunting season demonstrated an effect (p < 0.001) on protein and hydroxyproline contents in the longissimus thoracis et lumborum (LTL) and affected dry matter, protein and hydroxyproline contents (p < 0.05, p < 0.001 and p < 0.01, respectively) in BF muscles, and differences in the colour of muscles were also observed. The shear force in the Warner-Bratzler (WB) test was higher (p < 0.001 and p < 0.01, respectively) for LTL and BF muscles during the first hunting season. The hunting season did not affect the total SFA in the intramuscular fat (IMF) of all the tissues, but it affected levels of monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acids in the muscles. No differences were found in the total saturated fatty acids (SFA) of both muscles between the sexes, but females demonstrated lower (p < 0.05 and p < 0.01, respectively) and more favourable n-6/n-3 PUFA ratios in the muscles and fat and a lower (p < 0.05) thrombogenic (TI) index in the LTL compared with males.

Prediction of fatty acid composition in intact and minced fat of European autochthonous pigs breeds by near infrared spectroscopy.

The fatty acids profile has been playing a decisive role in recent years, thanks to technological, sensory and health demands from producers and consumers. The application of NIRS technique on fat tissues, could lead to more efficient, practical, and economical in the quality control. The study aim was to assess the accuracy of Fourier Transformed Near Infrared Spectroscopy technique to determine fatty acids composition in fat of 12 European local pig breeds. A total of 439 spectra of backfat were collected both in intact and minced tissue and then were analyzed using gas chromatographic analysis. Predictive equations were developed using the 80% of samples for the calibration, followed by full cross validation, and the remaining 20% for the external validation test. NIRS analysis of minced samples allowed a better response for fatty acid families, n6 PUFA, it is promising both for n3 PUFA quantification and for the screening (high, low value) of the major fatty acids. Intact fat prediction, although with a lower predictive ability, seems suitable for PUFA and n6 PUFA while for other families allows only a discrimination between high and low values.

Cranial Morphology of Lithuanian Indigenous Wattle Pigs and Their Hybrids with Wild Boar.

The diversity of domestic pig breeds and their hybridization increases the variety of phenotypes expressed in hybrids. The aim of this study was to quantify the differences of cranial morphologies between local Lithuanian Indigenous Wattle pigs and theirhybrids with wild boar. A total of sixteen craniometric measurements were performed on the lateral, ventral and dorsal sides of 71 skulls of Lithuanian Indigenous Wattle pigs and their hybrids, including 1/4 wild boar (WB), 1/2 wild boar and 3/4 wild boar genotypes. The weight of the skull was affected by the genotype, live weight and sex of the animal. The size of the skull, particularly related to skull length parameters, increased consistently with the increase of the wild boar proportion in the hybrids. However, the Sus scrofa genotype did not affect the skull height. Clear discrimination was possible between the local Lithuanian breed pigs and their hybrids with different proportions of wild boar and between individual groups of hybrids. The most correct classification was determined on the basis of the overall and length parameters of the crania. This could contribute to better management and utilization of hybrids.

Effects of Dietary Rapeseed (Brassica napus), Hemp (Cannabis sativa) and Camelina (Camelina sativa) Seed Cakes Supplementation on Yolk and Albumen Colour and Nutritional Value of Yolk Lipids in Estonian Quail Eggs.

The aim of this study was to investigate the effects of supplementing commercial diets with rapeseed, hempseed and camelina seed cakes on the yolk and albumen colour and nutritional value of yolk lipids in Estonian quail eggs. A total of 585 eggs were used to evaluate egg weight, yolk and albumen pH and colour, proximate yolk composition, cholesterol content and fatty acid composition in the yolk lipids of three Estonian quail groups each fed a diet supplemented with 10% rapeseed, hemp or camelina seed cakes. The higher (p < 0.01 and p < 0.05, respectively) lightness (L*) of the yolk was detected in the group of quail fed the diet supplemented with rapeseed and camelina cakes compared to the hempseed addition. Meanwhile, the albumen lightness in the rapeseed group was higher (p < 0.01) in comparison to the camelina group. A lower (p < 0.001) yolk negative a* value was estimated in the hemp group than in the groups fed rapeseed and camelina seed cake supplements, while the rapeseed group demonstrated lower (p < 0.001) albumen yellowness (b*) and colour saturation (C) in comparison to the other groups. The highest and lowest proportions of total saturated (SFAs)and monounsaturated (MUFAs) fatty acids, respectively, were found in the yolk lipids of quails fed a mixture supplemented by hemp cake. A higher (p < 0.05) proportion of polyunsaturated fatty acids (PUFAs) was only found in the hemp group compared to the camelina group. The highest and lowest (p < 0.001) n-6/n-3 PUFA ratios were found in the yolk lipids of quail receiving mixtures supplemented with rapeseed and camelina cakes, respectively. The yolk of the quail from the rapeseed group showed more favourable lower and higher (p < 0.01 and p < 0.05, respectively) atherogenic index (AI) and hypocholesterolemic/hypercholesterolemic (h/H) ratio compared to the hemp and camelina groups. The lower yolk cholesterol content was found in the eggs of the quail fed the diet supplemented with rapeseed cake compared to the eggs of the quail which were fed the diets containing more n-3 PUFAs from the addition of hemp and camelina cakes (p < 0.05 and p < 0.01, respectively).

Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data.

Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krskopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products.

Effects of Dietary Rapeseed and Camelina Seed Cakes on Physical-Technological Properties of Goose Meat.

The objective of the present study was to investigate the effects of commercial diet supplemented with rapeseed and camelina seed cakes on the physical and technological attributes of goose meat quality. The breast and thigh muscles from thirty geese of both sexes of the Lithuanian native breed Vistines fed the diet containing either rapeseed cake (group 1) or camelina cake (group 2) at the age of 13 weeks were used for the evaluation of physical and technological attributes. The diet did not affect the colour of goose meat; however, females showed higher (p < 0.05) values of breast yellowness (b*) and hue angle (h). The camelina group demonstrated higher (p < 0.001) cooking losses of breast and thigh muscles and also higher (p < 0.05) EZ drip loss and thawing loss of thigh muscles compared with the rapeseed group. Females had higher (p < 0.05) cooking loss of the breast, whereas males had higher (p < 0.05) cooking loss of the thigh. The growth rate of geese and their slaughter time showed an effect (p < 0.05 and p < 0.01, respectively) on pH of thigh muscles. Higher (p < 0.01) hardness of the breast muscle in the camelina group compared with the rapeseed group was detected by the texture profile analysis (TPA) as well as other parameters such as cohesiveness and gumminess, chewiness. Despite some differences in technological meat quality attributes, the quality of goose meat produced with diet supplementation of 10% of rapeseed cake and camelina seed cake can be considered as suitable.

Present Conservation Status and Carcass and Meat Characteristics of Lithuanian Vistines Goose Breed.

The aim of the present study was to identify the conservation status of Lithuanian local Vistines goose breed and evaluate the carcass and meat quality characteristics in the breast and thigh depending on the sex. The status of the Lithuanian Vistines goose breed was evaluated by monitoring of the birds, which are included in the breeding system. Twenty geese from the nucleus flock at the age of 10 weeks and reared using a commercial concentrate diet ad libitum were used for the carcass and meat quality evaluation. Due to fluctuations in the numbers of geese and reproduction of purebred birds on a largest scale from the nucleus flock, the status of Vistines goose population remains critical-maintained. The difference in the live body weight between males and females was insignificant, whereas males showed higher carcass weight (p < 0.05), including the weight of breast, wings, thighs and neck. The sex did not affect the meat quality parameters, but the anatomical location of muscles has appeared to show a high effect. Thigh muscles had lower (p < 0.01 and p < 0.001, respectively) protein and cholesterol, and higher (p < 0.001) intramuscular fat contents compared with the breast. Thigh muscles also showed higher (p < 0.001 and p < 0.01, respectively) pH and EZ drip loss, but lower (p < 0.001) cooking loss compared with the breast. The breast was characterized by a higher (p < 0.001) shear of force and toughness with Warner-Bratzler test and higher (p < 0.001) hardness detected by texture profile analysis (TPA) compared with the thigh. Breast lipids had higher (p < 0.001) proportion of total saturated and polyunsaturated fatty acids, whereas the thigh was characterized by a higher proportion of monounsaturated fatty acids. Atherogenic (AI) and thrombogenic (TI) indexes were higher (p < 0.001) and hypocholesterolemic/hypercholesterolemic (h/H) ratio was lower (p < 0.001) and less favourable in the breast compared with the thigh. Despite the muscle type differences, goose meat of the local conserved breed exhibited good quality and expected enhancing impact on consumer health.

Pork Consumption Frequencies, Attitudes and Sensory Acceptance of Traditional Products in Lithuania.

Finding a niche for the wider use of local pigs highlighted the need for information about consumer attitudes regarding pork and traditional products and the acceptability of fatter meat. With the aim to ascertain pork consumption frequency and Lithuanian consumer attitudes towards traditional pork products, as well as acceptability of traditional sausages from the meat of Lithuanian White pigs, a questionnaire-based survey and consumer sensory tests were conducted. A total of 136 meat consumers participated in the study. Respondents reported that they consume fresh or processed pork from 1 to 10 times weekly. Male respondents were more familiar with Lithuanian local pig breeds, while female respondents demonstrated knowledge of pork products. Boomer generation (1946-1964) respondents mostly (χ2 = 29.53, df = 10, p < 0.001) had pork at home compared with the respondents of younger generations. There were no significant differences in the blind sensory acceptance between sausages made in a traditional way and cold-smoked with different quantity of salt and commercial sausages of premium quality, while conventional hot-smoked sausages had lower (p < 0.001) overall acceptance. The highest (p < 0.005 and p < 0.01, respectively) acceptance for salt reduction in traditional sausages was demonstrated by the X generation (1965-1980) consumers compared with older boomer and subsequent Y (1965-1980) generations.

Effect of Gender on Meat Quality from Adult Obsolescent Horses.

The objective of the study was to assess the influence of gender, age, and carcass weight on the properties of meat from adult horses slaughtered in Lithuania. M. pectoralis profundus of twenty-six obsolescent horses from 3 to 21 years of age were used in the experiment. Gender appeared to affect the horse meat properties. Stallions demonstrated (p < 0.01 and p < 0.05, respectively) lower content of dry matter and also considerably lower (p < 0.001 and p < 0.01) intramuscular fat content compared with mares and geldings and higher (p < 0.01) cholesterol content compared with mares. The meat of stallions showed the highest pH; however, a significant (p < 0.01) difference was obtained only in comparison with mares. Meat lightness (L*) and yellowness (b*) of stallions were lower (p < 0.05) compared with geldings. Meat toughness of stallions was also lower (p < 0.01) than the meat of mares and geldings. The highest (p < 0.05 and p < 0.01, respectively) proportion of total polyunsaturated fatty acids (PUFA), higher (p < 0.05) and more favorable PUFA/SFA ratio, and also the highest (p < 0.05) but least favorable n-6/n-3 PUFA ratio, were detected in the muscles of stallions compared with mares and geldings. The differences in horse ages did not exhibit any effect on the properties of M. pectoralis profundus. Despite the age differences at the decline of horse life, the properties of the horse meat exhibited good quality and showed that horse meat is potentially highly beneficial to human health.

Fatty Acid Composition of Cannabis sativa, Linum usitatissimum and Camelina sativa Seeds Harvested in Lithuania for Food Use.

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.

Pork Quality of Two Lithuanian Breeds: Effects of Breed, Gender and Feeding Regimen.

The diversity of breeds is an important factor influencing carcass and meat quality traits that are also associated with other different effects. The objective of this study was to investigate the effects of breed, gender, and feeding level in the finishing phase on the carcass and meat quality of Lithuanian White and Lithuanian Indigenous Wattle pigs reared indoors. After 60 kg weight, half of the animals from both breeds were fed a restricted diet of approximately 82% of average ad libitum feeding intake, and the other half of pigs were further fed ad libitum to the end of the experiment. Feed restriction during the finishing phase decreased daily gain and weight of pigs at slaughter, and backfat thickness at the tenth rib (p ˂ 0.001, p ˂ 0.01, and p ˂ 0.05, respectively). Lithuanian White pigs demonstrated higher (p ˂ 0.001) growth rate, live body weight at slaughter and carcass weight, and had a higher (p ˂ 0.01) length of carcass and loin area and lower (p ˂ 0.05) backfat thickness at the last rib and at two points at the lumbar area compared with Lithuanian Indigenous Wattle pigs. The semimembranosus muscle of Lithuanian White pigs had relatively (8.1%) lower (p ˂ 0.001) proportions of saturated and 41.2% higher (p ˂ 0.001) proportions of polyunsaturated fatty acids compared with the pigs of the Lithuanian Indigenous Wattle breed, whereas in the longissimus muscle and subcutaneous tissue, the breed only affected the n-6/n-3 ratio (p ˂ 0.01 and p ˂ 0.001, respectively). Gender showed an effect on saturated fatty acids in all the studied tissues, however, the effects on polyunsaturated fatty acids were found in the semimembranosus muscle and subcutaneous tissue (p ˂ 0.05 and p ˂ 0.001) and the effects on monounsaturated fatty acids was found only in the semimembranosus muscle (p ˂ 0.01). These differences in the fatty acid composition of the semimembranosus muscle and subcutaneous tissue of females exhibited more favorable lipid quality indices compared with castrated males (p ˂ 0.001). The semimembranosus muscle of Lithuanian White pigs also showed more favorable lipid quality indices in relation to healthy nutrition compared with Lithuanian Indigenous Wattle pigs (p ˂ 0.001). This study is one of the steps toward the development and utilization of endangered breeds. The obtained information can be used to increase choice in pork production and consumption, and provides new insights for research into the conservation of local breeds.

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources.

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a "One Health" perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a "One Health" perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.

Fatty Acid Composition of Meat and Edible Offal from Free-Living Red Deer (Cervus elaphus).

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.

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems.

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, Krskopolje 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 (HP) and fixation index (FST)] and group-based FST 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.

Diversity across major and candidate genes in European local pig breeds.

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, Krskopolje (Krskopoljski), 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.