Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds.

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states.

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.

Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip.

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 FST outlier 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.

Can innovations in traditional pork products help thriving EU untapped pig breeds? A non-hypothetical discrete choice experiment with hedonic evaluation.

The EU is supporting measures that stimulate enhanced value-added products in order to conserve local and threatened livestock breeds. Several Traditional Pork Products (TPP) and Innovative Traditional Pork Products (ITPP) with health innovations from four untapped pig breeds in Spain (Porc Negre Mallorquí), Croatia (Turopolje), Italy (Cinta Senese) and Slovenia (Krskopolje) were analysed. Consumers' "Non-hypothetical" willingness to pay (WTP) and hedonic evaluation were investigated. An integrated experimental approach using two Non-Hypothetical Discrete Choice Experiment (NH-DCE) was carried out before and after a hedonic evaluation test. Results showed that the health innovative products (ITPP) received similar and even lower WTP than the "control" products (TPP) from the untapped pig breeds. The TPP outperformed products enriched with healthy ingredients or with reduced undesirable compounds. The potential demand for traditional and "unaltered" product from the rustic pig breeds could contribute to their conservation. A market niche exists, where consumers appreciate these high-quality products and where no "add-ons" are required to enhance their uptake.

Signatures of de-domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution.

Autochthonous pig breeds are usually reared in extensive or semi-extensive production systems that might facilitate contact with wild boars and, thus, reciprocal genetic exchanges. In this study, we analysed variants in the melanocortin 1 receptor (MC1R) gene (which cause different coat colour phenotypes) and in the nuclear receptor subfamily 6 group A member 1 (NR6A1) gene (associated with increased vertebral number) in 712 pigs of 12 local pig breeds raised in Italy (Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano and Sarda) and south-eastern European countries (Krskopolje from Slovenia, Black Slavonian and Turopolje from Croatia, Mangalitsa and Moravka from Serbia and East Balkan Swine from Bulgaria) and compared the data with the genetic variability at these loci investigated in 229 wild boars from populations spread in the same macro-geographic areas. None of the autochthonous pig breeds or wild boar populations were fixed for one allele at both loci. Domestic and wild-type alleles at these two genes were present in both domestic and wild populations. Findings of the distribution of MC1R alleles might be useful for tracing back the complex genetic history of autochthonous breeds. Altogether, these results indirectly demonstrate that bidirectional introgression of wild and domestic alleles is derived and affected by the human and naturally driven evolutionary forces that are shaping the Sus scrofa genome: autochthonous breeds are experiencing a sort of 'de-domestication' process, and wild resources are challenged by a 'domestication' drift. Both need to be further investigated and managed.

Vascular smooth muscle mechanics in isolated perfused segments of carotid arteries.

BACKGROUND: We hypothesized that smooth muscle contraction and relaxation responses in a muscle bath (isometric tension) would be different than responses of intact vessels (isotonic tension). METHODS: Bovine carotid artery contractile responses to the catecholamine, norepinephrine, and smooth muscle relaxant, 3-isobutyl-1-methylxanthine, were examined in strips of vessels in a muscle bath and in intact whole vessels in an isolated perfused whole-vessel perfusion apparatus. RESULTS: The maximal tension in the muscle bath depended on the length of the strip. The responses of whole vessels to increasing pressure was curvilinear. The maximal decrease in vessel diameter in intact vessels in response to the catecholamine and norepinephrine occurred at low intraluminal pressures. The dose-response curve to norepinephrine was shifted to the left in intact vessels compared with strips of vessels in the muscle bath, which suggests that whole vessels were more sensitive to norepinephrine. The maximal increase in diameter to increasing intraluminal pressure occurred in the presence of the phosphodiesterase inhibitor, 3-isobutyl-1-methylxanthine, which suggests that there was significant intrinsic tone in the vascular smooth muscle. CONCLUSIONS: These results suggest that there are differences in the contractile properties of the vascular smooth muscle that are related to the ex vivo system used to examine smooth muscle responses. Responses obtained in isolated perfused whole vessels may more closely approximate in vivo responses.

Endothelial-dependent vasodilation is associated with increases in the phosphorylation of a small heat shock protein (HSP20).

PURPOSE: Increases in the phosphorylation of a small heat shock protein (HSP20) are associated with cyclic nucleotide-dependent vasorelaxation. The effect of pressure and flow on vessel diameter was studied. We hypothesized that physiologic conditions that induce vasorelaxation would lead to increases in HSP20 phosphorylation. METHODS: Flow-dependent changes in vessel diameter, at different intraluminal pressures, were measured with a laser optical micrometer in intact bovine carotid arteries. Experiments were performed in the presence and absence of norepinephrine (10(-5) mol/L). Increases in the phosphorylation of HSP20 were determined with isoelectric focusing immunoblots. RESULTS: The increase in vessel diameter was most significant at low intraluminal pressures (20 mm Hg), high flow rates (200 mL/min), and in the presence of the vasoconstrictor norepinephrine (10(-5) mol/L). The addition of methylene blue (a guanylate cyclase inhibitor) completely inhibited flow-induced vasodilation. Under conditions in which maximal flow induced vasodilation occurred, there were significant increases in the phosphorylation of HSP20. CONCLUSION: Flow-dependent vasodilation in isolated perfused segments of bovine carotid arteries was maximal when the intraluminal pressures were low and when the vessels were precontracted with norepinephrine. Flow-dependent vasodilation was inhibited by methylene blue and was associated with increases in the phosphorylation of HSP20, suggesting that the vasodilation was mediated by endothelial production of nitric oxide.