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 F_ST 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.

Encuesta de datos demográficos y fenotípicos de razas locales de cerdos del proyecto TREASURE

Este trabajo presenta los resultados de una encuesta de datos demográficos y fenotípicos de 20 razas locales de cerdos en estudio en el proyecto H2020 TREASURE y incluí información de: parámetros demográficos, características morfológicas principales, parámetros reproductivos, informaciones adicionales a nivel de los efectivos (ex. Temperamento, instalaciones, prácticas de cubrición), orígenes y desarrollo de las razas. Casi todas las razas (18 de 20) tienen libro genealógico, aunque su fecha de inicio varía mucho (de 1980 a 2006). El número de hembras reproductoras varía de 24 (Moravka) a más de 200 mil cabezas (Ibérico). La relación macho/hembra varía mucho con los valores más altos verificados en las razas italianas muy probablemente debido a una política diferente relativamente al registro de animales. Casi todas las razas tienen programas de conservación, aunque pocas están interesadas en otras técnicas de conservación y sólo en menos que 5 razas los datos relativos a número de efectivos y de coeficiente de consanguinidad están fácilmente disponibles. Los valores medios para números de pezones, tamaño de camada y lechones destetados son de 12, 8 y 6, respectivamente con un grande potencial para mejora. El escenario descrito es altamente diversificado y esta colecta de datos representa el punto de partida para una marca colectiva debajo del parasol del proyecto TREASURE.

Concentrations of lipoproteins in the serum of wild boar and Lithuanian pig breeds followed by principal component and cluster analyses to demonstrate the differences among genotypes

With the aim of evaluating serum cholesterol and triglyceride concentrations in Lithuanian wild boar and Lithuanian pig breeds, twelve gilts from three genotype groups were used in the experiment. Only the concentration of high-density lipoprotein (HDL) was significantly higher in the serum of wild boar than in serum of domestic pig breeds (P < 0.05). Factor loadings of the principal components (PCs) revealed that lipoproteins were positively related in PC1 for wild boars but associations between lipoproteins of domestic pigs varied differently in PC1 and PC2. Cluster analysis showed a greater distance between wild boar and domestic pigs than that between two domestic pig breeds.