The footprint of recent and strong demographic decline in the genomes of Mangalitza pigs

Altres ajuts: The authors also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016-2019 (SEV-2015-0533) grant awarded to the Centre for Research in Agricultural Genomics (CRAG). Tainã Figueiredo Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education of the Federal Government of Brazil. Thanks also to the CERCA Programme of the Generalitat de Catalunya.The Mangalitza pig breed has suffered strong population reductions due to competition with more productive cosmopolitan breeds. In the current work, we aimed to investigate the effects of this sustained demographic recession on the genomic diversity of Mangalitza pigs. By using the Porcine Single Nucleotid Polymorphism BeadChip, we have characterized the genome-wide diversity of 350 individuals including 45 Red Mangalitza (number of samples; n=20 from Hungary and n=25 from Romania), 37 Blond Mangalitza, 26 Swallow-belly Mangalitza, 48 Blond Mangalitza × Duroc crossbreds, 5 Bazna swine, 143 pigs from the Hampshire, Duroc, Landrace, Large White and Pietrain breeds and 46 wild boars from Romania (n=18) and Hungary (n=28). Performance of a multidimensional scaling plot showed that Landrace, Large White and Pietrain pigs clustered independently from Mangalitza pigs and Romanian and Hungarian wild boars. The number and total length of ROH (runs of homozygosity), as well as FROH coefficients (proportion of the autosomal genome covered ROH) did not show major differences between Mangalitza pigs and other wild and domestic pig populations. However, Romanian and Hungarian Red Mangalitza pigs displayed an increased frequency of very long ROH (>30 Mb) when compared with other porcine breeds. These results indicate that Red Mangalitza pigs underwent recent and strong inbreeding probably as a consequence of severe reductions in census size

Romanian wild boars and Mangalitza pigs have a European ancestry and harbour genetic signatures compatible with past population bottlenecks

We aimed to analyse the genetic diversity of Romanian wild boars and to compare it with that from other wild boar and pig populations from Europe and Asia. Partial sequencing of the mitochondrial encoded cytochrome b (MT-CYB) gene from 36 Romanian wild boars and 36 domestic pigs (Mangalitza, Bazna and Vietnamese breeds) showed that the diversity of Romanian wild boars and Mangalitza pigs is fairly reduced and that most of the members of these two populations share a common MT-CYB haplotype. Besides, in strong contrast with the Bazna animals, Romanian wild boars and Mangalitza swine did not carry Asian variants at the MT-CYB locus. The autosomal genotyping of 18 Romanian wild boars with the Illumina Porcine SNP60 BeadChip revealed that their genetic background is fundamentally European, even though signs of a potential Near Eastern ancestry (~25%) were detectable at K = 4 (the most significant number of clusters), but not at higher K-values. Admixture analysis also showed that two wild boars are of a hybrid origin, which could be explained by the mating of feral animals with domestic pigs. Finally, a number of Romanian wild boars displayed long runs of homozygosity, an observation that is consistent with the occurrence of past population bottlenecks and the raise of inbreeding possibly due to overhunting or to the outbreak of infectious diseases.This article was published under the frame of the European Social Fund, Human Resources Development Operational Program 2007–2013, project no. POSDRU/159/1.5/S/132765 awarded to VB. Part of the research presented in this publication was funded by grant AGL2013-48742-C2-1-R awarded by the Spanish Ministry of Economy and Competitivity to MA. We also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016-2019 (SEV-2015-0533) grant awarded to the Center for Research in Agricultural Genomics.Peer reviewe

Mitochondrial and SNP data analysis confirm the complex origin of Bazna pigs from Romania

Resumen del póster presentado a la 37th International Conference on Animal Genetics (ISAG), celebrada en Lleida (España) del 7 al 12 de julio de 2019.Bazna is a native pig breed from Romania with a black coat and white belt. It has a very tasty and marbled meat, which is much appreciated by the local consumers. The story of the Romanian Bazna breed goes back to 1872 when it is documented the first crossing between a Berkshire boar and Mangalitza sows in Transylvanian region. Subsequently these populations were infused in different episodes with cosmopolitan pig breeds. Currently there are 78 Bazna sows and 14 boars registered in the herd book. Therefore the historical data suggest an admixed origin of Bazna pigs. To verify this hypothesis we sequenced the mitochondrial Cytochrome b gene in Bazna versus Red Mangalitza and Vietnamese pigs. Additionally, using the Illumina Porcine SNP60 Bead-Chip, we have genotyped a larger panel of breeds i.e. Bazna pigs versus Mangalitza group (Red, Blonde and Swallow-belly) and a cosmopolitan group (Hampshire, Landrace, Large White and Pietrain). The NJ tree generated using mitochondrial DNA data evidenced 2 district clusters i.e. European (Mangalitza) and Asian (Vietnamese). Some of the Bazna pigs clustered tightly within the Mangalitza group, suggesting the maternal contribution of Mangalitza sows to Bazna breed formation, while some of them formed distinct sub-clusters, suggesting additional, but still European, maternal lineages. On the other hand, several Bazna pigs clustered in the Asian group, an observation which is consistent with the presence of Asian alleles in the contributing British breeds. By using SNP data we built an MDS plot, in which Bazna and Hampshire pigs occupied an intermediate position between the other 2 groups, one composed of Mangalitza pigs and the other one including cosmopolitan breeds. The Structure analysis indicated a probable contribution of Mangalitza pigs to the formation of the Bazna breed and at the same time it was evident the contribution of the British breeds, which is historically documented. Due to its superior meat quality Bazna pigs can well be the next fatty pig success story, after Iberian and Mangalitza breeds, if conservation and reproduction plans are implemented

Red and blond Mangalitza pigs display a signature of divergent directional selection in the SLC45A2 gene

The Mangalitza lard-type pig breed is well known for its fat appearance and curly hair, and it is mainly distributed in Eastern Europe. Four main lines were created in the nineteenth century by artificial selection: Blond Mangalitza, Black Mangalitza, Swallow-Belly Mangalitza and Red Mangalitza. The Swallow-Belly line has a black coat combined with yellow-blond throat and underbelly. In the current work, we aimed to investigate if the colourations of Mangalitza pigs are genetically determined by one or a few loci whose frequencies have been modified by artificial selection. The results of selection scans, with HapFLK and BayeScan, and of a GWAS for coat colour highlighted the existence of one region on SSC16 (18–20 Mb) with potential effects on hair pigmentation (Red vs. Blond contrast). The analysis of the gene content of this region allowed us to detect the solute carrier family 45 member 2 (SLC45A2) locus as a candidate gene for this trait. The polymorphism of the SLC45A2 locus has been associated with reduced levels or the absence of melanin in several mammalian species. The genotyping of four missense polymorphisms evidenced that rs341599992:G > A and rs693695020:G > A SNPs are strongly but not fully associated with the red and blond coat colours of Mangalitza pigs, a result that was confirmed by performing a haplotype association test. The near fixation of alternative SLC45A2 genotypes in Red and Blond Mangalitza pigs provides a compelling example of the consequences of a divergent directional selection for coat colour in a domestic species.Part of the research presented in this publication was funded by grant AGL2013–48742-C2–1-R awarded by the Spanish Ministry of Economy and Competitivity, and by projects TKISSE and TGENRE supported by the Hungarian Ministry of Agriculture. We also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Centre of Excellence Severo Ochoa 2016-2019 (SEV-2015-0533) grant awarded to the Centre for Research in Agricultural Genomics. Tainã Figueiredo Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education of the Federal Government of Brazil. Maria Gracia Luigi-Sierra was funded with a fellowship Formación de Personal Investigador (BES-2017-079709) awarded by the Spanish Ministry of Economy and Competitivity. Thanks also to the CERCA Programme of the Generalitat de Catalunya.Peer reviewe

The footprint of recent and strong demographic decline in the genomes of Mangalitza pigs

Altres ajuts: The authors also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016-2019 (SEV-2015-0533) grant awarded to the Centre for Research in Agricultural Genomics (CRAG). Tainã Figueiredo Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education of the Federal Government of Brazil. Thanks also to the CERCA Programme of the Generalitat de Catalunya.The Mangalitza pig breed has suffered strong population reductions due to competition with more productive cosmopolitan breeds. In the current work, we aimed to investigate the effects of this sustained demographic recession on the genomic diversity of Mangalitza pigs. By using the Porcine Single Nucleotid Polymorphism BeadChip, we have characterized the genome-wide diversity of 350 individuals including 45 Red Mangalitza (number of samples; n=20 from Hungary and n=25 from Romania), 37 Blond Mangalitza, 26 Swallow-belly Mangalitza, 48 Blond Mangalitza × Duroc crossbreds, 5 Bazna swine, 143 pigs from the Hampshire, Duroc, Landrace, Large White and Pietrain breeds and 46 wild boars from Romania (n=18) and Hungary (n=28). Performance of a multidimensional scaling plot showed that Landrace, Large White and Pietrain pigs clustered independently from Mangalitza pigs and Romanian and Hungarian wild boars. The number and total length of ROH (runs of homozygosity), as well as FROH coefficients (proportion of the autosomal genome covered ROH) did not show major differences between Mangalitza pigs and other wild and domestic pig populations. However, Romanian and Hungarian Red Mangalitza pigs displayed an increased frequency of very long ROH (>30 Mb) when compared with other porcine breeds. These results indicate that Red Mangalitza pigs underwent recent and strong inbreeding probably as a consequence of severe reductions in census size

Analysing the diversity of the caprine melanocortin 1 receptor (MC1R) in goats with distinct geographic origins

In humans, the variability of the melanocortin 1 receptor (MC1R) gene has been associated with geography, being mainly determined by the amount of exposure to sunlight. Studies performed in pigs have also evidenced the existence of a geographic component in the distribution of MC1R haplotypes, probably as a consequence of an ancient split between Asian and European wild boars. Herewith, we have partially resequenced the caprine MC1R coding region in 58 goats from distinct geographic locations i.e. Colombia, Italy, Spain, France, Greece, Romania, Iran and Africa. The resulting dataset was merged with 39 previously published caprine MC1R sequences and a median joining network was built. This phylogenetic analysis did not yield any evidence of a relationship between geography and the clustering of caprine MC1R sequences, a result that was confirmed by performing a Mantel test with a previously published dataset of nine goat breeds (N = 319) with available MC1R genotypes. The majority of caprine MC1R variation was non-synonymous (c.676A > G, c.748G > T, c.764G > A and c.801C > G) and predicted to have functional effects. An analysis of goat MC1R sequences with the PAML 4 software provided evidence that two SNPs (c.764G > A and c.801C > G) might evolve under positive selection. The apparent lack of any link between caprine MC1R variation and geography might be explained by a complex array of factors including artificial selection for pigmentation phenotypes and recent divergence amongst goat breeds.We acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016–2019 (SEV-2015-0533) grant awarded to the Center for Research in Agricultural Genomics. Taina F Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education (MEC) of the Federal Government of Brazil.Peer reviewe

Author Correction: Hotspots of recent hybridization between pigs and wild boars in Europe

The original version of this Article contained a typographical error in the spelling of the author Vlatka Cubric-Curik, which was incorrectly given as Vlatka Cubric-Curic. This has now been corrected in the PDF and HTML versions of the Article, and in the accompanying Supplementary Information file.</p

Hotspots of recent hybridization between pigs and wild boars in Europe

After a strong demographic decline before World War II, wild boar populations are expanding and the species is now the second-most abundant ungulate in Europe. This increase raises concerns due to wild boar impact on crops and natural ecosystems and as potential vector of diseases. Additionally, wild boar can hybridize with domestic pigs, which could increase health risks and alter wild boar adaptive potential. We analysed 47,148 Single Nucleotide Polymorphisms in wild boar from Europe (292) and the Near East (16), and commercial (44) and local (255) pig breeds, to discern patterns of hybridization across Europe. We identified 33 wild boars with more than 10% domestic ancestry in their genome, mostly concentrated in Austria, Bosnia and Herzegovina, Bulgaria and Serbia. This difference is probably due to contrasting practices, with free-ranging vs. industrial farming but more samples would be needed to investigate larger geographic patterns. Our results suggest hybridization has occurred over a long period and is still ongoing, as we observed recent hybrids. Although wild and domestic populations have maintained their genetic distinctiveness, potential health threats raise concerns and require implementation of management actions and farming practices aimed at reducing contact between wild and domestic pigs.</p

Hotspots of recent hybridization between pigs and wild boars in Europe

After a strong demographic decline before World War II, wild boar populations are expanding and the species is now the second-most abundant ungulate in Europe. This increase raises concerns due to wild boar impact on crops and natural ecosystems and as potential vector of diseases. Additionally, wild boar can hybridize with domestic pigs, which could increase health risks and alter wild boar adaptive potential. We analysed 47,148 Single Nucleotide Polymorphisms in wild boar from Europe (292) and the Near East (16), and commercial (44) and local (255) pig breeds, to discern patterns of hybridization across Europe. We identifed 33 wild boars with more than 10% domestic ancestry in their genome, mostly concentrated in Austria, Bosnia and Herzegovina, Bulgaria and Serbia. This diference is probably due to contrasting practices, with free-ranging vs. industrial farming but more samples would be needed to investigate larger geographic patterns. Our results suggest hybridization has occurred over a long period and is still ongoing, as we observed recent hybrids. Although wild and domestic populations have maintained their genetic distinctiveness, potential health threats raise concerns and require implementation of management actions and farming practices aimed at reducing contact between wild and domestic pigs

Effekten av offshoring på löner i utvecklingsländer

Av den ökade globala handeln under de senaste åren kan slutsatsen dras, att vi är mer öppnaoch att den globala marknaden växer sig allt större. År 1960 låg handeln av BNP i världen pårunt 24%, och 2016 uppgick andelen till 56%. Utifrån detta har människor möjlighet att handla,arbeta och bo i andra länder, men påverkas lönen av denna öppenhet? Enligt teorin så kommer faktorpriserna, priserna på till exempel arbetskraft, kapital och jord attutjämnas vid en ökad handel mellan länder. Vid full frihandel, skulle arbetskraften av sammaslag få samma lön över hela handelsområdet. Denna studie har undersökts hur offshoring påverkar lönen för låg- medel- och högutbildade iåtta utvecklingsländer under perioden 1995-2009. Offshoring är ett begrepp som betyder attman flyttar verksamheten utomlands. Ett exempel är när ett företag väljer att flytta sinproduktion utomlands, där arbetskraften är lägre. Resultatet visade att offshoring hade en positiv effekt på lönen för alla tre utbildningsgrupperoch att skillnaden av effekten av offshoring mellan utbildningsgrupperna var väldigt liten