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

Altres ajuts: European Social Fund, Human Resources Development Operational Program 2007-2013, project no. POSDRU/159/1.5/S/132765We 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

A high throughput genotyping approach reveals distinctive autosomal genetic signatures for European and Near Eastern wild boar

The lack of a Near Eastern genetic signature in modern European porcine breeds indicates that, although domestic pigs from the Fertile Crescent entered Europe during the Neolithic, they were completely replaced by their European counterparts in a short window of time. Whilst the absence of such genetic signature has been convincingly demonstrated at the mitochondrial level, variation at the autosomal genomes of European and Near Eastern Sus scrofa has not been compared yet. Herewith, we have explored the genetic relationships among 43 wild boar from Europe (N = 21), Near East (N = 19) and Korea (N = 3), and 40 Iberian (N = 16), Canarian (N = 4) and Mangalitza (N = 20) pigs by using a high throughput SNP genotyping platform. After data filtering, 37,167 autosomal SNPs were used to perform population genetics analyses. A multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK showed that Near Eastern and European wild boar populations are genetically differentiated. Maximum likelihood trees built with TreeMix supported this conclusion i.e. an early population split between Near Eastern and European Sus scrofa was observed. Moreover, analysis of the data with Structure evidenced that the sampled Iberian, Canarian and Mangalitza pigs did not carry any autosomal signature compatible with a Near Eastern ancestry, a finding that agrees well with previous mitochondrial studies

Organisation nucléaire et expression des gènes des protéines du lait

National audienc

Organisation nucléaire et expression des gènes des protéines du lait

National audienc

A high throughput genotyping approach reveals distinctive autosomal genetic signatures for European and Near Eastern wild boar

The lack of a Near Eastern genetic signature in modern European porcine breeds indicates that, although domestic pigs from the Fertile Crescent entered Europe during the Neolithic, they were completely replaced by their European counterparts in a short window of time. Whilst the absence of such genetic signature has been convincingly demonstrated at the mitochondrial level, variation at the autosomal genomes of European and Near Eastern Sus scrofa has not been compared yet. Herewith, we have explored the genetic relationships among 43 wild boar from Europe (N = 21), Near East (N = 19) and Korea (N = 3), and 40 Iberian (N = 16), Canarian (N = 4) and Mangalitza (N = 20) pigs by using a high throughput SNP genotyping platform. After data filtering, 37,167 autosomal SNPs were used to perform population genetics analyses. A multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK showed that Near Eastern and European wild boar populations are genetically differentiated. Maximum likelihood trees built with TreeMix supported this conclusion i.e. an early population split between Near Eastern and European Sus scrofa was observed. Moreover, analysis of the data with Structure evidenced that the sampled Iberian, Canarian and Mangalitza pigs did not carry any autosomal signature compatible with a Near Eastern ancestry, a finding that agrees well with previous mitochondrial studies

Structure-based estimation of the admixture proportions of 83 individuals belonging to ten <i>Sus scrofa</i> populations.

<p>The method of Evanno <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055891#pone.0055891-Evanno1" target="_blank">[38]</a> indicated that the most likely number of clusters was K = 4, but Admixture analysis and a plot of the log likelihood of each K-value (see Supplementary Information) pointed to K = 5 as the most likely number of clusters. WB = wild boar.</p

Multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK.

<p>This graph displays the genetic relationships between Near Eastern, Korean and European wild boar and Iberian, Canarian and Mangalitza pigs.</p

Observed and expected heterozygosities of Near Eastern (NEWB) and European (EUWB) wild boar and Iberian (IB) and Mangalitza (MA) pigs¹.

1<p>Far Eastern wild boar and Canarian pigs were not included in this analysis because of insufficient sample size.</p

Pairwise F_ST-values between Near Eastern (NEWB) and European (EUWB) wild boar and Iberian (IB) and Mangalitza pigs (MA)¹^,².

1<p>Far Eastern wild boar and Canarian pigs were not included in this analysis because of insufficient sample size.</p>2<p>*** <i>P</i>-value<0.001.</p