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

TESTING OF TWO PROTOCOLS FOR GENOTYPING THE LEPTIN GENE LOCUS AND BODY MEASUREMENT IN MARAMURES BROWN AND ROMANIAN BREED CATTLE

The body measurement of Maramures Brown breed and Romanian Siemmental and testing twoprotocols for emphasizing the leptine gene in order to perform associations with some beef productiontraits within further studies were the aims of our research. The blood DNA extraction was performedaccording to the protocols proposed by Yves Amigues and genotyping protocols was proposed byLeifers and Pomp et al. The body weight is within standards. The analyzed protocols used for leptinegene emphasizing led to satisfactory results, which will enable us to perform further research in orderto make associations between this possible marker gene and some body traits

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

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

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

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

Maximum likelihood trees constructed with TreeMix depicting splits and migration events (m = 1–4) between six <i>Sus scrofa</i> populations: 1, Near Eastern wild boar; 2, Mangalitza pigs, 3, Canarian pigs; 4, Iberian pigs; 5, European wild boar; 6, Korean wild boar.

<p>Edges, whose color ranges from red to yellow depending on the weight of the migration event (measured as the fraction of alleles coming from the parental population), indicate the direction of gene flow between populations. Probabilities associated with each migration event are represented by <i>P</i>-values in bold.</p