Dataset Information

Contact Zone of Asian and European Wild Boar at North West of Iran.

ABSTRACT: Wild boar (Sus scrofa) are widely distributed throughout the Old World. Most studies have focused on Europe and East Asia with the genetic diversity of West Asia being less well studied. In particular, the genetic variability and genetic structure of the Iranian populations are not yet known; gaps which prevent scientists from resolving the genetic relationships of the Eurasian wild boar. This paper is the first attempt to provide information about genetic relationships among modern Iranian populations of the Eurasian wild boar (S. scrofa) by sequencing 572 bp of the mitochondrial (mt) DNA control region. As a result of this investigation, it was discovered that Iran contains not only Middle Eastern haplotypes, but also shares haplotypes with Europe and East Asia. The Italian clade, which is endemic in Italy, is not identified in Iran, while all other clades, including Asiatic, European, Near East 1, and Near East 2 are found based on the phylogenetic tree and median-joining network. The results of this study illustrate that north west of Iran (specifically Southwest Caspian Sea) is the contact zone between the Asian (Near Eastern and Far Eastern), and the European clades. In light of the fact that the domestication of pigs occurs in Anatolia, this finding is important.

SUBMITTER: Khalilzadeh P

PROVIDER: S-EPMC4956230 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Contact Zone of Asian and European Wild Boar at North West of Iran.

Khalilzadeh Parinaz P Rezaei Hamid Reza HR Fadakar Davoud D Serati Malihe M Aliabadian Mansour M Haile James J Goshtasb Hamid H

PloS one 20160721 7

Wild boar (Sus scrofa) are widely distributed throughout the Old World. Most studies have focused on Europe and East Asia with the genetic diversity of West Asia being less well studied. In particular, the genetic variability and genetic structure of the Iranian populations are not yet known; gaps which prevent scientists from resolving the genetic relationships of the Eurasian wild boar. This paper is the first attempt to provide information about genetic relationships among modern Iranian popu ...[more]

PMID: 27442074

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Project description:Abstract The search for selection signatures in wild boars was meant to assist in identifying genomic regions associated with adaptation to environmental conditions. The aim of our study was to seek selection signatures in European wild boars of Russia. We studied 66 wild boars from 20 different regions in four different climatic zones. DNA samples were genotyped using Porcine SNP60 BeadChips and GeneSeek SNP-chips (Illumina, San Diego, USA). Quality control procedures were carried out resorting to PLINK v1.9; briefly, individuals with genotype call rates of < 0.8 and SNPs with call rates of < 0.3 or minor allele frequencies less than 0.99 were excluded. Also, we resorted to “–LD” to make prune filtering in Plink. In total 37065 markers from full subset of SNPs were used for subsequent analysis. We removed close relatives with enabling option --rel-cutoff 0.75. After filtering 11271 SNPs remained and total genotyping rate of obtained dataset was 98.4%. We subsequently identified SNPs, which had cross within log-likelihood ratio scores (LLRS) values > 2, in addition to integrated Haplotype Score (iHS) values > 2. After comparing 2 methods we detected 6 common elements in “IHS” and “LLRS” - ASGA0101898 – intergenic variant; H3GA0020102 – intergenic variant; ASGA0093835 - intron variant, RBFOX1 (RNA binding fox-1 homolog 1) is a Protein Coding gene, RNA-binding protein that regulates alternative splicing events by binding to 5’-UGCAUGU-3’ elements, regulates alternative splicing of tissue-specific exons and of differentially spliced exons during erythropoiesis; ASGA0098807 - DSG3 (Desmoglein 3) is a Protein Coding gene, component of intercellular desmosome junctions, involved in the interaction of plaque proteins and intermediate filaments mediating cell-cell adhesion; MARC0064247 – non coding transcript exon variant ENSSSCG00000035431, ASGA0020755 – intron variant, ARHGAP30 Rho GTPase activating protein 30). The result of the research will assist in revealing genetic regions associated with adaptation of the Russian wild boars. This research was supported by the Russian Scientific Foundation (RSF) within Project No. 19-16-00109.

Dataset Information

Contact Zone of Asian and European Wild Boar at North West of Iran.

Publications

Contact Zone of Asian and European Wild Boar at North West of Iran.

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