PSIX-26 - Genome-wide search for selection signatures in European wild boar

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.