Lack of polymorphism at the MC1R wild-type allele and evidence of domestic allele introgression across European wild boar populations

Abstract

Domestication promotes the emergence of novel phenotypic and behavioural traits in domesticated animals compared to their wild ancestors. We analysed variation at the melanocortin receptor I (MC1R) and nuclear receptor subfamily 6, group A, member 1 (NR6A1) genes in European wild boar populations, two loci which have been under strong artificial selection during domestication. These loci influence coat colour and number of vertebrae, respectively.A total of 145 wild boars were sampled throughout Europe, to evaluate frequency and spatial distribution of domestic alleles and patterns of hybridization between wild and domestic forms. Most of the wild boars (94%) were homozygous for the European wild-type (E+) MC1R allele. We did not observe any synonymous substitution in the European E+ allele, confirming its monomorphism even in areas known to be hotspots of wild boar genetic diversity. The remaining wild boars (6%) showed genetic introgression of three different European domestic alleles. No Asian MC1R allele was found in our sample.Furthermore, domestic NR6A1 alleles were observed in 6% of wild boars. Considering jointly the two loci analyzed, 11% of boars, sampled all over Europe, showed signs of recent or past introgression in their genome.These data agree with previous investigations on other molecular markers, confirming that, compared to Asian conspecifics, European wild boars have a relatively low genetic diversity, which is locally increased by the introgression of allelic variants from the domestic counterpart

High domestic pig contribution to the local gene pool of free-living European wild boar: a case study in Poland

“…The Polish WB populations we studied have some of Europe's highest levels of DS introgression. These levels are similar to those found in regions where DS are reared in semifree conditions (up to 10-20% in Canu et al 2016) or WB populations that have been restocked with captive-bred individuals that have been cross-bred with DS (27% in Frantz et al 2013). Since analysis using MC1R alleles is likely to severely underestimate the number of WB with a domestic ancestor (Frantz et al 2012, we cannot exclude the possibility that the real rate of introgression may be much higher than observed in this study.…”

“…In fact, introgression of domestic genes may reach much higher levels at very local scale (Fulgione et al 2016), especially in regions where open-air pig farming (Canu et al 2016) and/or hybridization in captivity (Gongora et al 2003;Canu et al 2014) and/or restocking with farmed WB that had been cross-bred with DS (Frantz et al 2012McDevitt et al 2013), are practiced.…”

“…A series of alleles of the MC1R gene have been found so far in pigs. The wild-type (E + ) allele has been identified in WBs, the Hungarian Mangalica DS breed and DS raised in free or semi-free conditions in Sardinia (Canu et al 2016). Meanwhile, in other DS breeds, because of different human needs or cultural preferences, domestication and human selective pressures caused coat color variation generated by non-synonymous mutations (Fang et al 2009;Li et al 2010).…”

“…However, because research to date is based on only 44 individuals, data on introgression into WB in Poland is inconclusive. While Babicz et al (2013) found three individuals with domestic alleles among 10 WBs from Lublin (eastern Poland), Canu et al (2016) found only one introgressed individual among seven Polish WBs. Neither Gongora et al (2003) (n = 15) nor Fang et al (2009) (n = 12) found evidence of hybridization among Polish WBs.…”

“…Sequence diversity at the melanocortin receptor 1 (MC1R ) locus is widely used to distinguish between meat originating from WB, DS, and their hybrids, as well as to detect introgression from DS into WB (Giuffra et al 2000;Koutsogiannouli et al 2010;Frantz et al 2013;Fontanesi et al 2014;Canu et al 2016). In addition, mtDNA sequencing, microsatellite genotyping, and a single-nucleotide polymorphism (SNP) assay have been used to look for evidence of introgression (Giuffra et al 2000;Scandura et al 2008, 2011b, Frantz et al 2012, 2013, Goedbloed et al 2013bHerreroMedrano et al 2013;Iacolina et al 2016b).…”