Signatures of de‐domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution

Abstract

Autochthonous pig breeds are usually reared in extensive or semi-extensive production systems that might facilitate contact with wild boars and, thus, reciprocal genetic exchanges. In this study, we analysed variants in the melanocortin 1 receptor (MC1R) gene (which cause different coat colour phenotypes) and in the nuclear receptor subfamily 6 group A member 1 (NR6A1) gene (associated with increased vertebral number) in 712 pigs of 12 local pig breeds raised in Italy (Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano and Sarda) and south-eastern European countries (Kr skopolje from Slovenia, Black Slavonian and Turopolje from Croatia, Mangalitsa and Moravka from Serbia and East Balkan Swine from Bulgaria) and compared the data with the genetic variability at these loci investigated in 229 wild boars from populations spread in the same macro-geographic areas. None of the autochthonous pig breeds or wild boar populations were fixed for one allele at both loci. Domestic and wild-type alleles at these two genes were present in both domestic and wild populations. Findings of the distribution of MC1R alleles might be useful for tracing back the complex genetic history of autochthonous breeds. Altogether, these results indirectly demonstrate that bidirectional introgression of wild and domestic alleles is derived and affected by the human and naturally driven evolutionary forces that are shaping the Sus scrofa genome: autochthonous breeds are experiencing a sort of 'dedomestication' process, and wild resources are challenged by a 'domestication' drift. Both need to be further investigated and managed.

Maternal genomic variability of the wild boar (Sus scrofa) reveals the uniqueness of East‐Caucasian and Central Italian populations

“…Throughout its history, the wild boar has been strongly influenced by human practices such as hunting, pig domestication, and animal translocation (Larson et al, 2005;Scandura, Iacolina, & Apollonio, 2011). Previous studies revealed the complex genetic structure of wild boar populations in Eurasia, including multiple domestication events and gene flow between wild boar and domestic pig breeds (Iacolina et al, 2016;Larson et al, 2005;Ramíres et al, 2009;Ribani et al, 2019;Šprem et al, 2014). Previous studies revealed the complex genetic structure of wild boar populations in Eurasia, including multiple domestication events and gene flow between wild boar and domestic pig breeds (Iacolina et al, 2016;Larson et al, 2005;Ramíres et al, 2009;Ribani et al, 2019;Šprem et al, 2014).…”

“…Thus, analysis of the changes in the geographical range of S. scrofa could aid our understanding of not only the global patterns of evolution and ecosystem change (Anijalg et al, 2018). Previous studies revealed the complex genetic structure of wild boar populations in Eurasia, including multiple domestication events and gene flow between wild boar and domestic pig breeds (Iacolina et al, 2016;Larson et al, 2005;Ramíres et al, 2009;Ribani et al, 2019;Šprem et al, 2014).…”

Matching STR and SNP genotyping to discriminate between wild boar, domestic pigs and their recent hybrids for forensic purposes

“…( 14,16,28 but see also 34,38,39 www.nature.com/scientificreports www.nature.com/scientificreports/ All reference pigs showed the domestic allele (T) at the NR6A1 gene (Table 5), except two individuals from family-owned farms that were pig × wild boar hybrids (T/C). Of these, one had already been identified by STRs.…”

“…Sequencing of MC1R on chromosome 6 in S. scrofa revealed a series of single-base substitutions corresponding to different E alleles with phenotypic effects 21,22 . The wild type allele E + (or 0101, sensu 13 ), determining a typical brownish-grey coat colour, is private to the European and Asian wild boar populations, and to the Hungarian Mangalica swine breed 13,14 . The variants E D2 (0301), E P1/2/3 (0501/0502/0503) and the recessive allele e (0401) are of domestic European origin, and determine different coat colours, from black to spotted, white, and reddish.…”

Differentiation between wild boar and domestic pig in food by targeting two gene loci by real-time PCR

“…The high frequency of the heterozygous C/T genotype in Turopolje, a domestic pig breed from Croatia, is in accordance with a very recent paper of the research group of Fontanesi. By genotyping 47 Turopolje individuals, the frequency of the T and the C allele were reported to be 0.57 and 0.43, respectively 19 .…”