Abstract
Wild boar and domestic pig breeds belong to the same species (Sus scrofa), so they can easily have viable offspring. This could be a problem in preserving the genetic lines of wild boars, keeping clean the food industry from lower-grade hybrid boar meat, and „producing” ethically questionable trophies, too. The aim of our study was to develop a cost-efficient, fast, easy and accurate marker set which can separate the wild boars from hybrids and domestic pig breeds.
 The InDel markers were developed using 59 full pig genomes of 17 different breeds (e.g. Duroc, Large White, Landrace, Mangalica, wild boar). Sequence differences between the genomes of wild boars and domestic breeds were identified in variant call files, and verified using the IGV software. Wild boar, mangalica and duroc specific primers to amplify the chosen InDel regions were designed using Primer3.
 After preliminary tests five markers were chosen, three wild boar specific, one Mangalica specific and one Duroc specific one. Fluorescently labelled primers were used to make the valuation easier and more accurate with capillary electrophoresis instead of gel-electrophoresis. The markers were optimised individually and in multiplex conditions and tested in samples of 11 breeds.
 In conclusion, a new, faster and cheaper set was developed to separate the wild boars from the hybrids and domestic breeds. Based on the preliminary testing on wild boars, duroc and mangalica breeds zero samples resulted false negative, so it is 100% accurate. In addition, it is a much more cost- and time-effective way than testing every single sample with STR sets.
Highlights
Domestic pig is one of the most important farm animals, providing more than hundred million tonnes of pork for meat consumption worldwide
We describe InDel discovery using a large number of genomic sequences from different pig breeds and wild boars
Five out of these genomic regions were specific for wild boar, the other were specific for different pig breeds
Summary
Domestic pig is one of the most important farm animals, providing more than hundred million tonnes of pork for meat consumption worldwide. Wild boar is the ancestor of pig, with a constantly increasing population in Hungary and across Europe (Csányi, 2014; Bieber and Ruf, 2005). In some wild boar preserves, they were crossbred because of the domestic pig’s better growth indices (reproduction rate, feed efficiency rate, etc.), degrading the “clean” wild boar populations. The wild boar-domestic pig hybrids poses a threat to the genetic diversity of boars. The nutrient contents of domestic pigs and hybrids differ from wild boars (Table 1) (Vörös, 2009)
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