Analysis of hybridization in French wild boar populations using genome-wide genotyping data

TL;DR

This study investigates hybridization between wild boars and domestic pigs in France using genome-wide genotyping, revealing moderate, often ancient hybridization with regional variations and recent hybrid cases mostly involving Asian pigs.

Contribution

It introduces a genome-wide SNP genotyping approach to analyze hybridization in French wild boars, overcoming limitations of cytogenetic methods and providing detailed hybridization insights.

Findings

Average hybrid rate of 15.8% over 12 years

Most wild boars had 0-18% domestic pig genome

Recent hybridization cases involved Asian pigs

Abstract

The "genetic purity" of French wild boar populations has been monitored since the 1980s based on a cytogenetic difference between wild boars and domestic pigs (36 and 38 chromosomes, respectively). This difference makes it possible to identify any boar with 37 or 38 chromosomes as "hybrid", without however being able to determine the origin (recent or ancient) of the hybridization, nor guarantee the "purity" of an animal with 36 chromosomes. Analysis of results of more than 4,600 tests performed over the last 12 years reveals an average "hybrid" rate of 15.8%, with high variability between populations. To analyse hybridization in greater detail and overcome inherent limitations of the cytogenetic approach, 362 wild boars recently collected in different regions of France were genotyped on a 70K SNP (GeneSeek GGP Porcine HD) chip. This study showed that for 96.4% of the wild boars analysed, includingmost of those with 37 or 38 chromosomes, the percentage of the genome of "domestic pig" origin varied from 0 to 18%. This suggests that hybridization is a fairly common phenomenon but of moderate intensity, and often ancient. Nevertheless, higher rates of hybridization have been observed in some regions such as Ard{\`e}che, and several cases of recent hybridization with domestic pigs were found in 3.6% of the wild boars analysed, most of them with pigs of Asian origin.