Understanding the Origin of Genetic Variations in Rare Breeds: the Importance of Gene-Flow and Demography

Domestic populations display a myriad of phenotypic variations. In farm animals, many of these variations are found in local/rare breeds. However, these populations are under threat due to the predominance of few breeds in industrial settings. Understanding the mechanisms that govern such phenotypic diversity is crucial to inform conservation efforts. To investigate this issue we sequenced over 100 pig genomes from diverse rare or commercial breeds as well as multiple populations of wild boars. We used this data to model the domestication history of pigs. Our results strongly support models involving gene flow between wild and domestic forms throughout history. Gene flow was high from wild to domestics but low the other way around. We also show that wild boars have undergone massive bottlenecks since domestication resulting in low effective population size. On the other hand, gene-flow have increased the effective population size of domestic pigs. Moreover, we show that besides for a few portions of the genome that are homogeneous among breeds due the their importance for maintaining domestic traits, genetic variations segregating between pig breeds were likely acquired through gene-flow from diverse local wild populations. Our complex picture of the domestication history of pigs demonstrates that domestic or wild boars should not be considered as genetically homogeneous groups. Instead, we argue that rare/local breeds can be seen as reservoirs for genetic variations that have been lost in the wild due to bottlenecks and should therefore be the focus of conservation efforts.