Hybrid origin of European commercial pigs examined by an in-depth haplotype analysis on chromosome 1.

Ole Madsen,Mirte Bosse,Richard P M A Crooijmans,Hendrik-Jan Megens,Yogesh Paudel,Martien A M Groenen,Laurent A F Frantz

doi:10.3389/fgene.2014.00442

Abstract

Although all farm animals have an original source of domestication, a large variety of modern breeds exist that are phenotypically highly distinct from the ancestral wild population. This phenomenon can be the result of artificial selection or gene flow from other sources into the domesticated population. The Eurasian wild boar (Sus scrofa) has been domesticated at least twice in two geographically distinct regions during the Neolithic revolution when hunting shifted to farming. Prior to the establishment of the commercial European pig breeds we know today, some 200 years ago Chinese pigs were imported into Europe to improve local European pigs. Commercial European domesticated pigs are genetically more diverse than European wild boars, although historically the latter represents the source population for domestication. In this study we examine the cause of the higher diversity within the genomes of European commercial pigs compared to their wild ancestors by testing two different hypotheses. In the first hypothesis we consider that European commercial pigs are a mix of different European wild populations as a result of movement throughout Europe, hereby acquiring haplotypes from all over the European continent. As an alternative hypothesis, we examine whether the introgression of Asian haplotypes into European breeds during the Industrial Revolution caused the observed increase in diversity. By using re-sequence data for chromosome 1 of 136 pigs and wild boars, we show that an Asian introgression of about 20% into the genome of European commercial pigs explains the majority of the increase in genetic diversity. These findings confirm that the Asian hybridization, that was used to improve production traits of local breeds, left its signature in the genome of the commercial pigs we know today.

Highlights

Domestication is a complex process that has major implications for both phenotypic and genetic variation
In this research we examine which process contributed most to the difference in genetic diversity between European commercial breeds and European wild boars
In the drawn-out process of domestication of the pig in Europe, the mixing of wild boar genetic variation from different regions in Europe, might explain the high diversity found in modern European pigs

Summary

INTRODUCTION

Domestication is a complex process that has major implications for both phenotypic and genetic variation. In this research we examine which process contributed most to the difference in genetic diversity between European commercial breeds and European wild boars. In the drawn-out process of domestication of the pig in Europe, the mixing of wild boar genetic variation from different regions in Europe, might explain the high diversity found in modern European pigs. We recently found that regions in the genome of Large White pigs that contain DNA that is shared with Asian pigs are generally more diverse than regions that do not share DNA with Asian haplotypes (Bosse et al, 2014a) It is unknown whether this is a direct result of the introgression (rather than, for example, incomplete lineage sorting). How much the introgressed Asian haplotypes contributed to variation in the genome of European commercial pigs remains an unanswered question. We make a contribution by analyzing the details of genetic diversity on chromosome 1 within and between groups of pigs and wild boars in Asia and Europe

MATERIALS AND METHODS

RESULTS AND DISCUSSION

CONCLUSIONS