Evolutionary History, Selective Sweeps and Deleterious Variation in the Pig

Whole genome sequencing of multiple individuals has revealed that each individual genome harbours a large number of deleterious variants. Nevertheless, the amount and distribution of such variants differs considerably depending on the history of the species or population studied. This not only relates to recent breeding practices of the population, but also to the population history of its source. How population bottlenecks during the domestication process and the subsequent development of specific breeds have impacted the occurrence of deleterious variants is an outstanding question. We have assessed the proportion of predicted deleterious variants within the genomes of domestic and wild pigs, to better understand how these deleterious variants have accumulated in our modern pig breeds. One of our focus points is understanding the genetic mechanisms that increase the amount of harmful mutations in commercial breeds.

Wild boar (Sus scrofa) originated in Southeast Asia some 3 to 4 Mya and over the past one million years colonized almost the entire Eurasian mainland. We have shown that the European and Asian wild boar populations that were the source of the domestication events diverged around 1 Mya resulting in very different minor allele frequencies at millions of genomic locations and over a million locations that are fixed for alternative alleles between these populations. Domestication took place some 9000 to 10,000 years ago independently in East Anatolia and in China. Following the initial domestication, the traits selected for, as well as how animals were kept, strongly differed in Europe and Asia, resulting in a large number of distinct pig breeds. Furthermore, the European breeds experienced a large influx of Asian haplotypes when, some 200 years ago, European breeders imported Chinese pigs to improve their local breeds. I will present a brief overview of how pig genomes evolved and how we used this genomic information to identify regions under selection during domestication and selection.

We have assessed the genetic background of European and Asian breeds and wild boars in terms of breed history and crossbreeding on a segment-by-segment basis so that the origin of each genomic segment can be assigned. This information is relevant for further steps in the identification of deleterious variants in the genome of individuals, and understanding how these variants have been introduced in the breeds.