Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA

Abstract

BackgroundArtificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity.Methodology/Main FindingsGenome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ∼2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar.Conclusions/SignificanceThese results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection.

Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof

“…It suggests that the actual effective size in the founder herd might be actually double, given that inbreeding coefficient of the sequenced animal is B0.39. When correcting for inbreeding, this diversity is comparable with that reported in other porcine species (Amaral et al, , 2011 or in humans.…”

Mining the pig genome to investigate the domestication process

“…Population differentiation analyses using genome sequences revealed that differentiation between European wild and domestic pigs is similar to or even lower than that observed among pig breeds (Amaral et al, 2011). Importantly, admixture analyses (Groenen et al, 2012) revealed significant gene flow from Chinese populations to Europe in the Pleistocene period and frequent recent admixture in domesticated pig breeds in Europe.…”

“…In addition, historical admixture with wild boars may have also had a role until a few hundred years ago (White, 2011;Goedbloed et al, 2013;Manunza et al, 2013). Amaral et al (2011) observed a positive correlation between the level of variability and recombination (also observed in Badke et al, 2012;Bosse et al, 2012 andEsteve-Codina et al, 2013), suggesting that selection (positive or negative) has an active role in shaping the variability of Sus scrofa and that interference among genomic positions has an impact on variability. The significant presence of candidate mutations that are functionally harmful suggests that many of the variants that have been artificially selected were new variants with strong effects (as indicated in Rubin et al, 2012).…”

“…The use of broadly reported QTL regions for a number of phenotypes affected by artificial selection has been the most commonly used (and perhaps the most robust) method to obtain such support. However, other approaches have also been used, such as Gene Ontology or pathway annotation, to detect enrichment in a given function (Amaral et al, 2011) or locate candidate genes associated with a trait of interest (a common method for selecting candidate genes in QTL studies). These other methods are more vulnerable to subjectivity and should be used carefully (Pavlidis et al, 2012).…”

“…Genome analyses have identified a number of regions and candidate loci that may be responsible, to some degree, for traits selected during and after domestication (Amaral et al, 2011;Mikawa et al, 2011;Ren et al, 2011;Rubin et al, 2012;Ai et al, 2013;Fan et al, 2013;Moutou et al, 2013;Wilkinson et al, 2013). In Table 2, genomic regions associated (directly or secondarily) with domestication traits are presented.…”