Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA

Abstract

Background: Artificial 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 findings: Genome 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/significance: These 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.

Figure 1. Schematic drawing showing the expected alignment between reads and the reference genome.

The colored bars represent the reads; each color corresponds to a different pig population. The reads originated from ∼150 bp fragments of RRL libraries of pooled DNA for each pig population. Therefore, for each read the identification is only available at the population level. Colored dots on the reads represent SNP positions.

Figure 2. Average nucleotide diversity per chromosome and sampled population.

Nucleotide diversity was estimated in non-overlapping 500 Kb windows (). A- Average overall chromosomes per population. B- Average per chromosome for each population. Vertical lines represent standard errors of the mean. C- Heatmap representing the p-values obtained from comparing the average per chromosome. D- Boxplot showing that centromeres and chromosome ends behave different in terms of nucleotide diversity.

Figure 3. Genome-wide variation of nucleotide diversity in the studied populations.

Each dot represents the observed nucleotide variation over a window of 500 Kb.

Figure 4. Correspondence analysis of population vs. genomic regions under selection and observed .

A- LT regions (regions with smaller than the lowest 95% C.I. boundary); B- HT regions (regions with larger than the highest 95% C.I. boundary); C- Genomic regions with significant high F_st values. Different color and point size indicate the relative contribution of each population to the space arrangement in the plot. Brown color and larger size indicates highest contribution, light blue and smaller size indicates smallest contribution.

Figure 5. Variation of along the wild boar SSC8 and SSC7.

Blue bars represent point estimates for each 500 Kb window. Red lines represent confidence interval limits with a significance level of 95%. Green lines represent the average per window. The insets are enlargements of the orange boxes that show details of the variation of in genomic regions that deviate from the standard neutral model in all sampled populations. A- Detail of genomic regions with a significantly low and that potentially contains the KIT gene. B- Detail of genomic regions with a significantly high and that potentially contains the TRIM26 gene member of the SLA locus. C- Detail of genomic regions with a significantly low and that potentially contains the OR4K13 gene.