@article{amaral_genome-wide_2011,
Author = {Amaral, Andreia J. and Ferretti, Luca and Megens,
Hendrik-Jan and Crooijmans, Richard P. M. A. and Nie,
Haisheng and Ramos-Onsins, Sebastian E. and
Perez-Enciso, Miguel and Schook, Lawrence B. and
Groenen, Martien A. M.},
Title = {Genome-wide footprints of pig domestication and
selection revealed through massive parallel sequencing
of pooled {DNA}},
Journal = {PloS One},
Volume = {6},
Number = {4},
Pages = {e14782},
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.},
doi = {10.1371/journal.pone.0014782},
issn = {1932-6203},
language = {eng},
pmcid = {PMC3070695},
pmid = {21483733},
year = 2011
}