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A reduction of the footprint of selection may also be achieved by increasing the frequencies of a broad spectrum of QTL alleles slowly, instead of heavily selecting on the biggest QTL with the danger of a large selection footprint.
It became clear to us that, during the domestication process of the silkworm, 354 genes in the nuclear genome bear a strong human selection footprint [ 7].
Among the five candidate genes discovered in the proximity of outlier markers, we decided to examine further the cadherin (CAD) and leucine aminopeptidase (LAP) at the sequence and expression levels, to confirm or infirm the selection footprint.
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In cattle breeds, several commercially important traits with different genetic backgrounds have been intensively selected, but clear selection footprints have been detected only in those traits with monogenic inheritance.
The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity.
However, few studies have focused on porcine selection footprints, particularly on a genome-wide scale.
Currently, genome-wide scans in both cattle and humans showing positive selection footprints have been investigated.
We found positive selection footprints moderately frequently at the codon level in LSE genes (5.38% in average among the different species) but did not find any positive selection footprints on single-copy genes after manual curation.
Surveying for selection footprints across porcine genomes can be quite valuable for revealing the genetic mechanisms of phenotypic diversity.
Our results revealed a genome-wide map of selection footprints in pigs and may help us better understand the mechanisms of selection in pig breeding.
Yorkshire and Landrace may have selection footprints in their genome resulting from intensive selection for production attributes over the past few decades.
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