Next generation semiconductor based sequencing of bitter taste receptor genes in different pig breeds and populations and association study of identified polymorphisms using a DNA pooling strategy

In this work we amplified and sequenced 10 TAS2R genes (TAS2R1, TAS2R3, TAS2R4, TAS2R7, TAS2R9, TAS2R10, TAS2R16, TAS2R20, TAS2R38 and TAS2R39) in six pig breeds (Italian Large White, Italian Duroc, Italian Landrace, Pietrain, Casertana and Meishan) and in wild boars using the next generation semiconductor sequencing platform Ion Torrent PGM. The experimental design was based on a target PCR amplification step that was carried out on equimolar DNA pools from animals of the same breed or population. Moreover, two pools were prepared including DNA each from 50 Italian Large White pigs having extreme and divergent estimated breeding values for back fat thickness (BFT), as polymorphisms in TAS2R genes are associated with obesity and fat deposition traits in humans and other species. The other breed specific pools were prepared each with DNA from 5-15 animals. After barcoding of the different breed/population specific amplicons, the prepared library was sequenced using the Ion Torrent PGM sequencer.