Identification of damaging mutations in porcine taste receptor and appetite-reward genes by genome capture coupled with high throughput sequencing

Taste receptors (TASR) have been associated to taste/food preferences, infection and intoxication in mammals. On the other side, the genes involved in the appetite-reward (reward) circuitry are responsible for promoting the feed intake of palatable foods. Therefore, both gene groups are likely to have an important impact on pig production traits. We captured the coding sequence of 10 TASRs and 196 reward genes from per-breed pools of 304 pigs belonging to: (i) 10 breeds, (ii) 4 commercial populations with records on feed intake and (iii) F2 pigs from an experimental intercross population divided in two groups with extreme phenotypes for growth and obesity. These genes were sequenced in an Illumina HiSeq2000 and compared to the porcine reference genome. We found 218 TASR and 5,100 reward variants, 68% of which are not present in the dbSNP database. 10 TASR and 218 reward variants are predicted to have a high impact on protein sequence (frame-shift, stop gained, splice site donor, etc). Likewise, 127 TASR and 2,276 reward variants are predicted to moderately affect protein sequence (non-synonymous, in-frame indel, etc). To further understand the possible phenotypic relevance of these variants, we compared the allelic read count frequencies of the four commercial lines and the two phenotypically divergent F2 pig groups and found significant differences indicating that they could be of functional importance. We have selected the 128 most relevant variants with high and moderate impact covering all ten TASR and 64 reward genes for variant validation and future application in association studies.