BackgroundThe domestic pig (Sus scrofa) is both an important livestock species and a model for biomedical research. Exome sequencing has accelerated identification of protein-coding variants underlying phenotypic traits in human and mouse. We aimed to develop and validate a similar resource for the pig.ResultsWe developed probe sets to capture pig exonic sequences based upon the current Ensembl pig gene annotation supplemented with mapped expressed sequence tags (ESTs) and demonstrated proof-of-principle capture and sequencing of the pig exome in 96 pigs, encompassing 24 capture experiments. For most of the samples at least 10x sequence coverage was achieved for more than 90% of the target bases. Bioinformatic analysis of the data revealed over 236,000 high confidence predicted SNPs and over 28,000 predicted indels.ConclusionsWe have achieved coverage statistics similar to those seen with commercially available human and mouse exome kits. Exome capture in pigs provides a tool to identify coding region variation associated with production traits, including loss of function mutations which may explain embryonic and neonatal losses, and to improve genomic assemblies in the vicinity of protein coding genes in the pig.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-550) contains supplementary material, which is available to authorized users.

Serum urea concentrations were measured in Large White pigs from lines divergently selected for components of efficient lean growth rate and performance tested over three 14-d test periods starting at 30, 50, and 75 kg. Two methods of performance testing were used. Phase-fed pigs were fed to appetite isoenergetic diets differing in total lysine:energy ratio (0.58, 0.69, 0.81, 0.91, 1.01, 1.12, and 1.23 g/MJ of digestible energy), whereas diet-choice pigs were offered a choice of the 0.69 and 1.12 lysine:energy diets. Between test periods, all animals were fed one diet: 0.91 g of lysine/MJ of digestible energy. The study consisted of 230 boars and gilts with 150 pigs performance tested on phase-feeding and 80 pigs on diet-choice. The line selected for high lean food conversion had lower urea concentrations on each diet than the line selected for high lean growth rate, despite similar predicted lysine balances. Efficiency of lean growth rather than the rate of lean growth may be a better selection strategy in the context of nitrogen excretion. Urea concentrations at the end of each test period were correlated with lysine intake (0.33, 0.48 and 0.65; standard error, 0.08) and predicted lysine balance (0.39,0.44, and 0.64), but were uncorrelated with predicted lysine for protein deposition (0.01, 0.08, and 0.08) and maintenance. Urea concentration at the end of a test period was not a useful predictor of protein deposition, even after accounting for pretest variation in urea concentration and food intake during test. The expected response pattern of serum urea concentration to diets differing in total lysine:energy would be nonlinear, with the point of inflection occurring at the required dietary total lysine:energy for each genotype. However, there was no evidence of such an inflection point such that the prediction of lysine requirement from urea concentration was not possible for the selection lines in the study.

Summary Divergent selection over seven generations for daily food intake (DFI) and for two lean growth rate (LGA and LGS) selection objectives in pigs produced correlated responses in serum insulin‐like growth factor‐1 (IGF‐1) concentration. The LGA and LGS selection objectives were for lean growth, but with performance testing on ad libitum (LGA) or on restricted (LGS) feeding regimes. There were 342 animals in the study, with an average of 46 pigs in each selection line and 72 pigs in the control line. All animals were performance‐tested from 30 to 90 kg on an ad libitum feeding regime. Selection on DFI increased IGF‐1 at 6 weeks of age (158 versus 104 μg/l, SED 21; control 136 μg/l) and selection for high LGA increased IGF‐1 at 30 kg liveweight (202 versus 161 μg/l, SED 14; control 185 μg/l). At 6 weeks of age and at 30 kg of weight, there was no response in IGF‐1 with selection on LGS (128 versus 129 and 167 versus 153 μg/l, respectively) suggesting that IGF‐1 may not be a reliable physiological predictor of genetic merit for such a selection objective, which combined rate and efficiency of lean growth. IGF‐1 measured immediately prior to the start of performance test may be useful in determining which animals to performance test for a lean growth selection objective, whereas IGF‐1 measured at 6 weeks of age may be a useful physiological predictor of genetic merit for daily food intake during performance test.