The FAGenomicH project: a whole candidate gene approach to identify markers associated with fatness traits in pigs and investigate the pig as a model for human obesity

Fat deposition in pigs is a complex trait for which several studies in experimental populations have identified a large number of QTL, some of which segregating in outbred commercial populations. As pigs and humans have numerous physiological and phenotypic similarities for fat deposition, in order to identify the genetic factors affecting this trait in both species, it could be possible to take advantage of the results obtained in one species and, applying a comparative approach, transfer biological information to the other one, and vice versa. Therefore, such approach, on one hand, might provide useful information to improve selection efficiency in pig breeding and, on the other hand, could contribute to understand the genetic basis of human obesity and related diseases. With these aims, we designed a project based on a selective genotyping approach in commercial pig populations for which extreme and divergent groups of pigs have been chosen according to the estimated breeding value (EBV) for fat deposition traits. A candidate gene approach has been applied in order to identify markers associated with fatness in pigs. DNA markers are chosen and identified using different approaches: i) mutations already reported in pig genes affecting fat deposition; ii) discovery of new mutations in candidate genes by resequencing; iii) database mining. For the latter approach, a bioinformatic pipeline has been designed to mine pig sequences available in DNA databases. In the start up phase, about 560 Italian Large White pigs, selected according to their fatness EBV, are genotyped for more than 700 SNPs. Some preliminary results are reported. The project portal is: http://fagenomich.biocomp.unibo.it/