Sex determination tests in pigs as tools for quality control in sample identification in large genomic studies.

The increasing number of samples used for association studies in farm animals, the number of participating laboratories in such investigations and the involvement of several people and laboratory technicians in the sampling, labelling, storage, database codification, DNA isolation and analysis contribute to increase the risk of mistakes in the different sample handling stages. DNA analysis using the routine microsatellite panel for parentage verification could be used to obtain a fingerprinting of the samples but it cannot provide a quick and inexpensive way to verify if misclassification occurred. In order to verify the correct classification of a large number of male and female pigs sampled at slaughterhouses and to identify the sex of some animals for which gender was not recorded, we applied the amelogenin based sex determination method that we recently developed. The test analyses the fragment length difference between the AMELX and AMELY genes that are located on the X and Y chromosomes, respectively. The obtained PCR products can be easily resolved on polyacrylamide gels, agarose gels or by capillary electrophoresis using an automatic sequencer. Of the analysed animals, eight samples resulted misclassified, probably due to a frameshift between the sampling and the pre-available list of slaughtered animals. Their gender was also confirmed from a different DNA extraction and using other two sex determination methods based on the analysis of the ZFX and ZFY genes. Furthermore, other two samples for which gender was not recorded at the slaughterhouse were sexed using the amelogenin and ZFX/ZFY methods.