Genome-wide association analyses for several exterior traits in the autochthonous Casertana pig breed

Casertana is an autochthonous pig breed reared in the Central-South of Italy, mainly in extensive or semi-extensive production systems. A small number of animals are registered to the breed herd-book. The population of this breed is not completely fixed for several exterior traits, including ear size (small vs large), ear bearing (forward vs floppy), presence or absence of wattles and coat colour (black vs slate-grey) that we recorded in a total of 101 pigs from six different farms. All these pigs were also genotyped with the Illumina PorcineSNP60 BeadChip. Then, with the aim to identify DNA markers associated with these traits, we run four genome-wide association studies (GWAS) comparing pigs having different phenotypes for each of the four external traits. Genome-wide fixation index (F-ST) analyses were run to confirm the results. GEMMA software was used in the GWAS. Single nucleotide polymorphisms (SNPs) associated to the wattle trait were identified on porcine chromosome (SSC) 1 and SSC11. Markers associated to the coat colour trait were located on SSC6, SSC8, SSC14 and SSC15. These chromosome regions were confirmed by the independent F-ST analyses. F-ST did not confirm the signals detected for the two ear conformation traits. Candidate genes were identified according to the function of the annotated genes in the detected genome regions. Despite the small number of pigs that could be investigated, this study showed that autochthonous animal genetic resources might be useful to disclose genetic factors affecting traits that are not fixed in a population.