Genomic characterisation of pigmentation related traits in livestock

With the intense use of high throughput genomic technologies, our knowledge about the cattle and pig genomes has rapidly evolved. Over the last years, many investigations have been already carried out to identify major genes and mutations underlying different morphological, productive, and reproductive traits in cattle and pigs. This thesis is the result of research activities focused on the investigation of genomic features to find novel candidate gene markers associated with pigmentation in two Italian local cattle breeds (Reggiana and Modenese) and in an Italian heavy pig breed, the Italian Large White breed. In the first study that we proposed, we detected signatures of selection in the genome of these two autochthonous cattle breeds using genome-wide SNP information in comparative FST analyses. Results show top FST values detected for the melanocortin 1 receptor (MC1R) gene region on BTA18, and for the agouti signalling protein (ASIP) gene region on BTA13. The second aim of this thesis was to investigate the pigmentation process of the iris in the Italian Large White pig breed. This is a white-coloured breed not affected by albinism. For this aim, we carried out several genome-wide association studies using high density SNP datasets and designed to contrast groups of pigs with different colour of iris. The results indicated that the eye pigmented patterns, the total absence of pigmentation in the both eyes, and heterochromia iridis defect were associated with SNPs close to the SLC45A2 (on chromosome 16, SSC16), EDNRB (SSC11) and KITLG (SSC5) genes, respectively. In addition, other associated genomic regions with eye depigmented patterns were also identified. This thesis demonstrates how population genomic approaches designed to take advantage from the diversity between livestock genetic resources could provide interesting hints to explain pigmentation related traits not yet completely investigated in these species.