Genome-wide association studies for iris pigmentation and heterochromia patterns in Large White pigs

Coat colour in livestock speciesis one of the most distinctive traits that characterise many different breeds. Pigmentation does not affect only skin and hairs but also the eyes. Few genomic studies in cattle and horses also investigated iris pigmentation, but no similar studies was conducted in pigs thus far. In this study we analysed eye colour diversity in a Large White pig population (n=897) and reported the results of genome-wide association studies based on several comparisonsincluding pigs having four main eye colour categories(three with both pigmented eyes of different brown grades: pale, 17.9%; medium, 14.8%; and dark, 54.3%; another one with both eyes completely depigmented, 3.8%) and heterochromia patterns (heterochromia iridis, i.e. depigmented iris sectors in pigmented irises, 3.2%; heterochromia iridium, i.e. a whole eye iris of depigmented phenotype and the other eye with the iris completely pigmented, 5.9%). Pigs were genotyped with the Illumina PorcineSNP60 BeadChip and GEMMA was used for the association analyses. The results indicated that the eye pigmented patterns (different grades of brown pigmentation), the total absence of pigmentation in the both eyes, and heterochromia iridis defect were under controlled of SLC45A2 (on chromosome 16, SSC16), EDNRB (SSC11) and KITLG (SSC5), respectively. In addition, to new candidate associations for the eye depigmented patterns were also identified for SNPs on two SSC4 regions (including two candidate genes: NOTCH2 and PREX2) and on SSC6, SSC8 and SSC14 (including COL17A1 as candidate gene). This study provided useful information to understand the genetic mechanisms affecting eye pigmentation in pigs.