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This trait was first interpreted using simplistic genetic models but soon it was realised that it is more complex. In this study, we analysed eye colour variability in a Large White pig population (<jats:italic>n<\/jats:italic>\u00a0=\u00a0897) and report the results of GWASs based on several comparisons including 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 \u2013 depigmented iris sectors in pigmented irises, 3.2%; heterochromia iridum \u2013 one 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 <jats:italic>SLC45A2<\/jats:italic> (on chromosome 16, SSC16), <jats:italic>EDNRB<\/jats:italic> (SSC11) and <jats:italic>KITLG<\/jats:italic> (SSC5) affect the different grades of brown pigmentation of the eyes, the bilateral eye depigmentation defect and the heterochromia iridis defect recorded in this white pig population respectively. These genes are involved in several mechanisms affecting pigmentation. Significant associations for the eye depigmented patterns were also identified for SNPs on two SSC4 regions (including two candidate genes: <jats:italic>NOTCH2<\/jats:italic> and <jats:italic>PREX2<\/jats:italic>) and on SSC6, SSC8 and SSC14 (including <jats:italic>COL17A1<\/jats:italic> as candidate gene). This study provided useful information to understand eye pigmentation mechanisms, further valuing the pig as animal model to study complex phenotypes in humans.<\/jats:p>","DOI":"10.1111\/age.12930","type":"journal-article","created":{"date-parts":[[2020,3,31]],"date-time":"2020-03-31T09:12:58Z","timestamp":1585645978000},"page":"409-419","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Genome\u2010wide association studies for iris pigmentation and heterochromia patterns in Large White pigs"],"prefix":"10.1111","volume":"51","author":[{"given":"G.","family":"Moscatelli","sequence":"first","affiliation":[{"name":"Division of Animal Sciences Department of Agricultural and Food Sciences University of Bologna Viale G. 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