Different Founding Effects Underlie Dominant Blue Eyes (DBE) in the Domestic Cat

Abstract

During the last twenty years, minimal white spotting associated with blue eyes was selected by feline breeders to create the Altai, Topaz, and Celestial breeds. Additionally, certain breeders introduced this trait in their lineages of purebred cats. The trait has been called "dominant blue eyes (DBE)" and was confirmed to be autosomal dominant in all lineages. DBE was initially described in outbred cats from Kazakhstan and Russia and in two purebred lineages of British cats from Russia, as well as in Dutch Maine Coon cats, suggesting different founding effects. We have previously identified two variants in the Paired Box 3 (PAX3) gene associated with DBE in Maine Coon and Celestial cats; however, the presence of an underlying variant remains undetermined in other DBE breeding lines. Using a genome-wide association study, we identified a single region on chromosome C1 that was associated with DBE in British cats. Within that region, we identified PAX3 as the strongest candidate gene. Whole-genome sequencing of a DBE cat revealed an RD-114 retrovirus LTR (long terminal repeat) insertion within PAX3 intron 4 (namely NC_018730.3:g.206975776_206975777insN[433]) known to contain regulatory sequences. Using a panel of 117 DBE cats, we showed that this variant was fully associated with DBE in two British lineages, in Altai cats, and in some other DBE lineages. We propose that this NC_018730.3:g.206975776_206975777insN[433] variant represents the DBE^ALT (Altai Dominant Blue Eye) allele in the domestic cat. Finally, we genotyped DBE cats from 14 lineages for the three PAX3 variants and showed that they were not present in four lineages, confirming genetic heterogeneity of the DBE trait in the domestic cat.

Keywords: DBE; Waardenburg syndrome; coat colour; deafness; eye; feline; hair; pigmentation; white spotting.

Figure 1

DBE is present in various lineages of cats. (a–j) DBE phenotype in some feline breeding lines. (a) Altai cat. (b) Mixed-breed cat, daughter of the founding cat named Seymour. Note the sectorial heterochromia of both eyes. (c) British cat from the Nanotigr lineage. (d) British cat from the Igor lineage (e) British cat from the Nadeya lineage. (f) Persian–mixed cat from the Alaska lineage. (g) Founding female (named Marusya) from the Cyrridwen lineage. (h) Maine Coon cat from the Topaz lineage. All these cats were born to a DBE parent with minimal white spotting and to a non-DBE, non-white-spotted parent. They were therefore assumed not to be carrier of the w^S allele. (i) Maine Coon cat from the Dutch lineage. Note the large amount of white: this cat was tested heterozygous w^S/w⁺ for the white spotting locus. (j) Celestial kitten. Note the small white spot on the chin. (k) Partial pedigree tree of DBE lineages. Circles represent females; squares represent males. DBE cats with heterochromia or two blue eyes are depicted with fully filled symbols. The two Topaz founding cats are shown with their names (Roxi and Seymour) according to http://messybeast.com/blue-eye-breeds.htm, accessed on 11 April 2024. Roxi, the Celestial founding cat, and one of its litters are shown in blue and black. The cat that was whole-genome sequenced is shown with an arrow. Stars point out white-coated and deaf cats born to two DBE parents. Genotypes for the RD-114 LTR insertion are shown (+/+: wild-type; +/RD: heterozygous for the RD-114 LTR insertion; RD/RD: homozygous for the RD-114 LTR insertion). Genotypes for the FERV1 LTR insertion in the Roxi family are shown (+/+: wild type; +/FERV: heterozygous for the FERV1 LTR insertion; RD/FERV: compound heterozygous for both insertions). Latent cats are shown with a dot in their symbol. This pedigree tree was concordant with an autosomal dominant inheritance for DBE. A shared RD-114 LTR insertion among the Altai and the Seymour and Nanotigr British lineages suggests a common ancestor for these three breeding lines. Amelia, the DBE daughter of the founding male of the Nanotigr lineage (named Oliver) is shown. SH: shorthair, LH: longhair, BSH: British cat (shorthair or longhair).

Figure 2

At least three PAX3 variants are associated with DBE. (a,b) Manhattan plots of the GWAS. The plots represent the −log10 P_raw and −log10 P_Bonferroni values of each SNP included in the case–control association study. The association study compared 29 DBE cats with 37 control cats. A suggestive association with chromosome C1 was detected. The SNP with the highest association was chrC1.233232798!208720404 at position 208,720,404, with a P_raw value of 1.76 × 10⁻⁸ and P_Bonferroni value of 1.05 × 10⁻³ (Table S1). UN: unknown. (c) Presence (+) and absence (-) of the two FERV1 LTR and RD-114 LTR insertions in PAX3 intron 4 and the PAX3:c.937C>T exon 6 variant in 14 DBE breeding lines. As shown in Figure 1, the shared RD-114 LTR insertion among the Seymour and Nanotigr British lineages and the Altai breed suggests a common ancestor for these three breeding lines. Four breeding lines do not carry any of the three PAX3 variants, confirming genetic heterogeneity of the DBE trait in cats. DSH: domestic shorthair.