IBD-Mapping of Caprine and Ovine POLYCERATE Loci

Assuming autosomal dominant inheritance and genetic homogeneity in each of the species investigated, all polycerate animals share at least one copy of the same causative mutation and of a surrounding chromosomal segment inherited-by-descent from a common ancestor. Therefore, comparing SNP array genotyping data of two distantly related polycerate animals is expected to reveal a number of Mendelian incompatibilities (i.e., homozygosity for different alleles) throughout their genomes but not within shared IBD segments. Accordingly, we screened Mendelian incompatibilities in all the possible pair combinations of polycerate × polycerate (4H4H pairs) and polycerate × wild-type (4H2H) individuals. Pairs with a proportion of Medelian incompatibilities below 1 percent of the total number of markers tested were declared as constituted of parent and offspring and were not considered in the analysis. Then, for sliding windows of n markers (n set to 10 in goat and 50 in sheep, considering differences in marker density) we scored the numbers of 4H4H pairs and 4H2H pairs for which “no” versus “at least one” Mendelian inconsistency has been recorded. Finally, we compared the contingency tables produced using Fisher’s exact test.

Illumina GoatSNP50 BeadChip genotypes specifically generated for this research and Illumina OvineHD Beadchip genotyping data generated by two previous studies (Greyvenstein et al. 2016; Kijas et al. 2016) were considered in the analyses. Polled (i.e., hornless) animals were removed from the sheep data set. Markers with a minor allele frequency below 5% or which were called in less than 95% of the samples were eliminated. Moreover, in sheep, genotyping data were extracted for markers located in a 10-Mb region (Chr2:127,500,001–138,500,000 on Oar_v4.0 assembly) corresponding approximately to the HOXD gene cluster ±5 Mb and encompassing all the mapping intervals of the POLYCERATE locus reported in the literature (Greyvenstein et al. 2016; He et al. 2016; Kijas et al. 2016; Ren et al. 2016). The final data sets contained 111 cases, 87 controls, and 2,232 markers in sheep and 35 cases, 51 controls, and 48,345 markers in goat.