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A vision-impairing ocular disorder was observed in a local Japanese Black cattle population, and assumed to be an autosomal recessive disease based on the presence of a founder cow. A genome scan using seven affected half-sib pairs revealed a linkage to BTA5 (Zmax = 7.0, LODmax = 2.0), designated the bovine ocular disorder 1 (bod1) locus. Of the seven animals, three were heterozygous at the bod1 locus. Analysis in these three animals revealed linkage to markers on BTA18, and this locus was designated bod2. Detailed haplotype inspection of 16 affected animals indicated linkage to BTA5 in 12 animals, BTA18 in three animals, and linkage to both BTA5 and BTA18 in one animal. The bod1 locus was mapped to a 25 cM interval between DIK5237 and DIK5210 on BTA5 (Zmax = 17.0, LODmax = 11.8), and bod2 was mapped to a 7 cM interval between DIK5411 and INRA038 on BTA18 (Zmax = 13.0, LODmax = 4.0). This study demonstrated that the independent involvement of loss of function mutations in two loci is likely responsible for this genetic heterogeneity.