Genes on bovine chromosome 18 associated with bilateral convergent strabismus with exophthalmos in German Brown cattle

PURPOSE Bilateral convergent strabismus with exophthalmos (BCSE) is a widespread inherited eye defect in several cattle populations. Its progressive condition often leads to blindness in affected cattle and shortens their length of productive life. Furthermore, breeding with BCSE-affected animals is forbidden by the German animal welfare laws. We performed a mutation and association analysis for three candidate genes (troponin T type 1 [TNNT1], retinol dehydrogenase 13 [RDH13], and TCF3 fusion partner [TFPT]), which are located within the previously identified BCSE-linked region on the telomeric end of bovine chromosome 18 (BTA18). In addition, we developed single nucleotide polymorphisms (SNPs) within these three candidate genes and nine other genes that are contained in this genomic BCSE-region to perform association analyses with BCSE in German Brown cattle. METHODS We performed cDNA analyses of all three candidate genes using eye tissues of three affected German Brown cows and three unaffected controls. Furthermore, we screened the exonic and the adjacent genomic sequences of RDH13, TNNT1, and TFPT using four BCSE-affected and four controls of German Brown cattle. Here, we included all exons of RDH13 and those exons of TNNT1 and TFPT for which SNPs were detected by cDNA analyses. In addition, we developed 21 polymerase chain reaction (PCR) products for 17 more genes in the BCSE region and searched them for polymorphisms. All markers detected were genotyped in 48 BCSE-affected German Brown cows and 48 breed and sex matched controls and tested for association with BCSE. RESULTS In total, we detected 29 SNPs in 12 genes. In the coding sequence of the three candidate genes, we identified 10 exonic SNPs and a new splice variant of TNNT1. Four SNPs were associated with the BCSE phenotype in single marker-trait analyses. These SNPs were located within DHDH (dihydrodiol dehydrogenase dimeric), CPT1C (carnitine palmitoyltransferase 1C), TNNT1, and NALP7. The marker-trait association for haplotypes including five SNPs of CPT1C, SYT5 (synaptotagmin V), RDH13, and NALP7 (NLR family, pyrin domain containing 7) revealed a significant association with BCSE. We identified three individual haplotypes that were significantly associated with BCSE. These haplotypes spanned the region from 56.05 Mb to 62.87 Mb on BTA18. CONCLUSIONS The haplotype association analysis corroborated the results of the linkage study that the telomeric end of BTA18 harbors a gene responsible for BCSE and further refines the BCSE region to a 6.82 Mb interval ranging from 56.05 Mb to 62.87 Mb on BTA18.