Use of bovine exome sequencing and targeted genotyping to investigate recessive fertility defects HH2, HH3, and BH1 with the identification and validation of a putative causative HH3 mutation in SMC2. Bos taurus

The recent discovery of bovine haplotypes with negative effects on fertility in the Holstein and Brown Swiss breeds has allowed producers to identify carrier animals using current commercial SNP genotyping assays. This study was devised to identify the causative mutations contained within three of these haplotypes (Holstein haplotypes 2 and 3 and Brown Swiss haplotype 1) by combining bovine exome capture array with next generation sequencing. Of the 68,476,640 sequence variations identified only 1,311 genome-wide were concordant with the disease phenotypes in the 21 sequenced animals. Validation genotyping of 36 SNP identified only 1 variation that was concordant for Holstein haplotype 3 (HH3) and no variations for HH2 or BH1. The HH3 variation is a T/C SNP within exon 24 of SMC2 (Chr 8: 95,410,507 UMD3.1). This non-synonymous SNP in the NTPase domain of the encoded protein changes amino acid 1135 from a phenylalanine to a serine, which is predicted to be a non-neutral, non-tolerated, and evolutionary unlikely substitution according to SNAP, SIFT, and BLOSUM62 analysis, respectively. Since only exome capture sequencing was performed the true causative HH3 mutation might lie in a non-sequenced genomic location, but given the essential role of SMC2 for chromosome condensation and segregation during cell division, our findings strongly support this concordant SNP as the putative HH3 causative mutation. The lack of concordant variations for HH2 or BH1 strongly suggests that their causative mutation is in a non-exome region or in a exome region not covered by the capture array.