Y are you not pregnant: identification of Y chromosome segments in female cattle with decreased reproductive efficiency

Reproductive efficiency is of economic importance in commercial beef cattle production, since failure to achieve pregnancy reduces the number of calves marketed. Identification of genetic markers with predictive merit for reproductive success would facilitate early selection of females and avoid inefficiencies associated with sub-fertile cows. To identify regions of the genome harboring variation affecting reproductive success, we applied a genome-wide association approach based on the >700,000 SNP marker assay. To include the largest number of individuals possible under the available budget, cows from several populations were assigned to extremes for reproductive efficiency, and DNA was pooled within population and phenotype before genotyping. Surprisingly, pools prepared from DNA of low reproductive cattle returned fluorescence intensity data intermediate between fertile females and males for SNP mapped to the Y chromosome (i.e., male sex chromosome). The presence of Y-associated material in low reproductive heifers or cows was confirmed by Y-directed PCR, which revealed that 21 to 29% of females in the low reproductive category were positive by a Y chromosome PCR test normally used to sex embryos. The presence of the Y chromosome anomaly was further confirmed with application of additional Y-specific PCR amplicons, indicating the likelihood of the presence of some portion of male sex chromosome in female cattle in various beef cattle herds across the U.S. Discovery of this Y anomaly in low reproductive females may make an important contribution to management of reproductive failures in beef cattle operations.