Deletion on Chromosome 5 Associated with Decreased Reproductive Efficiency in Female Cattle

Reproductive efficiency (calves marketed per cow) is arguably the most economically important trait in commercial beef cattle production. Genomic tools could facilitate accurate selection tools for daughter pregnancy rate.  Copy number variation (CNV) is one form of structural variation that results in abnormal copies of DNA in the genome.  Using results of a previous genome wide association study based on mutli-animal pools and high density arrays, our lab reported a region between 25 and 70 Mb on chromosome 5 associated with reproductive efficiency.  To further evaluate this region for genomic variations such as CNV, we applied a genome-wide association approach based on a >700,000 SNP marker assay and PennCNV analysis to 68 Bos indicus cross females from a large commercial ranch in Central Florida.  A genomic segment located on chromosome 5, spanning the region of approximately 58.37-58.44 Mb (Bovine UMD3.1 assembly) was identified as containing a deletion associated with decreased reproductive efficiency.  A quantitative real time PCR test was developed to evaluate additional females in the Central Florida and US Meat Animal Research Center (USMARC) populations.  In low reproductive performance females, the frequency of the homozygous deletion was 7% (23/319) in the Central Florida population (Bos indicus cross) and 0% in the USMARC population (predominantly Bos taurus).  To date, we have not identified the deletion in Bos taurus cattle, suggesting that the deletion is specific to Bos indicus cattle.  This deletion provides a toll for reproductive efficiency in Bos indicus-influenced cattle.  USDA is an equal opportunity provider and employer.

Key Words: bovine, copy number variation, reproductive efficiency