Over the last 50 years, dairy farmers have enjoyed higher production from their cows in part from the use of superior, proven sires and artificial insemination. But, at the same time that milk production has increased, fertility in dairy cattle experienced an overall decline. A 5-year, multi-state, interdisciplinary project, integrated with Extension, is focused on the identification of genomic loci associated with fertility in dairy heifers and cows; discovery of functional single nucleotide polymorphisms (SNPs) associated with daughter pregnancy rate (DPR) and early embryo development; and evaluation of the efficiency and profitability of increasing fertility in dairy cattle using genetic selection tools. 

The Extension portion of the project just completed its second Genomics Road Show visiting California, Florida, Idaho, Texas, Washington and Wisconsin to discuss research findings and case studies with producers, veterinarians and allied dairy industry professionals. Current results from two USDA-funded grants in this area, and case studies from two genomic testing companies with data from real dairy herds, were presented.

What is depicted in Figure 1 – declining fertility as measured by DPR -- is why the USDA wanted to fund projects investigating how to improve fertility. The reason for the decline has long been thought to be related to selection for milk production, that is, by selecting for high milk production, we were selecting against fertility. Selecting for higher DPR bulls, however, became available in the early 2000’s and is likely one of the reasons for the upturn in fertility, perhaps along with increased health, management, and efficient synchronization protocols. This positive trend provided a further spark in interest to look at the cow side for fertility traits using genomics.

Because the bovine genome has been sequenced, researchers have the ability to look at the whole genome (GWAS or Genome-wide Associated Study) and evaluate specific locations (SNPs) along the cow’s DNA and try to associate those with specific phenotypes (a collection of observable traits – like milk production or conception to first service). For an introduction to genomics, see our article at.

What has recently been discovered by our group and others? We’ll briefly highlight some of the important findings to date. 

  • Since 2006, a number of specific genes associated with fetal abnormalities leading to abortion, embryonic death, or reduced fertility have been identified. 
  • In a GWAS study of Holstein highly fertile (pregnant to first AI) versus subfertile (conceived after 4th AI or never pregnant and culled) heifers, the heritability of fertility was 0.46 (about 46% of the differences observed in fertility may be attributable to genetic individual difference), leading us to conclude that there is ample opportunity to make gains in Holstein heifer fertility with genomic selection (Keuter et al., 2015). 
  • When looking at bull genomics: 40 SNPs were identified that were related to DPR and 29 of those 40 SNPs were not significantly related to production traits. Therefore, selection for fertility without negative selection for milk yield is possible (Cochran et al., 2013). 
  • On the cow side, of the SNPs found to be related to DPR in bulls by Cochran et al., 19 were significantly related to DPR in cows, indicating that SNPs associated with genetic estimates of fertility in Holstein bulls maintained their association in a separate population of cows (Ortega et al., 2015).

Nearly 2 million dairy cows, heifers, and bulls have been genomically tested. Genomic testing improves the reliability of the information about a young animal and can speed the genetic progress in the herd. The testing is predominantly done within the first few months of a heifer’s life. The information a producer gets back from the company conducting the test is a set of numbers associated with specific traits, like Net Merit $ or Fat. From that information, producers can rank their heifers by the traits or indices most valuable to their business. Producers have developed different strategies depending on their farms’ goals. Some want to improve the overall production of the herd, some want to improve longevity in the cows, some want to select for animals that will be of superior genetics for flushing embryos and selling genetics. Whatever the farm’s goals, all of the producers and consultants we’ve talked to have emphasized that the farm needs to have a plan for what to do with the information if they are going to genomically test their animals. 

In addition to fertility traits, health traits have recently been evaluated and incorporated into the genomic tests. Traits such as the risk for mastitis, lameness, metritis, retained placenta, displaced abomasum, and ketosis have been researched because of their effect on milk production, reproduction and culling. In general, these traits are combined in a health index to allow the producer to select for potentially “healthier” animals genetically.

The bottom line is, there are quite a number of traits in genomic tests available and, as a result of the two USDA funded projects, specific SNPs for fertility will be a great addition in the future.