The capacity of our cows to calve and raise their babies is what keeps the beef industry going. Fertility plays a critical role in maintaining a sustainable supply chain and ultimately ensuring a steady influx of beef animals to processors. 

However, managing fertility is not easy. Even with the reproductive technologies available today, fertility remains heavily influenced by a cow’s environment, making it difficult to separate the genetic from the nongenetic components.

Most fertility problems are often subtle and present themselves as a heifer that took longer to get pregnant or a cow that consistently breeds late in the breeding season. Some cows may require a third service when their contemporaries on average need only two cycles to conceive. 

In more extreme and costly situations, pregnancy is confirmed but is not carried to term, sometimes resulting in a stillborn calf. The longer it takes to identify the loss, the more expensive and challenging the issue becomes. 

Because fertility is dependent on so many factors, we can and should invest in management improvements, such as adjustments to breeding protocols and nutrition.  University extension networks are a great resource to find tools and management recommendations suitable for your region to improve breeding practices. Still, it is important to know they may not fully address reproductive challenges in a herd. 

What else can be done? Traits such as Functional Longevity (FL) and Heifer Pregnancy (HP) help to select for females that conceive earlier and will continue to do so throughout their lives. What we still cannot capture quite well with our current selection tools are the hidden losses and stillborn calves with or without physical abnormalities, and that is where research on haplotypes might shed light.

Haplotype vs. genetic conditions

It is helpful to know the difference between haplotypes and genetic conditions. 

With the phenotypes of genetic conditions governed by mutations or abnormalities in one specific gene, a gene that has lost its function or one that gained an entirely different purpose is more noticeable. When a genetic condition is affected by two or more genes (or several mutations across one gene), their identification is not so clear. 

As shown in Figure 1, haplotypes cover a larger portion of the genome than genetic conditions influenced by a single gene. Haplotypes carry groups of markers and genes inherited together, rather than a short slice. Because of that, haplotypes are more powerful tools when used to identify conditions caused by several local mutations.

The American Angus Association, its members, and commercial users of Angus genetics along with research institutions like the University of Illinois and University of Nebraska–Lincoln have been successful in identifying important genetic conditions affecting the Angus breed. Examples include neuropathic hydrocephalus (NH) and double muscling (DM). 

Haplotypes are not new to the animal breeding scene. In dairy, six different haplotypes linked to embryo loss were identified in Holstein cows since 2012. While their exact mechanism is not entirely known, their identification has allowed breeders to make better mating decisions by avoiding the mating of these haplotype carriers. If any were identified in an Angus population, similar steps could be taken to reduce the frequency of carriers.

Exploring the genomic and phenotypic database

To identify any rare but potentially lethal haplotypes, we not only need to identify the chunk of DNA that is passed down, but also to know when a DNA chunk is linked to a fertility problem. Just like genetic conditions, we may have recessive, additive or dominant haplotypes, meaning problems might only appear in animals that have two copies, or they might also be present in those that are carriers and have only one copy of the haplotype.

Of course, turning to the data submitted by Association members is a huge piece when investigating haplotypes and their effects on fertility in the Angus population. Breeding records, disposal or reason codes, and calf records submitted via Angus Herd Improvement Records (AHIR^®) provide Angus Genetics Inc. (AGI) researchers with the opportunity to test sires and dams to understand which combinations result in either a failed service or inviable calves. 

Besides mating information, the DNA samples submitted on sires and dams and any inviable calves allow us to build a databank and drill down further into the research. 

Current and future research

Because haplotypes can negatively affect several stages of gestation from embryo implantation to malformations and premature births, AGI is currently investigating the potential effects in all phases of breeding protocols. 

The most difficult part of looking for potentially lethal haplotypes is carriers or homozygous animals affected by them are probably deceased. As imagined, looking for something invisible in the populations becomes a monumental task and next to impossible to pull off without member reporting. 

To fill out this piece of the puzzle, AGI released the Haplotype Research Calf Death Report, available to Association members for submission of information and DNA samples for genomic testing at no cost. 

Reporting of stillbirth and early death calves (i.e., before weaning) are welcomed and greatly appreciated. More information can be found at www.angus.org/agi/research or with our customer service representatives. 

Other steps we will explore as part of this research initiative are sequencing key animals and measuring the effect of fertility haplotypes on production traits. This research is testament to the collaboration between Angus breeders and the Association for the greater good of the breed and the beef industry.