The primary goals of the BPC are to provide resources to research groups interested in the improvement of cattle genomics resources, and to provide a forum for discussing the creation of high-quality genome assemblies of cattle breeds to foster collaboration and to prevent duplication of effort where it is not beneficial. Our guiding principal is that open discussion of ongoing and proposed projects will enhance efficient use of limited global cattle genomics resources and reduce unhelpful competition between projects. In part this is purely selfish in the sense that we intend to develop a pangenome resource but want to maximize impact by focusing on breeds or species that don’t already have resources to develop reference-quality genome assemblies. Below we discuss what resources we plan to contribute, how we think they can be useful, and who we anticipate can benefit from them either directly or indirectly. We begin with a brief overview from our perspective of the successes of animal agriculture.
Improvements in Livestock Breeding Fuel Food Production
Many of the existing breeds of cattle can trace their origins to only a handful of centuries in the recent past! Most breeds were developed in specific geographic locations around the world, and were specialized for milk, meat or draft animal production based on the needs of the surrounding landowners. Many of the farmers that raised livestock in these times practiced early forms of selective breeding by choosing mating pairs of cattle that had higher performance than their peers in the herd. It wasn’t until the turn of the twentieth century that animal breeding was turned into a mathematical science by the calculation of “values” for each parent. This resulted in large gains for milk and meat production in specific breeds of cattle.Modern animal breeding
Modern animal breeding
Modern animal breeding has benefited from several key innovations, including:
Artificial insemination: allowing high performance bulls to contribute their genetic material to the population at a faster rate.
Computer algorithms: which calculate “breeding values” for each animal to allow for targeted matings.
Genotyping chips: that can measure the genetic “relatedness” of animals in a rapid fashion so that farmers can best decide how the animal should be bred, or if the animal should remain in the herd!
The latter innovation of using animal genotypes has been the most recent development to benefit cattle dairy and beef production systems. By targeting specific DNA bases in the cattle genome that tend to be variable, geneticists can approximate a cow’s/bull’s full genome sequence and use that information to determine how closely related they are to high performers on a national level. In dairy systems, a farmer can now assess the potential lifetime production of a calf only weeks after she is born just by taking an ear punch tissue sample and sending it to a genetics lab. This is of critical importance to the producer, as raising a calf is a two year investment! If she ends up costing the producer more than she produces in product, that can make a difference between profitability and bankruptcy.
The cattle genome sequence
In order to track these variable DNA bases, scientists first needed to find out where they were located across the cattle genome. This is why a large collaboration was formed in 2004 to sequence the cattle genome and make it available to the public. Due to limitations in technology at the time, scientists had to select one animal of one breed to be the “reference cow” for the future genetic map. This cow, L1 Dominette, was from a famous line of Hereford cattle that was highly inbred. This feature made her a natural fit for the genome sequencing strategy at the time, as inbred individuals were easier to assemble into genomes.
However, this also meant that all comparisons of subsequently sequenced cattle would be against a reference to the Hereford breed’s genome. Any novel sequence in another breed’s genome would be difficult to identify on the map, and likewise, any Hereford-specific DNA would look like a big deletion of sequence. This presents a bigger problem when the DNA from Zebu cattle subspecies, or other distantly related Bovids, are aligned to the current cattle genome.
It is becoming increasingly clear that – while Dominette’s genome has served us well to this point – her genome sequence isn’t representative of the breadth of diversity of all cattle in the world. A resource that would encompass all of the variation and possible DNA sequence of cattle breeds and Bovini species would be termed a Pangenome
What Resources are We Looking to Develop?
Our primary products are reference genomes for popular cattle breeds. We define a reference genome as a representative, high quality “map” of the total DNA of an individual of that breed, that will be available for public use by the research community.
For this project, we want to sequence and assemble representative genome assemblies of many major cattle breeds that are in use in animal production systems throughout the world. We plan to use new DNA sequencing technologies and improved sequencing strategies to generate high quality reference genomes for these breeds.
Why are These Resources Useful?
One result of the success of modern genetics is that some breeds of specialized cattle have become much more numerous than other historical breeds. While overall production may be increased by this specialization and concentration, the concomitant decrease of overall diversity in the global population may result in the loss of alleles that might someday be important for further genetic advancement or disease/parasite tolerance. Moreover, the continued sequencing of new cattle samples throughout the world has revealed deficiencies in using only one cattle breed as a reference animal, as up to 2% of the genome sequence of certain individuals may not be present on the cattle reference genome. While this missing sequence is not guaranteed to impact animal production in all cases, it may hide genes that give certain breeds their distinguishing characteristics or improve their production. By creating new reference genomes for these breeds, we could track these new genes for potential production improvements, while identifying breeds with unique alleles to support conservation efforts.
If we achieve only a 2% improvement in production efficiency per year by tracking these new sites, that will result in a doubling of production within a 36-year time-frame.
Who will Benefit from These Resources?
At the present stage of the project, we are seeking members of the cattle research community that have samples from breeds of interest, but lack the resources to translate those samples into reference-quality genome assemblies.
As such, our primary stakeholders are the members of the cattle research community themselves, as our assemblies will benefit current and future research into the major cattle breeds. Just as the 2009 cattle reference genome publication spurned a new era in cattle genomics research, we hope that our reference assemblies will greatly benefit future research in cattle.
Ultimately, our hope is that these research results will translate into functional improvements that can be used by the international cattle industry by enabling better targeted genomic selection. If farmers can more rapidly identify high-performing animals and mate them to other high-performers, this will greatly increase the rate of genetic improvement of cattle, in general.
It is also possible that our new references could uncover genome regions related to methane emissions, and alleles contributing to aspects of sustainability such as improving ability to use low-quality forage, tolerating drought or parasites, or enhancing reproductive capacity. By reducing emissions and improving the sustainability of cattle livestock systems, we can ensure that producers remain competitive in a changing global environment.