About This Project

Ask the Scientists

What is the context of this research?

Ruminants like cattle, sheep, and goats play a critical role in sustainable agricultural systems by converting renewable resources from rangeland and crop residues into food and fiber for humans. However, outbreaks of animal disease cause pain and suffering and diminish agricultural sustainability. As researchers work to understand the beneficial effects that natural genetic variation has on disease, comparing gene sequences from related species to helps identify the underlying mechanisms of disease.

This comparative genomics approach is most effective when researchers are able to access gene sequences from many species on different branches of the evolutionary tree. Major international genome projects have provided a fantastic, but short, list of genomes for grazing and browsing animals separated by 15 to 30 million years of evolution. These include cattle, sheep, goat, water buffalo, yak, and bison. Unfortunately, these species represent only 2% of the surviving ruminant species and are a only small slice of evolutionary history.

Our ability to produce affordable whole genome sequence data has dramatically increased with advances in high throughput, Next Generation Sequencing. However, the first step after generating the sequence is to map it to a reference genome. This is a major disadvantage for those researchers who are interested in the many species who don't have reference genomes yet. As a result of this barrier there is much less sequence data generated for many important species.

In recent work in our labs, we have demonstrated that sequence reads from sheep could be mapped to the reference genome of cattle to identify variants between sheep and cattle, as well as variants that occur within the sheep species. With this approach, we demonstrated that a great deal can be learned for a species that does not have a reference genome. Variation within and between species can be identified by mapping reads to a related species with a good reference genome.

The nilgai (Boselaphus tragocamelus) is a unique ruminant species in the Bovinae subfamily and the only member of genus Boselaphus. Compared to cattle, it represents the most distant genus of the ten genera within the Bovinae. It is the largest Asian antelope weighing more than 600 pounds and native to most of India. Nilgai (also known as blue bull) were imported to the U.S. and released in South Texas in the 1930's. The current population in this region is estimated to be around 30,000 and the animal to be sequenced for this project comes from this population.

What is the significance of this project?

Upon successful completion of this project, we will have generated enough whole genome sequence for the nilgai to identify most of its genes for comparison to cattle. Thus, for any mapped gene, we will be able to identify differences between cattle and nilgai. We will also have identified variation within the nilgai species based on one animal (heterozygous sites). When we made a similar comparison with a single sheep, we found millions of species differences between cattle and sheep and more than a million heterozygous sites in just one animal.

By making the data immediately public, we will advance research on nilgai, cattle, and all the Bovinae. If successful, it is possible that many other exotic ruminant could benefit by using a similar approach. This would leverage the high-dollar domestic livestock genomes for advancing genomics research in the remaining 98% of the wild ruminant species, many of which need conservation.

What are the goals of the project?

The goal of this project is to generate ten-fold whole genome sequence data for an individual nilgai. This data will then be mapped to the reference genome for cattle, and made immediately available via Intrepid Bioinformatics for public use without restriction. It can then be used to find nearly any gene in the nilgai genome and compare its sequence to that in other ruminants like cattle, sheep, goats, yak, water buffalo and bison. This data set will be the first of many that we hope to collect among ruminants in order to broaden the scope of our search for meaningful variation that has evolved across these species.