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Wanted: Functional Variants for Genome Alberta Project

Cattle in the fieldWe all want the same things in life: Peace, good health and functional variants that influence key traits in beef cattle. Okay, maybe not ALL of us want that last one, but for members of a certain Genome Alberta and ALMA project, it’s top of the list. As they seek to develop and apply more accurate genomically-enhanced breeding values for traits that will benefit the commercial cattle industry, researchers have identified functional variants as an important part of the puzzle. And perhaps the best place to start that quest is with a simple question:

What the heck are functional variants?

“Like all species, cattle differ from each other on the DNA level,” said Dr. Paul Stothard, a co-investigator for Activity 1 of the project.

 “Most of those differences don’t influence physical characteristics; that is, they are not functional variants.

Very important variants

First, as Dr. Stothard explained, his team is trying to find all the sites in the genome that vary in beef cattle by using whole genome sequencing.

“Once we have that catalogue of variants, we can start predicting which ones influence traits and thus are functional variants.”

In the field of genetics, there seem to be breakthroughs on a regular basis, and Stothard’s team is also breaking new ground.

“In the past we have identified a relatively simple type of DNA difference called single nucleotide polymorphisms or SNPs. These are spots in the genome where some individuals have one type of DNA letter and others have a different sequence.”

Now, the Genome Alberta researchers are trying to expand their understanding of DNA variation by looking for structural variants, which involve a thousand or more nucleotides or DNA letters.

That’s where it really gets interesting.

Predicting success

“We will then generate a structural variant catalogue, combine it with a SNP catalogue and use software to predict which variants are likely to influence traits. We can even go a step further and predict which traits may be affected by functional variants, with one of them being feed efficiency.”

While it’s all highly technical, the goal is to produce practical benefits for the cattle industry.

“Once we have variant collections and predictions, we can provide that information to the downstream activities in the project and they can incorporate it into their prediction equations. In the end, this will lead to greater improvements in feed efficiency as the prediction equations perform better in terms of accuracy and their ability to work on different breeds or cross bred animals.”

 One constant in science is that the greater your sample size, the more confident you can be in your findings, and this project is no exception.

“At this stage we already have sequence data from 300 beef cattle from the Canadian Cattle Genome Project, and we are adding another 150 sequences to that, allowing us to build a more comprehensive catalogue of variants.”

And if you thought the Sears catalogue was a source of excitement, this one could surpass it.

“The fact that we are finally looking at structural variants is huge. For several years we’ve known where SNPs are located in the cattle genome, but we haven’t had enough sequence information to identify the larger structural variants.”

They’re not sure yet what they will find in terms of structural variants; they are, however, confident of one thing.

“Our starting point was feed efficiency, but it doesn’t end there. We can make use of this catalogue to target any trait of interest to the industry, from birth weight to carcass quality to average daily gain.”

So even if peace and good health prove elusive, functional variants that influence key traits in beef cattle are within our grasp.

A win is a win.

Wanted: Functional Variants for Genome Alberta Project

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