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The ABC’s of DNA Spell Success for Genome Project

As heartbreaking lines go, “you’re not my type” is up there with “it’s not you, it’s me”. But for researchers on a new joint project run by Genome Alberta and ALMA (Alberta Livestock & Meat Agency), getting genotypes right is a make-or-break element. In the quest to use genomics for developing multi-trait value indices that improve carcass quality and feed efficiency in cattle, it’s a lot like finding the love of your life: a worthy goal, but a journey that’s not for the faint of heart.

Genotyping in 4 easy (?) steps

The daunting task of genotyping all 7200 animals in the project falls to Delta Genomics. In her capacity as CEO and formerly Director of Operations with the company, Michelle Miller knows the steps well.

1. Inventory the samples

Similar to any process, where you end up has a lot to do with where you begin.

“When a sample arrives at the lab, we have people who receive, catalogue and inventory it,” said Miller, “so we record all the ID’s and store a portion of the sample for future use.”

2. Preparation and extraction

“For this project, we obtained a lot of blood samples in the first year,” said Miller.

Those samples that weren’t frozen for long-term storage went to the extraction team, where the process takes two days. By the end of it, they have DNA which can be forwarded to the genotyping team.

3. Genotyping

This is where things get labor intensive, as the genotyping team generates about 30,000 SNPs or data points on each animal over a period of three days. In total, the first three steps require about 10 days to complete. It’s a bit slower than on those crime shows where the DNA work starts and ends over a coffee break, but it’s pretty efficient for the real world.

From there, it’s on to the final step…

4. Data analysis

In work at the University of Alberta, breed composition is determined for each animal and from that, they also get a value for retained heterozygosity, which is similar to hybrid vigor.

“The way beef producers think of hybrid vigor is that the more diverse their animals are in genetic context, the better they perform,” said Miller. “What ‘better’ means depends on what a certain producer wants (performance traits, carcass traits, good breeders), so we’re able to quantify heterozygosity.”

They also conduct parentage analysis to determine which of the 2400 calves in the first year of the project belong to which bulls.

Right tool for the right job

Together, the four steps represent a lot of time and effort, but it appears to be time well spent.

“Without the lab work and the genetic information, it’s hard to produce an index with high accuracy,” said Miller. “We’re trying to provide commercial producers with a tool to rank their animals based on an index of how well they will perform at slaughter.”

While Miller concedes that you can also build an index by measuring traits and understanding pedigree, the accuracy will be low.

“By adding the genetic information we can increase the accuracy of prediction and make better breeding decisions when the animal is younger, even before he starts breeding. Without genetics, you may not be able to accurately assess a bull until he is 6 or 7 years old.”

A different breed of challenge

One obstacle researchers have had to overcome is that while breed associations in the purebred industry provide education and help members adopt new genetic technologies, the commercial side lacks that support right now.

“It means that the purebred guys are using these genomic tools and paying to use them, but in some cases their customers don’t understand the value,” said Miller. “We’re trying to bridge that gap by educating commercial breeders, giving them the tool and explaining how to use it and measure the results.”

As Miller explained, “we need to focus on the traits that commercial breeders value most, such as residual feed intake and carcass quality.”

Sometimes in the lab, it’s easy to lose sight of the big picture. For her part, Miller has that squarely in view and likes what she sees.

“The biggest thing about this project is the long-term implication. We have more people to feed every day and an increasing number are demanding meat products as a source of protein. By increasing the efficiency of food production we can play a big part in feeding the world for years to come, and that’s exciting.”

And with a full belly of beef, the next time your date says “I love you like a friend”, it might just be easier to swallow.

The ABC’s of DNA Spell Success for Genome Project

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