In everyday life, sequence is important: Look both ways BEFORE you cross the street. For the researchers on the Efficient Dairy Genome Project, which aims to boost feed efficiency and reduce methane emissions in dairy cattle through genomics, sequencing plays a critical role. And unlike crossing the street, it’s a lot tougher than it sounds.
The project was spearheaded by Dr. Filippo Miglior and Dr. Paul Stothard, and is funded by Genome Alberta, Genome Canada, Ontario Genomics, ALMA, the Canadian Dairy Network (CDN) and Grow Safe.
According to Adrien Butty, a Ph.D. student from Switzerland who is working on the project, one goal is to create a reference population of sequenced animals to improve the accuracy when they impute all of their animals at the sequence level.
Chief among the challenges with this approach is the cost.
“Although the costs of sequencing have come down over the last few years, sequencing is still really expensive at over $1,000 per animal,” said Dr. Christine Baes, Assistant Professor - Centre for Genetic Improvement of Livestock, Department of Animal Biosciences at the University of Guelph.
Chipping away
“For genetic analysis, we like to have large populations consisting of bulls and cows. To capture their genotype information, we use a high through-put and cost effective technology called the SNP chip [SNP stands for single-nucleotide polymorphism, which is a variation in a single nucleotide that occurs at a specific position in the genome].”
The SNP chip itself is a little piece of plastic on which extracted DNA material is placed for lab analysis.
“All of our bulls are genotyped with either high density chips containing 700,000 SNPs or medium density chips with 50,000 SNPs. Most of the cows are genotyped with a lower density chip,” said Dr. Baes.
Sequencing, on the other hand, is the ultimate SNP chip, providing all the genetic variants present in the DNA of an animal. In essence, sequencing provides the equivalent of 30 million SNPs – but the price is much higher than that of the SNP chip.
Compute & impute
“With imputation, we use the medium or high density chip information to infer what the full sequence of those animals looks like.”
Since sequencing everybody is too expensive, the group needed to find the optimal method for choosing which animals to sequence. They can eventually use that information as a basis for imputing the entire genotyped population for only a fraction of the cost.
And if they needed more challenges, selecting those animals is a big one.
“For this part of the project we wanted to select 50 additional animals to sequence.” said Butty. “These animals were chosen from a pool of 46,000 genotyped candidates born after 2011 in North America.”
“Unfortunately, we could only obtain DNA information on a fraction of those potential candidates,” said Butty.
That left them with a “mere” 6,700 animals from which to choose. They then applied three different algorithms based on the genotypic information of the animals to further whittle the field.
“We made our selection taking 450 previously sequenced animals into account. These animals are part of the 1,000 Bull Genomes Project, and provide a reference population for sequence information in dairy cattle.”
Sequencing 50 additional Holstein bulls will provide greater accuracy of imputation of rare variances within the genotype population.
The envelope please…
Now that they’ve found the 50 they want to work with, the intensive process of gathering the DNA of these animals and sequencing them begins (when do these people sleep?).
It sounds like a tall order, but much progress has already been recorded.
“With those 450 animals, we have most of the genetic diversity covered, something that really surprised me,” said Dr. Baes. “Now the finesse is in the details.”
By sequencing more animals, Dr. Baes explained that they can get a better grasp of rare variants.
“There are a million female animals in Canada right now and only a few of them are genotyped; that will change in the future and when it does, we will have good sequence information that we can use to impute and fill in the blanks.”
If they can impute the full sequence of the entire population, they hope it will allow for selection of the best cows that offer the greatest feed efficiency and the least methane emissions.
That could be of critical importance to the dairy cattle industry in Canada, and sequencing is a key part of making it happen. Of course, this doesn’t mean the sequence for looking both ways and then crossing the street isn’t important as well. If you doubt that, try reversing the order.