When the phrase “variety is the spice of life” was first used in a poem called The Task, did the author imagine that “variation” would one day become a key ingredient in the task of genomic research? We’ll never know for sure, but we do know that the study of structural variants is a key component of a new Genome Alberta research project. The study aims to develop and apply more accurate genomically-enhanced breeding values for traits that will benefit the commercial cattle industry.
To accomplish that goal, identifying and working with structural variants is critical.
That process is largely the focus of Dr. Kirill Krivushin, a postdoctoral fellow in the Stothard Research Group responsible for Activity 1 of the project.
“My work includes developing and running bioinformatics pipelines for mapping sequencing data (to a reference bull genome), as well as discovery and annotation of genomic structural variations (SVs) and single nucleotide polymorphisms (SNPs).”
Structural variations (SVs) are chromosomal rearrangements such as deletions, insertions and inversions that may affect the activity of particular genes or even whole metabolic pathways.
Finding your type
In essence, when looking for structural variants associated with a trait, researchers are trying to reveal a correlation between phenotype - traits of interest to industry such as carcass quality, feed efficiency and methane emissions - and genotype.
To illustrate the concept, Dr. Krivushin set out a fictional scenario:
“If we observe a duplicated gene across bulls of high carcass quality and only a single copy of the gene is observed in beef having moderate or low quality carcasses, there is a high chance that the structural variation has a functional impact. Thus we can say there is a clear ‘trait – SV’ correlation.”
It’s complex, time-intensive work, but discovery of genomic variations (SVs and SNPs) is essential to making further progress on the project as a whole.
“At this juncture, I have developed high throughput and scalable pipelines for mapping genomic data and finding structural variants. Also, I have made a tool for further post-processing of the data in order to reduce the rate of false positives.”
Taking bull genomes by the horn
So far, Dr. Krivushin has mapped over 130 bull genomes and detected thousands of potential structural variations. He is currently working on validation of the results and filtering out SVs of low confidence.
Working with such a huge data set is daunting. Since it cannot be processed on a single computer, it requires high performance computing clusters and storage space. Dr. Krivushin is grateful to WestGrid in that regard, as they bring together computing facilities, research data management services and a network of technical experts to meet the needs of researchers.
Even on days when those data sets and computing clusters weigh heavily on researchers, thoughts of the real world implications of their efforts help lighten the load.
“Nowadays, genomic analysis is used worldwide in the cattle industry. To stay competitive, Canadian beef producers should make use of state-of-the-art approaches for efficient resource management, cattle breeding and environmental sustainability.”
If they do, Dr. Krivushin sees a range of benefits.
“SVs and SNPs can be used for development of low-cost genotyping panels and new genomic-based value indices. The panels and indices will help to select the best (or at least better) bulls for breeding in order to get cattle with higher carcass quality and feed efficiency.”
“Overall, it will facilitate production of higher quality meat for less investment. In addition, it will help to reduce methane emission from livestock which goes along with recently introduced carbon tax policies in Alberta.”
So perhaps that poet had a different “variety” in mind. But if Genome Alberta researchers can achieve their goals, they could spice up the prospects of the beef industry for years to come.