RBST’s involvement in genomic projects has increased substantially and the opportunities this work offers are wide ranging. Senior Conservation Adviser Tom Blunt takes this opportunity to highlight some of the factors that need to be considered before undertaking a project.

Breeds that have been the subject of RBST’s genomic projects to date include the Exmoor pony, British Lop pig and, most recently, North Ronaldsay sheep. The opportunities for using genomics are extensive and range from full breed genome projects to a more targeted project to identify deleterious traits. The benefits are well recognised and there is certainly an increasing demand for RBST to help carry out such work – however, the costs are significant and these are often quite complex projects with a number of considerations to be taken into account.

Developing a plan
First and foremost, there is a need to develop a genomic project plan to determine what the objectives are and how they can be achieved. The key points that we have to consider are:

• What the objectives are and the stakeholders involved.
• The logistics of sample collection and the method to be used.
• Confirmation of the level of the genotyping required and identification of the appropriate specialist for analysis of the results.
• Detailed costings for each stage – including any trial work.
• How the results will ultimately be presented and used.

The key stages of the project are sample collection, genotyping of the samples, analysis of the results and, finally, their presentation.
Sample collection Identifying those animals to sample and the number required will depend on the objectives of the project, but they need to be selected to provide a true representation of the breed. Experience has shown that a whole genome project would require a minimum of 10% of the breed population to be sampled. However, the research organisations that we have consulted would encourage as many samples as possible to be collected to help produce a reliable set of results – without adequate samples, the project objectives will not be achieved.

There are a number of ways in which the individual animals can be sampled. These include, but are not limited to, hair, nasal swab, tissue sample and blood. The suitability and practicability of each method will depend on species but there are also legal consideration when it comes to tissue sampling. It is also important to ensure that those collecting the sample are provided with sufficient guidance on how to collect samples correctly to ensure that they are usable samples.
Before embarking on full-scale sample collection, experience has shown that it is advisable to carry out a small trial with whichever sampling method is planned to ensure its suitability for the main project. As well as confirming that the chosen method is the most viable, this helps with confirmation of project costings.

Sample genotyping
There are different genotyping arrays which can be used, dependent on species and project objectives. The more detailed analysis is, the more significant the cost becomes but it is important that cost does not become the sole focus when selecting the genotyping array. If it is the intention to compare the project results with data collection previously undertaken, it is important to ensure that a true comparison can be made by ensuring that the arrays used are compatible.
It is also worth taking a long-term view. It may be advisable to choose a more detailed genotyping array that will provide increased opportunities on which to base future genomic work.

Presentation
With any project, there will be a number of stakeholders involved, each of whom may have a different perspective on the project. Key to meeting everyone’s expectations is the process of determining a timescale with clear deadlines and agreeing how the results will be delivered at the start of the project.

No one should go into a research project with pre-conceived ideas of the outcome and, ultimately, the results may not provide the outcome a stakeholder wants to hear. If there is the possibility that the results may have a significant impact on current perceptions of the breed, all parties involved need to be aware of this and a plan needs to be in place to deal with it.

With the work we are doing, RBST recognises that we have much to gain through the increasing use of genomics. It is a complex science and projects require meticulous pre-planning and an understanding that the initial project may highlight a need for further work and further investment.

Genomics vs genetics
Genetics is a well-recognised term that refers to the study of genes and their roles in inheritance - the way that certain traits or conditions are passed down in the genes from one generation to the next.

Genomics is the all-encompassing term that takes into account all of the DNA in an organism’s genome – both the genes that code for proteins and the non-coding regions. It looks at how the genes are expressed and the interplay between different genes.

Whole Genome Sequencing (WGS) is a genetic testing technology that gathers comprehensive data on every gene and all of the chromosomes in the DNA. The analysis of a breed’s entire genomic DNA sequence of a cell at a single time provides the most comprehensive characterization of the genome, which is much more advanced than other technologies. It enables a better understanding of variations both within and between species.

Tom Blunt RBST Senior Conservation Adviser
[email protected]
March 2022