The aquaculture industry is ripe for the uptake of DNA-based technologies also known as genomics. The sector has observed and, therefore, learned lessons from the livestock industry where DNA tools are heavily applied, and genetic gains are no longer simulations on a computer screen.
Many aquaculture producers have questions and are seeking guidance to improve their genetics.
Before I charge ahead with my recommendations, I want to emphasize that the use of genomics will not make the need for collecting phenotypes or the need to improve a management system go away.
Economically important traits are complex in nature, which means that part of their outcome originates from improvements in genetics – through the observation of measurable traits and other breeding records – and part from improvements in management (i.e., health, nutrition), so investing in one while ignoring the other will not solve all your problems.
Genomics is just one tool in the box and does not replace good husbandry practices and a commitment at all levels of an organization to supporting the genetic improvement program.
The Difference Between Genetics and Genomics
Let me first make the distinction between the terms ‘genetics’ and ‘genomics’. These are different terms, but they complement each other when we talk about a breeding program.
A seller of broodstock will say ‘I sell genetics’. A geneticist will say genetics in terms of genetic merit (breeding values). Different roles, different definitions but all correct, in their own way.
Genomics, on the other hand, is a term associated with the structure of the DNA (i.e., the bases: As, Ts, Cs, and Gs), and the tools that allow us to profile the DNA are defined as genomics tools.
Every producer will benefit from using DNA technology in their breeding program. The level of benefit and the type of return on investment will depend on the tool – whether low density (LD), medium-density (MD), or high-density (HD) – that they use. Regardless of the tool, the application of DNA technology adds precision to a selection decision.
The type of tool to use is a function of how producers have structured their breeding programs; for example, if they have been collecting phenotypes and maintaining breeding records.
Below are the Top 3 Tools (genomics and bioinformatics) that any aquaculture producer should consider investing in:
The Top 3 AQUAArray Genomics Tools:
- Low Density (LD): for those dipping their toes in genomics without any knowledge of which populations they have (i.e., species or strains), we recommend a panel with less than 200 SNPs. It provides insights into the genetic architecture of the population and a basis for relatedness and inbreeding. This panel also allows for parentage testing, an important step in the calculation of EBVs (estimated breeding values), which is another way of saying genetic merit. Each species has its own LD panel.
- Medium-Density (MD): If you have been investing in high-density (HD) genotyping (see below) for a while and you have a solid knowledge of how your population is structured (i.e. level of linkage disequilibrium), then you should start thinking about a medium-density panel that can be imputed to your HD dataset to save cost while maintaining precision.
- High-Density (HD): The most powerful tool for a full-throttle, high-speed genetic improvement program. These panels have around 50,000 markers and can be used for parentage testing, genomic selection, marker-assisted selection, etc. Producers that have been, and are committed to, collecting phenotypic data are in the sweet spot for the use of this HD tool,
The Top 3 Bioinformatics Tools:
The bioinformatics tools provide actionable insights needed to move ahead, and without them, the tools I listed above are just a bunch of As, Ts, Cs, and Gs. Below is a list of analyses and applications coming from these genomics tools:
- A Genetic Overview (GO) Analysis: A powerful analysis that provides insights on the diversity and level of inbreeding between animals of a population. When combined with a strain ID analysis – it enables the differentiation between animals used in different production systems and markets. For example, Tilapia (the Nile vs Mozambique), Largemouth Bass (Florida vs Northern).
- Parentage Analysis: This analysis defines the pedigree of your animals, and it is – after you have been collecting phenotypic data – the first step for the calculation EBVs (genetic merit). It requires samples from the broodstock and its progeny.
- Genomic Selection: At this stage, the pedigree information and phenotypic data have been collected over many generations. Here we assign a value (+ or -) for each of the thousands of markers obtained from the HD SNP panel and that information is then added to the genetic evaluation. You may have heard of the term GE-EBVs (genomic-enhanced estimated breeding values). This is a more precise estimate of the genetic merit because of the power added by the DNA information.
Once you have decided which genomics tool best fits your needs, or you may also want to contact us to discuss more, it is time to collect a biological sample. This step cannot be ignored, and a misstep here can often mean low quality DNA yield and, therefore, no results. Fin clips (for finfish) or pleopods (for shrimp) are a great source of DNA. We guide our clients throughout sample collection and submission to ensure that we generate usable results.
What’s your weakest link?
A genomic tool will only be as good as your weakest link. So, if you have not already done so, there will come a time when you need to upgrade your management program (i.e., invest in better feed, monitor for pathogens, buy bigger or more tanks, modify your layout). To put it into layman’s terms, do not expect to reach the finish line by putting Porsche tires (HD tool) on your Volkswagen Beetle.
If your weakest link right now is in pathogen detection and monitoring, the best way is to couple one of the genomic tools above (LD, MD, or HD) with a panel for pathogen detection where you can choose which pathogen to test for. You may not need all of them, so it is important that you have an à al carte option rather than an ‘all you can eat’ buffet.
And, if you are noticing that you need help in multiple levels of your business (health, nutrition, genetics, genomics), an annual breeding contract that carries custom made recommendations would likely serve you better and qualified professionals are out there to help new entrants wade through all their options!
Dr. Elisa Marques has spent the last 15 years vigorously applying genomics tools in genetic improvement programs around North and South America. She is currently holding the Senior Director of Business Development position at the Center for Aquaculture Technologies (CAT).
Read more about our genotyping tools and services here.