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Brood program basics

March 23, 2023  By Ron Hill


photo: © konstantin baydin / Adobe Stock

Brood is an entire field unto itself, complicated and with high stakes. There are many intricacies to a brood program and many worthy books and papers on the subject. When looking at brood it can be difficult for the farmer to decide where to get started. The initial impulse for the farmer is often in favour of keeping brood, but the question is an essential one to explore for any farm. 

Should a farm have its own?
The answer, of course, is that it depends on the farm and the nature of the venture. Brood programs are expensive. They require specialized staff and contractors, specialized tools and analyses and a staffing commitment. Brood programs also take up space; rearing units with brood are not producing fish for direct profit. Brood programs provide a self-sufficient source of new fish, but is that a risk or a security? The difficulty and viability of egg production varies species to species. Inexperience with the species or inexperience with live feeds for larvae production create a steep learning curve that is likely to negatively affect production at least at the outset.

The cost of purchasing eggs or fingerlings from a reliable source must be weighed against the expense and risk of self-production. The nature and size of the source farm must also be taken into consideration. Quarantine for outbreaks in other regions that limit import of a species can be devastating for a farm that relies on imports. 

Setting up
“The first thing you need when setting up a brood program is clear goals,” says Mowi Canada West’s brood support specialist, Trevor Dawes. “What do you want your breeding program to accomplish and what traits are most desirable? From there, you start to work backwards through the planning from your desired end result back through the production cycle.” 

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Indeed, goal-oriented selection is the basis of any brood program. Whether it’s getting a better FCR from the stock, increasing stock resistance to disease or harsh conditions, or getting more top-quality colour fillets in the processing plant, brood goals are designed to increase efficiency and advance the ability of the company to growth their fish through genetic improvement of the fish stock.

Having decided to pursue a brood program and selected a goal or goals, detailed planning must be undertaken, as well as a thorough assessment of the current stock and facilities. For example, salmon farmers generally plan four to six years ahead, but planning needs will depend largely on the life history of the species reared.

“There are many traits that can be selected for including flesh colour, growth rate and disease resistance,” explains Dawes. “The goals of the program, and therefore the needs of the farming operation, determine the most desirable traits. Some traits like flesh colour or growth rate are easy for farmers to track and trace, others such as disease resistance can be hard to select for without the use of DNA analysis.” 

Program management
In general, there are two ways to manage brood: using genomics or not using genomics. Using genomics means matching and breeding fish based on genetic analysis of the species’ genes. Knowing the genes allows the farmer to breed fish with desirable genes to improve the stock performance and breed out undesirable traits.

The choice to use genetic analysis is very specific to the farm and farmer. The decision comes back to the goals of the breeding program, the size of the operation and the funding available. 

Using genomics
DNA analysis is incredibly helpful and is the best way to improve a breeding program. It is easy to use the eye test to select fish with outwardly desirable traits, but lose desirable traits that are unseen or worse, perpetuate unseen undesirable traits. Fish are PIT tagged, DNA sampled and sexed with an ultrasound are soon as size allows, with salmon or trout this is before they are one year old. The information is recorded along with the rest of the important details about the fish. At this point, geneticists can analyse the DNA and decide which fish they want to keep for breeding and backups, and let the farmer remove the undesirable brood and excess males from the brood program. These excess fish are usually added to a production group as the size is small.

Using DNA analysis, undesirable fish are removed from the population early in the life cycle allowing the brood program itself to be significantly smaller, take up significantly less space and allow greater mixing of groups since each fish can be identified by scanning the PIT tag.

Not using genomics
Not using genomics usually means the farmer will be following a ‘Do No Harm’ philosophy. A program without genomics relies on the farmer’s ability to select brood groups based on desirable traits and maintain family brood groups. These groups are managed to avoid inbreeding depression and are matched with other isolated groups for spawning. Tracking traits is a long-term process as analysis happens after the traits are expressed (fish must reach adulthood to be evaluated). This setup necessitates a much larger brood program with more individual tanks for keeping individual groups separate or rudimentary tagging (like fin clipping or coded wire tags) to allowing some mixing of groups.

A two female to one male breeding program allows the low-tech brood farmer to track traits. Paternal traits will be expressed in the offspring from both females while maternal traits will only be expressed by their own offspring. 

A low-tech approach can be very effective. There are many examples of successful brood programs that do not use genomics, but the ability to improve the stock is limited compared to using genomics.

Tools of the trade
These useful tools can help a farmer get the most out of their brood program: 

  • Ultrasound – used for sexing, allows farmers to remove excess males from the population and know the number of females. Knowing number of females allows farmer to anticipate number of eggs. Eliminating excess males from the brood population early allows more females to be stocked.
  • PIT tags – allow individual fish to be identified by scanning the implanted tag. Info can be recorded including sex, lineage, DNA etc. Fish can be placed in a mixed tank of brood as they can be re-identified with a scan.
  • Cryo milt – a great tool allowing desirable male milt to be used in multiple generations. Milt is cyropreserved and then thawed as needed. Useful as insurance against excess mortality or poor performance. 
  • Performance evaluation groups – PIT-tagged fish are sampled throughout the production cycle to see how they are perform under farm conditions at different life stages. 


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