Domestication, mating and selection, the basis of our life.
Selective Breeding is an activity that mankind has carried out instinctively since the first plant crops that sustained ancient civilizations. However, domestication of animals and adaptation to captivity has taken longer, except for the species that were employed for commercial uses such as horses, cattle, pigs, chickens, or our dear pets; dogs, and cats. Mating these domesticated populations with a systematic and scientific approach began in the 17th and 18th centuries, but in the case of aquaculture, the first modern breeding program in salmon wasn’t established until the 1970s. More and more, improved cultivation of plants and animals is recognized as essential to meet the requirements of growing human consumption, with aquaculture representing an important source of healthy protein and micronutrients.
When managing crops or culture systems of any kind, a founding population is established as a starting point followed by a further selection of animals with desired traits relevant for the efficiency of the process or consumer acceptance. The design of the crosses and the general strategies to reach the breeding goals varies considering the geographical area and its economic conditions, the species, the knowledge/expertise of the producers and the needs of the market.
Many farmers are up to date with new technologies for stocking at higher densities, animal nutritional requirements, and general management of commercial species. However, relatively few have taken the step of tracking and improving the genetic characteristics of their breeders and offspring as an essential part of their operations. The use of molecular markers is by far, one of the main scientific tools used to help manage breeding programs today.
The objective of this article is to help producers to understand:
- How they can have a snapshot of the genetic characteristics of their populations in captivity.
- Why this is important to sustain or improve levels of production.
Let’s start with the first question. The best way to get this snapshot is by doing a Genetic Overview (GO) analysis.
What is a GO analysis?
The Genetic Overview (GO) is a compelling analysis that is used to characterize populations in captivity that are often being managed for commercial purposes. Using state-of-the-art analytical techniques, the GO analysis report describes the levels of diversity, inbreeding, and kinship/relatedness, as well as the genetic structure of the sampled population.
The data required to complete a GO analysis is genetic marker information (genotypes or genetic fingerprints) taken from a subsample of individuals within a population. While there are several genetic marker types available that can be used for this analysis, the single nucleotide polymorphism (SNP) is the most desirable type because SNPs are much more abundant in the animals’ genome than other types of markers. SNPs are also easily assayed and scored in a high-throughput and cost-effective manner. The larger the number of SNPs that are used, the more detailed the genetic fingerprint that is generated and the greater the amount of information that can be learned about the genetic structure of a population. A Genetic Overview can be conducted with as few as 150 SNPs per animal and up to as many as 50,000 SNPs per animal or more. The choice of how many SNPs to use will be dependent on the objectives of the analysis and the complexity of the breeding populations being investigated; it can be customized for any program, any species, and any budget.
Why completing a GO analysis is important to sustain or improve levels of production?
The short answer is because the GO analysis can reveal a management strategy that you cannot see just by using your naked eyes and selecting the best animals only using their appearance, but let’s expand on that.
Have you ever heard the phrase “the DNA does not lie?”. We use it frequently because sometimes not even the current owner of the farm knows about the previous history of the breeding line(s) they have. Whether the animals were taken from the natural environment and adapted to captivity, bought from another farm, or donated from an experimental unit in a scientific institution, there will be a genetic fingerprint that can describe the ancestral origin and current composition of this population. However, although useful, there is even more information that the GO analysis can reveal.
The key information is the genetic variability and the levels of consanguinity, briefly defined as inbreeding and relatedness/kinship in the population.
Concerning genetic diversity, one of the foundations of a strong and productive breeding program is good genetic diversity in the breeding population. This allows producers to make good progress when selecting for a variety of commercial traits and it is also a buffer against inbreeding building up in the population. Understanding genetic diversity can lead to strategic discussions, such as whether to merge various lines in a breeding program or, whether outside genetics should be added to increase diversity. Assessing diversity can also serve as a benchmark to manage against loss of diversity (an increase of homozygosity) over time.
Most of the deleterious traits in living organisms are produced by homozygous variants, including several “per-se” genetic diseases or susceptibility to acquired infections from the environment. When mating among related individuals is carried out, or during self-fertilization (for example in plants or in the case of the aquatic environment, some types of mollusks) the number of homozygous variants is enhanced, that is, consanguinity is raised. This leads to lines of less vigor, lower reproductive success and, in the worst-case scenario, these homozygous variants can be lethal leading to the potential loss of pure lines.
Documentation of pedigree linked to the performance of the offspring is a very common practice in breeding management. It has been shown, though, that these types of records captured using traditional methods can accumulate between 2 and 10 % error. Additionally, for aquatic species that can produce thousands of descendants and systems that can accommodate several breeders, the use of molecular markers such as SNPs to track the pedigree, is justified and highly recommended.
Finally, when selecting animals with better performance/efficiency for desirable traits, it is possible to inadvertently breed animals with similar genetic composition and/or higher relatedness. When this process is repeated for several generations, the number of genetic variants can decrease, and homozygosity can accumulate if the spawning plans and the selection process is not well managed. This loss in variability can lead to a genetic bottleneck of the population together with an increase in inbreeding/relatedness, and the legitimate threat of population collapse.
In summary, for a genetically healthy population, high diversity and low consanguinity is most suitable. Owing to the advances in DNA technology that has enabled the development of cost-effective tools for identifying SNP genotypes, the ability to measure and trace diversity and consanguinity in captive populations is available to anyone wishing to better manage the genetic health of their population now and in the future.
A Genetic Overview (GO) provides a snapshot of the genetic characteristics of a population. It is advisable to complete a Genetic Overview analysis prior to implementing a breeding program to understand the level of diversity and relatedness and, the history that the DNA reveals about previous management and origin of the lines. Thereafter, adopting GO into a hatchery management strategy will enable the evaluation of the impact of selection on the genetic quality of the breeding lines over time, guide the mating decisions to maximize diversity, and decrease the rate of inbreeding/relatedness to maintain the genetic health of a population.
Dr. Adriana Artiles is a Breeding Scientist at CAT. As part of the team, she brings her expertise and enthusiasm for both field and laboratory work to help clients worldwide to design, implement, and manage breeding programs for a variety of aquatic species.