Moving on to family selection in 2000, new traits came into the program related to harvest quality and disease resistance.
Since 2009, individual selection methods have significantly improved the precision of selection and thereby the genetic gains for important traits.
The Benchmark Genetics in-house breeding programs are all based on family selection.
For instance, our Atlantic salmon programs produce more than 800 families every year, each with a large number of individuals for further selection and testing.
Why family selection?
By comparing families for different traits that are important in commercial production, we can accurately identify families with specific genetic advantages. Family selection is especially crucial for traits that are difficult to measure on individuals or are destructively measured, such as fillet yield or color. Family selection is also an effective way of minimizing the levels of inbreeding, as we are in control of the pedigrees of each family.
In traits such as growth, where the phenotypes are easily measured on breeding candidates, individuals can be efficiently selected based on its performance. In recent years new genomic methods has been developed to identify individuals for breeding based on DNA sequence by genotyping. By understanding which genotypes (often using SNPs — single nucleotide polymorphisms) are associated with excellent performance in each trait, it is possible to screen populations for the best performing offsprings.
Genomic Selection is when a large number of SNPs are used on each individual. In some traits, where single SNPs are associated with a large amount of variation (often described as QTLs — Quantitative Trait Loci), individuals can be selected on a small number of SNPs. In both cases, genotyping has improved the effectiveness of selection by more accurately identifying the individuals with improved performance. This is particularly important in traits such as disease and parasite resistance.
The individual selection has been implemented in all of our in-house breeding programs across species.
A QTL is a position on the genetic sequence (genome) associated with a significant amount of variation of a trait. It is often identified using one or a small amount of SNPs. The QTL suggests that a considerable gene is located close to that position on the genome. The SNPs are genetic markers for the QTL and can be used in a particular form of selection known as marker-assisted selection (MAS).
In Atlantic salmon, a significant QTL has been identified for resistance to IPN virus, which accounts for over 80% of the genetic variation in resistance. SNP markers for this QTL is used to identify and breed from resistant individuals in the nucleus and for commercial egg production, reducing the number of outbreaks of IPN.
Researchers continue to identify significant QTLs for other traits. Although in most traits, the majority of variation is accounted for by many genes where Genomic Selection is more effective.
Marker-assisted selection for larger QTLs is a very effective method for traits where a major gene accounts for the majority of genetic variation. In most traits, however, genetic variation is controlled by a large number of genes, each with a small effect. For these traits, Genomic Selection (GS) is more effective in identifying individuals for breeding. Genomic Selection (GS) is a more comprehensive methodology than QTL and is better adapted to traits that are controlled by many genes. Using advanced genetic methods, we can successfully select parent animals with the most suitable genes for commercial offspring production.
Our breeding programs for Atlantic salmon are internationally recognized for the offspring quality — rapid growth coupled with delayed sexual maturity, disease and parasite resistance and outstanding flesh quality.
Sea-lice is a significant challenge in salmon farming. Benchmark Genetics started using family selection for sea-lice resistance as early as 2007. Because sea-lice is a complex trait, we switched to Genomic Selection in 2015. Since then the rate of genetic gain in sea lice resistance has been more than three times greater.