Nick Boddicker, PhD, Genesus Inc.
Genesus has written a number of articles on the importance of genomic information to improve genetic gain. That is because genomic information can greatly improve the accuracy of estimated breeding values (EBVs), particularly for lowly heritable traits (total number born), traits that can only be collected on the carcass (pH, color, etc), sex limited (litter traits), or difficult/expensive to measure (feed intake). Furthermore, this is the most important benefit to genomics because it ultimately benefits our customers.
Genotype information has additional benefits and uses as well. One is managing the level of inbreeding in a population. This is not an issue at the multiplication or commercial level because, by definition, animals crossed with a different breed yield offspring that are not inbred. Furthermore, Genesus maintains large purebred populations, which mitigates increases in inbreeding. Nonetheless, inbreeding can have a negative effect on genetic improvement because it decreases genetic variation, which is an important metric in the genetic improvement equation.
Gene discovery, using genome wide association analyses, is another benefit of genotype information. Gene discovery is scanning the genome for regions that have significant effects on economically important traits. With routine genotyping on hundreds of animals every week, Genesus has started to identify genes for novel traits, such as sow lactation efficiency and disease resilience.
Lastly, genotype information can give way to the discovery of lethal mutations. Lethal mutations in genes occur when a specific combination of alleles results in the death of an animal, typically before it is born. If a particular genotype combination is absent from a population, this region could be a candidate for a lethal mutation. For example, assume the sire and dam are genotype AB for a gene. Because the parental alleles at a gene are randomly allocated to offspring, the expected frequency of the genotypes in the offspring would be 25% AA, 50% AB or BA, and 25% BB. If the BB genotype is absent from the surviving offspring, this gene would be a candidate for a lethal mutation, i.e. animals with BB genotype die in utero. Lethal mutations have been reported to account for a reduction in total number born by 2.97 pigs per litter (Derks et al., 2017). Nearly 3 pigs less per litter has a significant impact on profitability for a producer. Identifying lethal mutations requires a large number of animals with genotype information. Genesus has a capability to do these analyses because of the hundreds of animals genotyped every week and are doing such in our Duroc population and will be analyzing our Landrace and Yorkshire populations as well.
Genesus continues to do cutting edge research to benefit its customers. This includes identifying and incorporating new technologies into our breeding program, along with identifying new analyses and uses for our current technologies.
Derks et al. A systematic survey to identify lethal recessive variation in highly managed pig populations. BMC Genomimcs 2017.
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