July 18, 2021

Animal Breeding and Genetics Symposium II

Animal Breeding and Genetics Symposium II

Integration of Quantitative Genetics and Epidemiology: Why Selection Against Infectious Diseases Is More Promising Than We Think – Dr. Piter Bijma, Wageningen University

The Animal Breeding and Genetics Symposium II at the 2021 ASAS National Meeting on Saturday, July 17th, began with Dr. Bijma discussing why selection against infectious diseases is more promising than currently believed. Infectious diseases are a great concern in agriculture as they lead to production losses and costs of treatment causing economic damage. Genetic selection has been used as a strategy to combat infectious diseases in agriculture. The current breeder’s perspective focuses on the binary disease status of the individual and the low heritabilities suggest the rate for genetic improvement is restricted; however, Dr. Bijma explained that a proper quantitative genetic theory that includes transmission dynamics within a population is lacking. He then went on to discuss the results from integrating quantitative genetic analysis of binary disease status with epidemiological models of transmission. The ordinary breeding value that determines individual phenotype and the breeding value that determines response to selection for prevalence differ by a factor of prevalence (P), implying that the breeding values that determine response to selection increase strongly when prevalence goes down showing that there is more genetic variation and higher variability than we think from our ordinary breeding values. This suggests that the genetic variance that determines the potential response of prevalence to selection may largely be due to indirect genetic effects, which are hidden to ordinary genetic analysis. Overall, there is either way more genetic variation for response to selection than we think, or there must be some other key factor that we are overlooking. This suggests that selection against infectious diseases is actually more promising than currently believed.

Insights into Complex Traits from Human Genetics – Dr. Kathryn Kemper – University of Queensland

Dr. Kemper began her presentation by defining a complex trait: traits that are influenced by many genetic and environmental factors. This implies that there are simple (or Mendelian) traits that exist. A classic Mendelian trait in livestock is the poll locus in cattle, where there is a strong predictable correlation between genotype and phenotype. In humans, an example would be Huntington’s disease that has an autosomal dominant pattern of inheritance. It is a classic single gene disorder, but there are polygenic components to consider when understanding the disease outcome. Dr. Kemper explained that simple traits are increasingly hard to find as a polygenic background of ‘modifier effects’ seems to operate in many cases such as Huntington’s disease and BRAC1/BRAC2 mutations. She then discussed how most traits are complex traits and while livestock industries have been able to implement genomic selection for genetic improvement, genomic selection provides little insight into the genetic mechanisms underlying variation in complex traits. Human genetics, on the other hand, has fixated on understanding genetic architecture and the origins of quantitative trait variation. Dr. Kemper then analyzed various examples from human genetics that have helped to form our understanding of the nature of variation in complex traits and realize that simple traits do have more complex genetic architecture than assumed. She also explained how massive data sets and huge sample sizes are allowing us to start to address and understand more about effects that are harder to quantify. Performing similar studies in livestock will potentially be helpful to better understand and predict complex traits in livestock.

The Saga of Just One QTL; From Laying Hen Bone Strength to the One Carbon Cycle – Dr. Ian Dunn, University of Edinburgh

Dr. Dunn continued the discussion on what makes complex traits complex by focusing on bone health in laying hens. Eggs are very economical, a well-balanced source of protein, and consumed in large quantities across the world, heightening the importance of hen and bone health. Bone quality in laying hens is a growing welfare and economic concern in the industry. While there are many factors that can exacerbate bone fractures such as environmental conditions, management, housing, activity, and growth, past research has shown genetic factors have an important influence on bone quality. Previously, a quantitative trait locus (QTL) of large effect was detected on chicken chromosome 1. Dr. Dunn explained how they then fine-mapped the QTL on chromosome 1 to understand its function in terms of gene expression and physiology. Some of the results he discussed included detecting several single nucleotide polymorphisms on chromosome 1 that had significant associations with tibial breaking strength and transcriptome profiling of the tibia from high and low bone strength genotype revealed a highly differentially expressed gene at the locus, cystathionine beta synthase (CBS). This brought in the link between laying hen bone strength and the one carbon cycle as CBS is a component of one carbon metabolism. Plasma homocysteine concentration, the substrate of CBS, was much higher in the low bone strength genotype, leading the researchers to question if they could change homocysteine concentrations with nutrition to improve bone quality. Eventually, they discovered that feeding betaine would reduce plasma homocysteine concentrations and improve bone quality. By gaining more information about the QTL on chromosome 1, a nutritional and genetic solution was discovered to potentially improve bone quality. These are just some components of a complex trait and further research needs to be conducted to understand more factors that determine skeletal quality genetics to improve hen bone health and overall welfare.

Awardee Talk: Genetic Improvement of Disease Resilience – Dr. Jack Dekkers, Iowa State University

After returning from a short break, Dr. Dekkers was presented with the Bouffault International Animal Agriculture Award for his scientific contributions through research that will have many long-term benefits for both developing and under-developed countries. Congratulations, Dr. Dekkers! He then began his presentation by explaining the difference between resistance (the ability of an animal to prevent pathogen infection/limit replication), tolerance (the ability to maintain performance as pathogen load increases), and resilience (the ability to maintain performance as pathogen exposure increases). Infectious disease is one large cost component to the swine industry due to reduced performance, reduced animal welfare, loss of pigs due to mortality, and others. There are strategies that exist to reduce the incidence and impact of infectious diseases such as vaccination, veterinary treatment, biosecurity, and selection for genetic resistance; however, each of these strategies have their own limitations causing commercial pigs to continue to be exposed to and infected by pathogens. If complete resistance is not reasonable, selecting for resilience could potentially be beneficial to allow these animals to have the ability to clear an infection while still maintaining performance and therefore, may be a useful target for inclusion in breeding programs. Dr. Dekkers then explained how the use of a natural polymicrobial disease challenge model was used to collect disease resilience data and develop indicators of resilience that could then be used to select for disease resilience. Day-to-day feed intake patterns were found to be correlated with disease resilience and can be measured on healthy pigs to ultimately predict resilience of their offspring. Genetic selection can have an important role in developing pigs that are more resilient to multiple diseases and further research needs to be conducted to determine other potential indicator traits for disease resilience that can be collected in nucleus herds as well. Even though disease resilience is a complex genetic trait, it will be important to include in breeding programs.

Invited Speaker – The Use of Sensors for Phenotyping: Estrus and Thermotolerance - Dr. Ronaldo Cerri, University of British Columbia

Dr. Cerri concluded the symposium by introducing the topic of phenotyping with the use of sensors specifically for estrus and thermotolerance. Estrus detection is a critical component of reproductive programs in dairy cattle, yet visual estrus detection is difficult especially when there is a lower intensity of estrous expression and when the duration is short. Previous studies have provided evidence that expression of estrus tends to have a beneficial effect on fertility. This link then highlights the importance of behavioral estrus, where important physiological effects linked to estrus and fertility can be captured by a behavioral trait. There are currently all sorts of sensors used for precision dairy farming such as pedometers, accelerometers, video analysis, and GPS. These activity monitors could help to capture the various intensities and durations of estrus in dairy cattle as not all estruses are equal with some having a high intensity estrus and others having a low intensity estrus. The intensity and duration have a direct association on ovulation success, pregnancy loss, and pregnancy per artificial insemination, suggesting that utilizing sensors to measure estrous expression can potentially lead to better on-farm estrus detection, potential genetic selection for estrus expression, and hopefully overall improve herd reproductive efficiency and pregnancy outcomes.