Genetic Testing Large Animals Flashcards
Why do we do genetic testing
- health
- conformation/ apperance
- inheritance
- breeding value
- ancestry
- production
- inbreeding
Application of genetic testing
how we interpret genetic test results and what we do with them
- medical tx
- culling
- marketing
- rearing/ maintenance
- breeding
Who does gene testing
- breed associations
- internationa/ national associations
- genotyping companies
- AI companies
- Academic institutions
Uses of genetic testing
- depends on acceptance by general public and for industry adoption and use of it
- can be used by individual or by a group
- can be used to educate the public vs to educate a user
genetic test pricing
high density= higher number of markers= higher price= higher accuracy
- realistically the accuracy is fairly close and for the 5% difference in accuracy most consumers will go with lower density and lower price
DNA sample options
- hair
- blood
- tissue
- nasal swab
- semen
genetic merit
what is the genetic value of the animal; objective score of that animals value
- estimate for this evolved from looking at phenotype and pedigree
- now look at phenotype genotype and pedigree this allows you to estimate values of traits not exhibited (ex milk production in bulls)
parent average
genetic average of each parent’s genetic value; assumes offspring inherit exactly 1/2 of parents genetic merit for all traits and that parents are 100% correctly IDed
estimation of genetic merit
- genotypic value
- breeding value
- progeny difference= transmitting ability
- producing ability
genotypic value
value of an individuals genes on their own performatnce
breeding value
value of an individuals genes on their progeny’s performance
progeny difference= transmitting ability
expectation of what progeny inherits from their parents
producing ability
performance potential of an individual for a repeated trait (Ie milk production in a dairy cow)
progeny testing vs genomic prediction
investment progeny testing= time and cost or raising animal and progeny until performance evaluated
investment genomic prediction= genomic research, industry infrastructure, producer buy in
genomics- has better accuracy of genetic merit and trait selection, lets you evaluate merit of young stock, validate parentage, check for cacciers for genetic conditions
genomic prediction
- need a reference population so take all of these cows who’s phenotypes for things like milk production have been recorded and genotype them
- get prediction equations associations between SNP and phenotypes (what marker indicates what phenotype) and look at how that gives genetic merit
- once you have reference pop must still keep sequencing because populations change
Rate of genetic change equation
Expected genetic progress per year= { (square root of genetic variance) (selection differential ie intensity) (square root of accuracy)}/ generational interval
genetic variance
variation in population due to genetics; includes heritability (h^2) of trait
* we can not change this*
selection differential
intensity of selection; how selective we are when making mating decisions
accuracy
how certain we are about our estimate of an animals genetic merit
generation interval
time between generatiosn
what’s included in genetic evaluations
- conformation/ type traits
- produciton traits
- health traits
what drives genetic change
elite animals
performance index
optimized for general improvement of production, health, and conformation net merit (parent transmitting ability x economic value)= most common
targeting indexes
uses subset of traits to improve a targeted subject like cheese merit (emphasis on protein and fat %), fluid merit (emphasis on milk yield), grazing merit (emphasis on fertility), calving ability (emphasis on easy and alive calf birth), fertility index (emphasis on conception rate)
individual traits
looks at individual traits under umbrellas of production traits, health traits, and conformation/type traits
inbreeding
looks at potential loos per 1% inbreeding increase in different traits
- inbreeding can lead to inadvertent propigation of deleterious mutations
does carrier status affect genetic merit of an animal
no because even if they are a carrier they are fine; farmer may use this to decide who to breed to and who not to breed to
genetics limitations
- genetics if foundation for potential but without good management won’t reach that potential
- there will always be outliers who over or under reach potential
- farms who don’t use genetic testing will still improve because of industry improvements just slower
who do you genotype
bulls, cows, heifers, calves; depends on what is important to you and what you want to test for, this very much depends on farm and what their focus is
proven vs young bulls
proven bulls have more reliabilityy in estimation of genetic merit because have phenotypic along with genomic data; higher probability of progeny having expected genome merit (85-90% reliability)
young bulls- reduce generation interval and increase genetic change but genomic estimation of merit less than those of proven estimates (70% reliable)
- can have diff people choosing bulls can be choosing bull for individual cow or for group of cows in the herd
how do you increase the rate of genetic change
reduce generation interval and increase selection intensity
commercial marketing
can use genetic testing to try to back using your bulls or cows ect. saying they have better ____ trait; can also look at niche marketing for things like no horns (good for animal welfare dehorning concerns and not having to pay for man power to dehorn); can also increase thrermotolerance
industry impact of genetic testing
- increased genetic merit of individuals
- reduced genetic interval
- reduced cost (less progeny testing, merit of young animals)
- inbreeding management (preventing propigation of recessive deleterious alleles)
American Quarter Horse Association
- offers 5 panel genetic tests; tests are more expensive than cow test for many fewer traits looked at
HYPP
impressive syndrome; AQHA designated this a genetic deffect; all impressive descents has to be be tested for the ex and have parentage verified and results on registration; any horse who is homozygous dominant can’t be registered
genetic testing in horses
can look at coat patterns and to see if carriers for genetic dx or not and a few other traits like curiosity/ villagence/ myostatin/ speed, gait; lordosis (curvature of spine); no genetic merit application in horses yet
genetics in goat and sheep industry
they’re stuck on what is important and can’t agree
successful application of genomics
- industry infrastructure
- extensive historical data
- wide spread use of AI
- high value of animal
- generation interval that can be impacted
- large scale gain in industry (variable gain on farm depending on implementation)
Challenges of genomics
- standardization of phenotypic data (its subjective)
- industry consensus on trait prioritized
- initial cost investment
- implementation across management systems
- inbreeding
New traits
these are v convient but can be v costly to keep track of and breed into a line who were is the line of value it brings vs what it costs
Traits of current interest:
- feed efficiency
- Heat tolerance
- Complex dx
- consumer valued traits
Considerations for new trait selection
- value of trait
- initial research investment
- cost of long term phenotyping
genetically modified vs genetically enginered
some companies trying to separate the two for public perception improvement
GMO:
- technique to genetic engineering that introduces genetic material often from another organism tends to have bad reputation
Genetic engineering
- gene editing process that enables use of genes already native to plants or animal that could be introduced via conventional cross breeding
