Traditional and genomic selection Flashcards
If clones all have the same DNA why is there variation?
- Due to complex traits such as environmental factors
What are complex (polygenic) traits influenced by?
- influenced by both genotype and environmental factors
- P = G + E
If you had two cows with the same genetic worth - Why might they different for milk yield?
- farm (diet, management, veterinary care…)
- age
- time of year
- breed ( though most selection is done within breeds)
In order to accurately estimate the genetic merit of animals what should we do?
- we should compare them under the same environment or adjust for known environmental factors via statistical modelling
How is traditional selection done?
- record performance and use pedigree information to derive breeding values
- assigning numbers to animals for genetic traits
- breed the best animals overtime
What is genomic selection?
- make selections based in the genomewide profiles of the animals tested
- can use a combination of traditional and genomic
What is the breeding value (BV)?
- the animals value as a parent
- the sum of all the genes affecting the traits we want to select
How do we work out predicted transmitting ability (PTA)?
= 1/2 of the EBV
What is GEBV or gEBV?
- genomic EBV
What is heritability (H2)?
- the proportion of the trait that is genetic
- usually given as a value from zero = low to 1 = high
- higher heritability is better
What heritability score is ideal and up?
- want 0.2 (20%) or higher
What are the different ways we can estimate the BV (breeding value)?
- progeny test
- performance test
- pedigree
What is the most accurate way to estimate breeding value?
- the progeny test
What is the progeny test?
- taking a number of sires and mate to random females (average to population) and compare mean performance of progeny from each sire
What does the progeny test allow for?
- measures the breeding value directly and provides a definition of breeding value
What is breeding value strictly related to?
- related to superiority (or inferiority) with respect to the population mean
What is transmitting ability (TA)?
- value of the genes that, on average, are passed on
What is BV related to in terms of TA?
- BV = 2 x TA
What can we predict if we know the value of the animals genes?
- we can predict that on average, it passes genes to its offspring worth half that value
- because it passes on half its genes
If we know the BV’s or TA of the parents what can we predict for the progeny?
- we can predict the BV of their progeny
What are the units of BV?
- kg
- litres
- seconds
What is a performance test?
- measure individuals performance relative to the performance of its contemporaries
What should be considered in a performance test?
- same environmental opportunity
- assume that better performance = better genes (on average)
- avoid preferential treatment
What equation can be used for BV in performance tests?
- BV = h2 x (individual performance - population mean)
Where may performance test be difficult to use?
- progeny may be difficult to test where you have to wait for a certain age
- for example in racehorse progeny you would have to wait for the progeny to get to 10-15 years of age before you could test the quality of his progeny
How would you predict progeny BV?
- 0.5 BV of sire and 0.5 BV of dam
= progeny BV
Under what conditions would you use the performance test?
- performance measure on individuals directly
- heritability is moderate to high
Under what conditions would you use the progeny test?
- traits cant be measured directly (sex limited, post mortem traits)
- heritability is low
What would need to be considered before using a progeny test?
- cost
- generation intervals
- gain per year
What is the difference between BV in progeny tests vs performance tests?
- progeny test measures BV directly
- performance test predicts BV
A good performance test ranks animals how?
- in the same way as a progeny test
Why do we refer to estimated breeding valves in both the progeny and performance tests?
- because both methods involve sampling to estimate rather than a direct measurement
What does a pedigree evaluation use?
- list of ancestors and relatives
- use performance records of relatives compared to their contemporaries
What test is a from of pedigree evaluation?
- progeny test
What do they say:
1. A pedigree test tells you
2. A performance test tells you
3. A progeny test tells you
- what to hope for
- predict what you might get
- what you have
What combination greatly improves the prediction of the outcome of mating?
- a combination of pedigree and EBV’s of animals in that pedigree
What test would you use on young animals?
- performance test
What tests would you use on breeding stock?
- performance and progeny test
What would you use for a pedigree?
- information from relatives
What does BLUP stand for?
- Best Linear Unbiased Prediction
What does BLUP use?
- statistical estimation of BVs
- uses all information from relatives
- correction for environmental factors
What might happen to estimated breeding values is environmental impact is high?
- animals with a higher breeding performance might look like they have lower EBV
What do breeding schemes allow for?
- allows farmers to compare herd to national trend
- schemes like AHDB
What is a phenotypic (rp) correlation?
What’s the scale for this?
- correlation between phenotypes for two traits measured on the same animal
- scale = -1 through 0 to +1
- 0 = no correlation
- 1 = correlation
What is a genetic correlation (rg or ra)?
- show the genetic merit (EBVs) of two traits measured on the same animal show the same variation
What are environmental correlations?
- common environmental effects cause correlation between two traits
What is genetic correlation caused by?
- pleiotropy = one gene that controls multiple traits of same set of gene results a set of traits
What can result from genetic selection?
- indirect selection an indicator of the thing we want to improve
- genetic antagonism
- selection for more than one trait at a time
The selection index is the most effective method of selecting for what?
- for selecting for more than one trait at a time
What should a selection index include?
- should include all traits of economic importance of breeder
- weighted according to economic value
What should a selection index account for?
- accounts for heritability, correlations among traits, economic values, and can include information from indicator traits not in the selection objective
What do we used to screen tens or hundreds of thousands of markers across the genome?
- large scale (genome-wide) DNA microarrays or SNP chips
How do you work out a predicted response in genome selection?
= selection intensity (heritability of trait)
Genome predictions are good but they aren’t as accurate as performance testing.
What is the advantage of genomic predictions?
- because you can select purely on genotype you can trade off lower accuracy for saving in time and money
What is genomic selection now widely used in?
- range of animal and plant breeding programmes and for multi-trait improvement
What is genetic selection using SNP markers used for in companion animals?
- to eliminate or select for mainly mendelian traits
What are examples of mendelian diseases?
- myotonia
- Duchenne muscular dystrophy
What are examples of mendelian traits?
- coat colour
- hair length
- dwarfism
