Traditional and genomic selection Flashcards
(58 cards)
1
Q
If clones all have the same DNA why is there variation?
A
- Due to complex traits such as environmental factors
2
Q
What are complex (polygenic) traits influenced by?
A
- influenced by both genotype and environmental factors
- P = G + E
3
Q
If you had two cows with the same genetic worth - Why might they different for milk yield?
A
- farm (diet, management, veterinary care…)
- age
- time of year
- breed ( though most selection is done within breeds)
4
Q
In order to accurately estimate the genetic merit of animals what should we do?
A
- we should compare them under the same environment or adjust for known environmental factors via statistical modelling
5
Q
How is traditional selection done?
A
- record performance and use pedigree information to derive breeding values
- assigning numbers to animals for genetic traits
- breed the best animals overtime
6
Q
What is genomic selection?
A
- make selections based in the genomewide profiles of the animals tested
- can use a combination of traditional and genomic
7
Q
What is the breeding value (BV)?
A
- the animals value as a parent
- the sum of all the genes affecting the traits we want to select
8
Q
How do we work out predicted transmitting ability (PTA)?
A
= 1/2 of the EBV
9
Q
What is GEBV or gEBV?
A
- genomic EBV
10
Q
What is heritability (H2)?
A
- the proportion of the trait that is genetic
- usually given as a value from zero = low to 1 = high
- higher heritability is better
11
Q
What heritability score is ideal and up?
A
- want 0.2 (20%) or higher
12
Q
What are the different ways we can estimate the BV (breeding value)?
A
- progeny test
- performance test
- pedigree
13
Q
What is the most accurate way to estimate breeding value?
A
- the progeny test
14
Q
What is the progeny test?
A
- taking a number of sires and mate to random females (average to population) and compare mean performance of progeny from each sire
15
Q
What does the progeny test allow for?
A
- measures the breeding value directly and provides a definition of breeding value
16
Q
What is breeding value strictly related to?
A
- related to superiority (or inferiority) with respect to the population mean
17
Q
What is transmitting ability (TA)?
A
- value of the genes that, on average, are passed on
18
Q
What is BV related to in terms of TA?
A
- BV = 2 x TA
19
Q
What can we predict if we know the value of the animals genes?
A
- we can predict that on average, it passes genes to its offspring worth half that value
- because it passes on half its genes
20
Q
If we know the BV’s or TA of the parents what can we predict for the progeny?
A
- we can predict the BV of their progeny
21
Q
What are the units of BV?
A
- kg
- litres
- seconds
22
Q
What is a performance test?
A
- measure individuals performance relative to the performance of its contemporaries
23
Q
What should be considered in a performance test?
A
- same environmental opportunity
- assume that better performance = better genes (on average)
- avoid preferential treatment
24
Q
What equation can be used for BV in performance tests?
A
- BV = h2 x (individual performance - population mean)
25
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
26
How would you predict progeny BV?
- 0.5 BV of sire and 0.5 BV of dam
= progeny BV
27
Under what conditions would you use the performance test?
- performance measure on individuals directly
- heritability is moderate to high
28
Under what conditions would you use the progeny test?
- traits cant be measured directly (sex limited, post mortem traits)
- heritability is low
29
What would need to be considered before using a progeny test?
- cost
- generation intervals
- gain per year
30
What is the difference between BV in progeny tests vs performance tests?
- progeny test measures BV *directly*
- performance test *predicts* BV
31
A good performance test ranks animals how?
- in the same way as a progeny test
32
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
33
What does a pedigree evaluation use?
- list of ancestors and relatives
- use performance records of relatives compared to their contemporaries
34
What test is a from of pedigree evaluation?
- progeny test
35
What do they say:
1. A pedigree test tells you
2. A performance test tells you
3. A progeny test tells you
1. what to hope for
2. predict what you might get
3. what you have
36
What combination greatly improves the prediction of the outcome of mating?
- a combination of pedigree and EBV's of animals in that pedigree
37
What test would you use on young animals?
- performance test
38
What tests would you use on breeding stock?
- performance and progeny test
39
What would you use for a pedigree?
- information from relatives
40
What does BLUP stand for?
- Best Linear Unbiased Prediction
41
What does BLUP use?
- statistical estimation of BVs
- uses all information from relatives
- correction for environmental factors
42
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
43
What do breeding schemes allow for?
- allows farmers to compare herd to national trend
- schemes like AHDB
44
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
45
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
46
What are environmental correlations?
- common environmental effects cause correlation between two traits
47
What is genetic correlation caused by?
- pleiotropy = one gene that controls multiple traits of same set of gene results a set of traits
48
What can result from genetic selection?
1. indirect selection an indicator of the thing we want to improve
2. genetic antagonism
3. selection for more than one trait at a time
49
The selection index is the most effective method of selecting for what?
- for selecting for more than one trait at a time
50
What should a selection index include?
- should include all traits of economic importance of breeder
- weighted according to economic value
51
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
52
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
53
How do you work out a predicted response in genome selection?
= selection intensity (heritability of trait)
54
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
55
What is genomic selection now widely used in?
- range of animal and plant breeding programmes and for multi-trait improvement
56
What is genetic selection using SNP markers used for in companion animals?
- to eliminate or select for mainly mendelian traits
57
What are examples of mendelian diseases?
- myotonia
- Duchenne muscular dystrophy
58
What are examples of mendelian traits?
- coat colour
- hair length
- dwarfism
