Genetics Flashcards
The skills of animal breeding lie in:
Knowing what changes will be worthwhile, correctly and efficiently identifying the genetically superior animals, identifying the most genetically and economically efficient way of mating the selected animals
One of the basic requirements for effective selection program?
There must be genetic differences between animals in order to make genetic improvement. Genetic Variation.
What is genetic variation directly linked to?
Heritability. If there is high heritability (>25%)- then selection will be effective in improving the genetic composion, moderate heritable 10-25%- possible but slower and harder to achieve, low heritability < 10%- difficult since there are only small genetic differences between animals
Where there are unfavorable correlated responses (e.g. productivity and fertility), how do you approach this?
Develop a selection index that optimizes overall response in the two or more trains of interest OR you can develop separate lines that excel in one or a few compatible traits… For example, develop terminal sire lines and maternal lines– terminal sire line in meat selected for larger size and good carcass attributes, while the maternal lines for reproductive rate and feed efficiency
What to account for to maximize efficiency:
cost of measurement of teach trait, number of animals to be measured, rate of dissemination of improved genes
What are estimated breeding values?
Phenotypic measurements. Estimationof breeding value based on an animal’s phenotype alone can be quire accurate for highly heritable traits. However, animals need to be compared across flocks and genetic and environmental influences need to be disentangled.
What is Best Linear Unbiased Prediction (BLUP)?
More sophisticated statistical model, BLUP uses all available information about an animal’s breeding value, including data on related animals
What are the two most important limiting factors in a breeding program?
Reproductive rate of breeding animals and uncertainty about their true genetic merit
What are common investments in breeding programs?
Trait measurement and genetic evaluation and to technology used to increase reproductive rates
Animal breeding in a nutshell
Where to go–> breeding objective–> how to get there (velocity)–> trait measurement (which traits, which animals, males v. females, progeny test), EBVs (phenotypes, pedigree, BLUP, genetic markers), reproductive technology–> Selection/ Culling/ Mating
What are the problems with British bulldog breeding?
Skull should be very large- larger the better- dystocia, fetopelvic disproportion
What are the problems with Dachshunds?
The whole trunk should be long; prolapsed intervertebral disc
What are the problems with miniature poodle?
“fine legs”– fractures
What are the problems with pugs breeding standards?
Eyes very large globular in shape- exopthalmus, keratitis
What are the important aims for a breeding objective?
Focused, quantified, timelined
What is a breeding objective?
Provides the direction for the whole program by defining the set of characters that we wish to improve by breeding. The more trains one attempts to improve, the less progress will be made in any single trait.
Response to selection- quantative genetics equation
R= (((im x rm) + (if x rf))/ (Lm+Lf))* SDG i= intensity r= accuracy genetic SD L= generation interval
For cattle and sheep, a well designed breeding program should deliver what percentage of improvement annually?
2% (22% over 10 years)
How are quantative trais determined?
Combined action of many alleles at many loci, most of which have a small effect. Minimum 30 genes for all traits.
Non-genetic factors equation?
P= G+ E P= phenotypic value- the performance of an individual in relation to a particular character G= genotypic value- the avg. performance of a particular genotype (determined at conception) E= Environmental deviation (either +ve or -ve)
What does inferior recessive alleles mean for future generations?
An animal may have fabulous genotypic value- but it may have many more inferior recessive alleles that may have no effect on itself but will affect a population of offspring
What is the genotypic value equation?
G= A+D+I A= breeding value (additive effect) D= dominance (+ ve or - ve) I= Epistasis (interaction between genes) D and I depend on the arrangement of genes within a genotype, breeding value does not.
Phenotypic value equation?
P= A+D+I+E
What are you trying to do when selecting animals for breeding?
Trying to increase the frequency of favourable genes
EBV?
Series of clues of the true breeding value- clues come from progeny testing or the animal’s own phenotypic performance or the performance of other relatives or genetic tests or preferably a combo of all available clues
How are EBVs expressed?
Deviations from the mean value of a reference population
How do you combine all these EBVs to pick the “best” animals?
Weighting each EBV by economic value and summing the lot up– Index selection (always more efficient than alternative methods of integrating the information)
What is an animal’s breeding value (A)?
Not the same as genotypic value. Breeding value is directly proportional to the number of favourable genes- genotypic value depends on the arrangement of those genes.
What is heratability (h^2)?
The proportion of the phenotypic variance attributable to variance in breeding balues. OR the proportion of phenotypic superiority (inferiority) of parents that is seen in their offspring).
What is the equation for heritability?
h^2= Va/Vp, Variance of breeding value/ variance of phenotypic value. h^2 must be between 0-1, if it is 0 then breeding value makes no contribution to Vp thus genetic progress is not possible in this trait.
If it is 1 then the observed variation in the trait would be due to variation in breeding values alone- no such case exists. (the higher, the more rapid the genetic progress possible)
What is a small heritability?
Less than 0.10 are small- consider non-genetic methods of improvement. Fertility and reproductive traits tend to have small h^2.
What is a large heritability?
More than 0.30 are large. Product quality traits tends to have a large h^2- fibre diameter, wool, protein, milk, marbling
What has moderate h^2 (0.2 approx)?
Growth, body weight
How is heritability measured?
By measuring the performance of many offspring of parents with known performance- deviation from mean performance is the measure
How is heritability estimated?
Using information from all forms of relationships- offspring, half-sibs, full-sibs. Sophisticated algorithm called REML is used for this purpose.
Predicting response to selection- aiming for largest possible response to selection program- what is genetic variance?
A measure of the variance in additive genetic values within the population of animals. Heritability is a normalized indicator of genetic variance. The greater the genetic variance, the greater the potential for improvement.
What populations will have less genetic variance?
Inbred populations, small populations, highly selected populations
What is accuracy?
Series of clues EBVs- because true acuracy is unknown (A)- ranked according to EBV- weighted- and then selected.
How do you improve accuracy?
Moving from visual to direct measurement, accounting for environmental factors, measuring correlated traits, repeat measurements, progeny testing, accounting for performance of other relatives, utilization of genomics….. if accuracy is poor, all EBVs will be close to zero.
What is G X E interactions?
When the genetic ranking of an individual is different in different environments. e.g. Dairy industry USA EBVs vs. Australian EBVs.
Disease, climate, and management variations may contribute to GxE interactions- adaptation of genotypes to particular conditions. Selection for performance is generally most effective if it takes place in an environment similar to that of the enterprise
What is meant by genetic correlation between traits?
Selection for one character almost always produces a change in another character. Some expected, some unexpected.
What is a phenotypic correlation?
The extent to which two traits are phenotypically related- phenotypic and genotypic correlation for the one set of traits can be very different. i.e. strong phenotypic correlation between bodyweight and fleeceweight but no genotypic correlation
PHENOTYPE INCLUDES GENES AND ENVIRONMENT
What is repeatability?
The correlation between any two measurements of the same character on the one individual. For example, repeatability of most production traits is quite high, if an animal has superior phenotypic value (milk yield for example) in its first measurement it is highly likely to be superior at later measurements- no need to measure again
What are some considerations of progeny testing?
Progeny testing a very large number of progeny is the most accurate method of estimating breeding values, but detrimental increase in generation interval often outweighs the accuracy benefit- resulting in a reduction in genetic response–> accurate EBVs should exist before widespread industry use of any sire/dam
What is pedigree selection?
Selection based only on performance of ancestors. Common in horses. Never as accurate as mass selection. Remote ancestors next to useless. Only sensible when selection has to be made before candidates performance can be measured.
What is genetic marker assisted selection?
Need numerous markers to improve accuracy of selection for any given trait- not one or two. Requires sacrifice of the animal. Full panel of markers for all important traits would potentially have very large impact by reducing generation interval (early, accurate selection)
How do we combine every bit of information we have to get the most accurate information?
BLUP
What is BLUP?
Best Linear Unbiased Prediction, sophisticated statistical model widely used that combine all available clues to obtain the most accurate EBV possible. Increasing accuracy gives more spread in EBVs- ranking of animals genetic merit will be improved. Also allows measurement of genetic progress over time- by monitoring progeny.
What is the range in average generation interval in sheep flocks?
Slow turnover flocks- ewes lamb for the first time as 3yo, sold as CFA as 7yo- rams 2-5 yo (avg. L= 4.11 years)
Rapid turnover flock- ewes lamb at 2yo- CFA(cast for age) as 5 yo- rams 2 & 3 yo only (avg. L= 2.97 years)
What is selection intensity?
A measure of the expected superiority, in standard deviations, of the selected animals. Varies inversely with the proportion of candidate animals that are selected for breeding. If 100% of animals are selected for breeding, there is zero selection intensity, as p (phenotype) increases, I (epistasis- interaction between genes) increases.
What are some influences on selection intensity?
Fecundity, fertility- more fecund- greater intensity possible. Most mammals- the rate and direction of genetic progress largely driven by male selection. Im»_space; If
What is the aim of MOET?
Improve female fecundity (actual reproductive rate of an animal) and thus selection intensity in females
Since Im»_space; If, what does this cause on commercial farms?
Breed female stock; buy males in
How does selection intensity change as proportion selected decreases?
Selection intensity increases
What are the two major problems with small population size?
Inbreeding and genetic drift
What is an effective population size?
Only those who contribute to the next generation genetically (not their actual census size). Ne
What is determined by the effective population size?
Determines the rate and impact of negative genetic processes
Why is Ne less than N?
Unequal sex ratio, population subdivision, non-random mating, other factors
What is Ne in a seal colony with 4 adult males and 100 breeding females?
(4 (4*100))/ (4+100)= 15.38
What does inbreeding result in?
Decreased performance (inbreeding depression)- possibly present as poor reproductive performance, Increased homozygosity (reduced heterozygosity) in the population- increase in incidence of recessive genetic disorders
How do you measure inbreeding?
Inbreeding coefficient needs to stay below 1%, preferably below 0.5% per annum. Generally for every 1% increase inbreeding coeffecient, 1% decrease in reproductive traits occurs. 1% per annum increase inbreeding coefficient can almost negate any genetic progress from selection.
What does the effective population size need to be in order to keep the inbreeding coefficient below 1%? How about 0.5%
50/L (L= avg. generation interval). 100/L to keep it below 0.5%
How many lethal recessive alleles does any normal animal carry?
About 20 lethal recessive alleles
