Final - Lecture 5 Flashcards
What is key to calculating EBVs
The contemporary group
Deviation
direction in which we want to change the phenotype
EBV calculation that doesn’t need a group that has grown up in the same environment?
Height in miniature donkeys - not fully grown until 3 years
Repeatability
likelihood of an individual repeating a phenotype (e.g. racing horses - how likely that horse of running a similar race, of similar distance is in a similar time)
Heritability
proportion of phenotype passed on through generations
Accuracy is referred to as
Risk
0-0.99
Why is heritability divided by 2?
Only half genome from either parent
Who determines relative emphasis?
breeder
Where does phenotypic variation come from?
- scientific literature
- calculated from sample
What does calculating EBVs for a generation lead to?
Consistency
- breeding program will move steadily in wanted direction (maintaining productivity)
QTL detection steps
- find a marker or many markers
- genotype a “population” for the marker(s)
- use statistics to associate marker genotypes with differences in phenotypes
- test on another population id possible
What is required in order to generate genotypes using molecular genetic markers?
polymorphisms within region of the genome that is of interest
What is involved in individual locus genotyping?
M and m - marker loci
Q and q - QTL (known)
What can be used for QTL detection?
Linkage
- disequilibrium = marker association maintained
If QTL and marker are linked, comparing MM and mm is equivalent to comparing QQ and qq
Are results accurate if marker is far from QTL?
No
When will the marker be close to the QTL in dog breeds?
If the the marker is consistent across every single breed
- linkage phase is reliable
What affects recombination rate?
distance between the loci
When do we want to use marker assisted selection?
- traits with low heritability
- sex limited traits (e.g. milking in bulls)
- traits that require sacrificing animal (e.g. use of carcass)
- traits expressed later in life (e.g. late onset of disease, PRD)
Why do we want to use marker assisted selection?
Increase genetic progress
- intensity, accuracy, variation, time
How well does marker assisted selection work?
- results vary
- can increase efficiency and reduce cost for same response
- planning horizon matters
Mating scheme strategies
- maximum progress (high heritability traits, elect for best phenotypes)
- avoid inbreeding (pedigrees)
- minimum progress
- move ahead and fix mistakes (move breed forward in some areas (skill), but correct for bad traits)
High heritability traits
conformation
Low heritability traits
reproduction, health, temperament
Positive assortative mating
mating best to best
e. g. racing speed - best EBV = positive
e. g. racing time - best EBV = negative (lowest racing time)
Best EBV
most appropriate EBV for goal of trait
Corrective mating
selecting for some characteristics to move forward, but correcting flaws
- +ve to +ve and then +ve to -ve to correct
- typically female population is corrected by choice of males
Negative assortative mating
Mating the best to worst
- eliminates tails and brings everything to the middle of graph
Random mating
assigning mated as random (typically does’t avoid inbreeding)
Genetic conservation
random mating with regard to phenotype (don’t keep track)
Rotational mating
mate multiple sires to avoid inbreeding
Line breeding and ling crossing
mate best to best within line
-increase inbreeding that exploit to generate some heterosis
E.g. thoroughbred breeding
Backcrossing (grading up)
mate back to a specific breed to increase % of pure bred
- avoid inbreeding by importing from unrelated individuals
E.g. beef cow breeding
What must the mating scheme be modified for?
- single vs. multi birth species
- maternal input
- breeding interval
mating scheme for single vs. multi birth species?
Multiple males to breed one female
mating scheme when considering maternal input?
modify generation interval
Breeding interval is shorter in?
litter bearing species
Find a marker or many markers
candiate gene approach (look in area of a known gene) or anonymous markers (SNP “chip)
Genotype “population” for marker(s)
Generate large number of parent-offspring sets with phenotypes
Use recombination rate to map genotypes
Determine c from parent-offspring genotypes and calculate distances for all possible marker pairs
Use statistics to associate marker genotypes with differences in the phenotypes
See if average phenotype of MM individuals minus average phenotype of mm individuals is statistically significantly different from zero
Test on another population (if possible)
Repeat process on another, unrelated group of individuals to see if linkage phase is the same
Steps to lead to maximum longterm success as a QTL?
- A QTL needs to have a marker with a stable linkage phase in the population
- having a 2nd marker locus class by can help to monitor crossovers between markers which may affect QTL linkage phase
- Marker genotyping needs to be done in such a way that there is a negative and positive control such that genotyping result cannot be mis-read
- Quality assurance program to make sure the same received is the one that a genotype is generated for
- statistical analysis reported for QTL to make sure what is being calculated and reported is significantly correct
- see if marker(s) was/were tested on another population
