Final - Lecture 5

Question 1

What is key to calculating EBVs

Answer 1

The contemporary group

Question 2

Deviation

Answer 2

direction in which we want to change the phenotype

Question 3

EBV calculation that doesn’t need a group that has grown up in the same environment?

Answer 3

Height in miniature donkeys - not fully grown until 3 years

Question 4

Repeatability

Answer 4

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)

Question 5

Heritability

Answer 5

proportion of phenotype passed on through generations

Question 6

Accuracy is referred to as

Answer 6

Risk

0-0.99

Question 7

Why is heritability divided by 2?

Answer 7

Only half genome from either parent

Question 8

Who determines relative emphasis?

Answer 8

breeder

Question 9

Where does phenotypic variation come from?

Answer 9

• scientific literature

- calculated from sample

Question 10

What does calculating EBVs for a generation lead to?

Answer 10

Consistency

- breeding program will move steadily in wanted direction (maintaining productivity)

Question 11

QTL detection steps

Answer 11

1. find a marker or many markers
2. genotype a “population” for the marker(s)
3. use statistics to associate marker genotypes with differences in phenotypes
4. test on another population id possible

Question 12

What is required in order to generate genotypes using molecular genetic markers?

Answer 12

polymorphisms within region of the genome that is of interest

Question 13

What is involved in individual locus genotyping?

Answer 13

M and m - marker loci

Q and q - QTL (known)

Question 14

What can be used for QTL detection?

Answer 14

Linkage
- disequilibrium = marker association maintained

If QTL and marker are linked, comparing MM and mm is equivalent to comparing QQ and qq

Question 15

Are results accurate if marker is far from QTL?

Answer 15

No

Question 16

When will the marker be close to the QTL in dog breeds?

Answer 16

If the the marker is consistent across every single breed

- linkage phase is reliable

Question 17

What affects recombination rate?

Answer 17

distance between the loci

Question 18

When do we want to use marker assisted selection?

Answer 18

• 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)

Question 19

Why do we want to use marker assisted selection?

Answer 19

Increase genetic progress

- intensity, accuracy, variation, time

Question 20

How well does marker assisted selection work?

Answer 20

• results vary
• can increase efficiency and reduce cost for same response
• planning horizon matters

Question 21

Mating scheme strategies

Answer 21

• 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)

Question 22

High heritability traits

Answer 22

conformation

Question 23

Low heritability traits

Answer 23

reproduction, health, temperament

Question 24

Positive assortative mating

Answer 24

mating best to best

e. g. racing speed - best EBV = positive
e. g. racing time - best EBV = negative (lowest racing time)

Question 25

Best EBV

Answer 25

most appropriate EBV for goal of trait

Question 26

Corrective mating

Answer 26

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

Question 27

Negative assortative mating

Answer 27

Mating the best to worst | - eliminates tails and brings everything to the middle of graph

Question 28

Random mating

Answer 28

assigning mated as random (typically does't avoid inbreeding)

Question 29

Genetic conservation

Answer 29

random mating with regard to phenotype (don't keep track)

Question 30

Rotational mating

Answer 30

mate multiple sires to avoid inbreeding

Question 31

Line breeding and ling crossing

Answer 31

mate best to best within line -increase inbreeding that exploit to generate some heterosis E.g. thoroughbred breeding

Question 32

Backcrossing (grading up)

Answer 32

mate back to a specific breed to increase % of pure bred - avoid inbreeding by importing from unrelated individuals E.g. beef cow breeding

Question 33

What must the mating scheme be modified for?

Answer 33

- single vs. multi birth species - maternal input - breeding interval

Question 34

mating scheme for single vs. multi birth species?

Answer 34

Multiple males to breed one female

Question 35

mating scheme when considering maternal input?

Answer 35

modify generation interval

Question 36

Breeding interval is shorter in?

Answer 36

litter bearing species

Question 37

Find a marker or many markers

Answer 37

candiate gene approach (look in area of a known gene) or anonymous markers (SNP "chip)

Question 38

Genotype "population" for marker(s)

Answer 38

Generate large number of parent-offspring sets with phenotypes

Question 39

Use recombination rate to map genotypes

Answer 39

Determine c from parent-offspring genotypes and calculate distances for all possible marker pairs

Question 40

Use statistics to associate marker genotypes with differences in the phenotypes

Answer 40

See if average phenotype of MM individuals minus average phenotype of mm individuals is statistically significantly different from zero

Question 41

Test on another population (if possible)

Answer 41

Repeat process on another, unrelated group of individuals to see if linkage phase is the same

Question 42

Steps to lead to maximum longterm success as a QTL?

Answer 42

1. A QTL needs to have a marker with a stable linkage phase in the population 2. having a 2nd marker locus class by can help to monitor crossovers between markers which may affect QTL linkage phase 3. 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 4. Quality assurance program to make sure the same received is the one that a genotype is generated for 5. statistical analysis reported for QTL to make sure what is being calculated and reported is significantly correct 6. see if marker(s) was/were tested on another population