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MBG 4020 > Final - Lecture 5 > Flashcards

Final - Lecture 5 Flashcards

1
Q

What is key to calculating EBVs

A

The contemporary group

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2
Q

Deviation

A

direction in which we want to change the phenotype

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3
Q

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

A

Height in miniature donkeys - not fully grown until 3 years

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4
Q

Repeatability

A

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)

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5
Q

Heritability

A

proportion of phenotype passed on through generations

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6
Q

Accuracy is referred to as

A

Risk

0-0.99

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7
Q

Why is heritability divided by 2?

A

Only half genome from either parent

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8
Q

Who determines relative emphasis?

A

breeder

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9
Q

Where does phenotypic variation come from?

A
  • scientific literature

- calculated from sample

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10
Q

What does calculating EBVs for a generation lead to?

A

Consistency

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

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11
Q

QTL detection steps

A
  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
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12
Q

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

A

polymorphisms within region of the genome that is of interest

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13
Q

What is involved in individual locus genotyping?

A

M and m - marker loci

Q and q - QTL (known)

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14
Q

What can be used for QTL detection?

A

Linkage
- disequilibrium = marker association maintained

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

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15
Q

Are results accurate if marker is far from QTL?

A

No

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16
Q

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

A

If the the marker is consistent across every single breed

- linkage phase is reliable

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17
Q

What affects recombination rate?

A

distance between the loci

18
Q

When do we want to use marker assisted selection?

A
  • 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)
19
Q

Why do we want to use marker assisted selection?

A

Increase genetic progress

- intensity, accuracy, variation, time

20
Q

How well does marker assisted selection work?

A
  • results vary
  • can increase efficiency and reduce cost for same response
  • planning horizon matters
21
Q

Mating scheme strategies

A
  • 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)
22
Q

High heritability traits

A

conformation

23
Q

Low heritability traits

A

reproduction, health, temperament

24
Q

Positive assortative mating

A

mating best to best

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

25
Q

Best EBV

A

most appropriate EBV for goal of trait

26
Q

Corrective mating

A

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
27
Q

Negative assortative mating

A

Mating the best to worst

- eliminates tails and brings everything to the middle of graph

28
Q

Random mating

A

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

29
Q

Genetic conservation

A

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

30
Q

Rotational mating

A

mate multiple sires to avoid inbreeding

31
Q

Line breeding and ling crossing

A

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

32
Q

Backcrossing (grading up)

A

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

33
Q

What must the mating scheme be modified for?

A
  • single vs. multi birth species
  • maternal input
  • breeding interval
34
Q

mating scheme for single vs. multi birth species?

A

Multiple males to breed one female

35
Q

mating scheme when considering maternal input?

A

modify generation interval

36
Q

Breeding interval is shorter in?

A

litter bearing species

37
Q

Find a marker or many markers

A

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

38
Q

Genotype “population” for marker(s)

A

Generate large number of parent-offspring sets with phenotypes

39
Q

Use recombination rate to map genotypes

A

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

40
Q

Use statistics to associate marker genotypes with differences in the phenotypes

A

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

41
Q

Test on another population (if possible)

A

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

42
Q

Steps to lead to maximum longterm success as a QTL?

A
  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

MBG 4020 (9 decks)

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