6: Selection for Simply Inherited Traits

Question 1

Define simply-inherited vs polygenic traits and give e.g.

Answer 1

Simply: affected by one (or a few) genes, affected very little by environment, usually know genes/alleles involved
e.g. coat colour, horns

Poly: affected by many genes, affected by environment, might know a few of the genes/alleles
e.g. birth weight, litter size

Question 2

What is a recessive lethal condition

Answer 2

Two copies of a certain allele =death

Question 3

How could a trait come in both polygenic and simply-inherited varieties? E.g.?

Answer 3

Can be polygenic but with single genes that have large effects
e.g. height in cattle
e.g. muscle mass is polygenic but myostatin has large effect

Question 4

Qualitative vs quantitative? E.g.?

Answer 4

Quali: phenotypes chosen from few possible values / categories
e.g. coat colour

Quanti: phenotypes are scored numerically and are usually continuous
e.g. birth weight

Question 5

Polygenic traits are typically…

Answer 5

quantitative traits

Question 6

Example of a qualitative polygenic trait

Answer 6

Calving ease (assisted or unassisted)

Question 7

How do you go about selection for polygenic traits

Answer 7

1. infer the genetic merit of individuals for the trait based on phenotypes observed in the individual and/or relatives (calculate breeding values)
2. choose parents based on breeding values

Question 8

Why isn’t genotyping effective for polygenic traits

Answer 8

Usually poorly understood which genes affect the trait, and each has a small role, can’t just genotype a few loci to determine which animals carry desirable alleles

Question 9

What is breeding value

Answer 9

Value of an individual as a contributor of alleles to the next generation

Question 10

What is genotyping

Answer 10

determining which alleles are carried by an individual at one or more loci by examining the DNA in a biological sample

Question 11

How do we go about selection for simply-inherited traits

Answer 11

1. infer genotypes of selection candidates through phenotyping, genotyping or test crosses (test matings)
2. select animals based on those genotypes

Question 12

slide 8,9

Answer 12

look

Question 13

How effective is using phenotype for selection on traits with complete dominance

Answer 13

If desirable allele is recessive, we can impose strong selection using phenotype
If desirable allele is dominant, can only impose moderate selection bc of heterozygotes

Question 14

How effective is using phenotype for selection on traits with partial or no dominance

Answer 14

Very (each genotype has a unique phenotype)

Question 15

Example of selection based on phenotype

Answer 15

HYPP (hyperkalemic periodic paralysis) in horses (partial dominance): do not breed horses with twitching phenotype (H/H or n/H)

Question 16

Gaitedness in horses is controlled by which gene? How do we select for it

Answer 16

DMRT3
Phenotype hard to assess due to subtle effects on performance
Gene and alleles are known, so can genotype animals

Question 17

Blood disorder in Irish setters… How do we select against it

Answer 17

Canine leukocyte adhesion deficiency Type 1
Disorder is autosomal recessive, so disease absence can still be carriers
Genes and alleles are known, genotype dogs to select parents or make mating decisions

Question 18

Symptoms of CLAD Type 1

Answer 18

Abnormal blot clotting, recurrent infections, lameness

Question 19

How do we test mate (e.g.)

Answer 19

Wanna know if a black bull is BB or Bb, mate bull to red cow (bb) and if you see red calf you know its Bb
See only black calves, confidence in bull being BB increases

Question 20

How do you calculate ‘probability of detection’ (e.g. that the bull is BB)

Answer 20

1-0.5^n
n= number of test matings

Question 21

How are the genes behind simply-inherited traits identified

Answer 21

Genotype many individuals from each phenotypic group at numerous loci in the genome, compare genotypes (look for differences/similarities)

Verify through additional experiments

Question 22

Seven steps of genotyping

Answer 22

Decide on tests-> find lab->collect samples->(extract DNA->run genotyping assay-> report results)->make selection decisions

( ) lab

Question 23

What is the VGL

Answer 23

Veterinary Genetics Laboratory at University of California Davis

Offers tests for simply-inherited traits in variety of species

Question 24

In TaqMan SNP genotyping assay, how many probes? Bound by what? What do they do?

Answer 24

Two probes, one for each allele of target gene
- bound by diff fluorescent molecules (VIC or FAM)
- Quencher attached
- Probe binds locus with matching allele
- Forward primer anneals, DNA polymerase extends it and cleaves the probe when it reaches it, releasing fluorescent molecule
- fluorescent model drifts away from quencher, and emits detectable light

Question 25

How does the intensity of selection influence effectiveness

Answer 25

More intense selection leads to faster progress (e.g. no bb animals breed instead of 50% breed)

Question 26

Slides 29-32

Answer 26

Intensity of selection

Question 27

Why is it difficult to eradicate an unfavorable recessive allele

Answer 27

Can avoid using the recessive phenotypes in breeding (e.g. bb) but there will still be many heterozygotes (Bb) who are passing down their b’s

Question 28

Why not genotype all selection candidates to identify carriers? (4)

Answer 28

• costs (large populations)
• valuable animal may lose value if identified as carrier
• different levels of genomic technologies in dispersed populations (e.g. many breeders control small # dogs)
• genes involved may still not be known