Lecture 3 - Animal Breeding Flashcards by Aimee Supinski

What are polygenic traits?

Phenotypes that are influenced by multiple genes at once

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What are two other names for polygenic traits?

Complex traits or quantitative traits

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What is polygenic inheritance?

-Cumulative effect of two or more genes
-Multiple genes with codominant alleles. Allelic effects are additive

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What is an example of a human phenotype that is influenced by thousands of genes?

Height

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What is a continuous trait?

A trait that varies in severity in a continuous way. Usually has a mean represented at the peak of a bell curve

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What is a threshold trait?

A trait that is only expressed when it reaches a threshold value through the additive affects of alleles (ex. cancer)

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What is the formula for calculating phenotypic variance (Vp)?

Vp = genetic variance (Vg) + environmental variance (Ve)

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What is the formula for calculating heritability (h^2)?

h^2 = Vg/Vp

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What is heritability?

The proportion of phenotypic variance due to genetic effects. Specific to a population at a given time

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Why is heritability specific at a given time?

-Changes in environment
-Differences between allele frequencies in populations

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If the h^2 of human height is ~0.80, then what percent of variation is due to genetics?

80%

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What is the breeders equation?

R = h^2 x S, where R is the response to selection and S is the selection differential

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What is the breeders equation used for?

To predict evolution

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What does it mean if h^2 is zero?

There is no evolution or selection occurring

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What does a larger h^2 indicate?

That genetic and phenotypic gain (heritability) is occurring at a faster rate

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What is the response to selection (R)?

Change in population phenotypic mean in the next generation

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What is the selection differential (S)?

Difference between a populations mean phenotype and the mean phenotype of selected individuals

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What do you need to estimate h^2?

Phenotypic records for many individuals
Variation in relatedness

What is an animal model in pedigree-based relatedness?

A statistical approach which uses info from all pairwise relationships in a populations pedigree (ex. parent-offspring, full-sibs)

What should selection be based on?

Genetic merit and not phenotype

How can an animals breeding value be estimated?

By combining information about its own phenotype as well as the phenotypes of its relatives

What is EBV?

Estimated Breeding Value

How can EBV accuracy be improved?

Genotypes at some of the genes influencing the selected trait(s) are known (marker-assisted selection)

What is progeny testing?

Estimating breeding value of an animal based on the success of its offspring.

What are the downsides to progeny testing?

Takes a long time to test the progeny and a therefore a long time between selecting a sire and their offspring being born.

Quantitative trait locus (QTL)

A locus associated with variation in a quantitative trait.

Quantitative trait nucleotide (QTN)

A SNP responsible for variation in a quantitative trait

Genome-Wide Association Studies (GWAS)

GWAS tests many genetic variants across many genomes to find those associated with a specific trait or disease. The aim is to identify associations of genotypes with phenotypes by testing for differences in the allele frequency of genetic variants between individuals who are ancestrally similar but differ phenotypically.

Linkage disequilibrium (LD)

A non-random association of alleles at two or more loci on the same DNA strand (the amount that an allele of one genetic variant is inherited or correlated with an allele of a nearby genetic variant)

How does GWAS work?

1. Find SNPs in your population. 2. Obtain genotypes and phenotypes on a large number of individuals. 3. Identify loci showing strong statistical associations with phenotypes.

How do they determine which loci are associated with phenotypes in GWAS?

- Case controls (diseased vs. healthy) - Continuous traits - Extreme phenotypes

Manhattan plot

Dots above the threshold line are unlikely due to chance.

GWAS limitations

- Few regions reach statistical significance - False positives common --> replication/validation needed - Results often breed-specific - Significant associations rarely explain all of the heritability (known as the ‘missing heritability’ problem) --> most QTL have very small effects that do not reach statistical significance. - Very large sample sizes needed to detect loci having small effects (>50,000 individuals common in human studies) - Follow-up (and laborious) research typically needed to identify and confirm causative mutations

Marker-assisted selection can improve ____ by using ____ information

Marker-assisted selection can improve traditional selective breeding by using QTL/QTN information

Marker-assisted selection

Using known genotypes at genes influencing selected trait(s) to guide breeding

GEBV pros/cons

- Lower EBV accuracy than traditional progeny testing - Much cheaper and faster than progeny testing

Genomic EBV (GEBV)

GEBV predicts the breeding value of a newborn by looking at all SNPs and choosing the best newborns based on the GEBV (no phenotype information or progeny testing)

Does statistical significance matter for GEBV?

No, all SNPs are looked at regardless of whether they are statistically significant or not

What is the accuracy of GEBV?

75-85%

What is the accuracy of traditional progeny testing?

99%

What is the generation interval of progeny testing?

63 months (5y 3mo)

What is the generation interval of genomic selection?

21 months (1yr 9mo)