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Flashcards in AB&G - End-of-year Exam Revision Deck (56)
1

What is the equation for the annual response to selection?

R = phenotypic SD * selection intensity * heritability / generation interval

2

How would you calculate the correlated response on trait 2 by selecting on trait 1? How would you adapt that if you were asked to use DNA tests as the correlated trait (e.g. the DNA test accounts for 50% of the genetic variation)?

CR2,1 = genetic variation * selection intensity (trait 1) * phenotypic SD (trait 2) * sqrt(heritability of trait 1 * heritability of trait 2) / generation interval

Using DNA test:
- square root the genetic variation (sqrt(0.5))
- imagine a linear regression equation (r^2)
- r^2 is the correlation (the key is that its SQUARED)
- the h^2 (heritability) of a DNA test is 1

3

How do you calculate the generation interval?

Lf = (#1y.o females *1) + (#2y.o females*2) + (#3y.o females *3), etc / total number of females

Same for males

Average the two

4

What units is the generation interval in?

Years

5

What units is the response to selection in?

trait units /year

6

What is the equation for effective population size?

Ne = (4*s*d)/(s+d)

7

What is the equation for the change in inbreeding coefficient per generation?

Delta F = 1/(2*Ne)

8

How do you calculate selection intensity?

First calculate the proportion of progeny required as replacements (separately for male and female).

Find the corresponding selection intensity from the table.

Average the selection intensities

9

What are the 3 methods for multiple trait selection?

-----TANDEM SELECTION:
- selecting for one trait at a time, ignoring all others
- order the traits in terms of importance (value) and make selections based on the most important trait for a number of years
- Then the next important trait becomes the basis for selection, and so on.
> Advantages
- Easy
- Can make the maximum genetic improvement in 1 trait
> Disadvantages
- Can only focus on one trait at a time
- If traits are negatively correlated, can be taking 2 steps forward and one (or more) steps backward

-----INDEPENDENT CULLING
- pretty much happens in all breeding programs to some degree
- A proportion of animals are culled based on individual traits alone
> Advantages:
- Culling can follow the life cycle of the animal; e.g. culling at weaning, yearling, etc.
> Disadvantages:
- Its difficult to estimate the response to selection and how much pressure to put on each trait

-----INDEX SELECTION
- individuals are ranked based on numerous traits that are weighted on economic value
- selection is of those with the highest ranking
- Advantages
- captures the economic value of multiple traits, meaning animals can be selected based on their overall economic superiority
- Complicated

10

What is the difference between heritability and heterosis

-----HERITABILITY
- The proportion of phenotypic superiority of the parents that is seen in the progeny
- a function of additive genetic effects

h^2 = Va/Vp
= addative variance / phenotypic variance


-----HETEROSIS
- The increased performance of CROSSBRED progeny above the mean performance of the parents
- a function of non-additive genetic effects (i.e. dominance and epistasis)

= (crossbred mean performance - parent breed mean performance) / (parent breed mean performance) * 100

- crossbreds often don't out-perform parents on individual traits, but often do out-perform them on total productivity; e.g. Angus x Hereford, the progeny won't have better muscling than purebred Hereford
- Heterosis is reduced in subsequent generations (F2 = 25%:50%:25% heterosis)

11

Compare a single terminal cross and three-way cross

-----SINGLE TERMINAL CROSS
- e.g. (existing) purebred Jersey cows x Angus bull (terminal sire) ----> Market F1 progeny

> Advantage: individual heterosis completely utilised
> Disadvantage: no utilisation of maternal or paternal heterosis

- Best to use a female with superior material qualities and mate them to sires with superior growth and carcass qualities (complementarity)


-----THREE-WAY CROSS
- The same as the single terminal cross, but instead of the F1 progeny going to market, they're mated with another (the terminal) breed, then those progeny are marketed
e.g. existing purebred Jersey cow x Angus ----> F1 progeny x Wagyu bull -----> Market progeny

> Advantages:
- all individual heterosis utilised
- maternal heterosis from crossbred female utilised
- complementarity
> Disadvantages:
- having to maintain another (crossbred) herd
- purchasing female F1 replacements
- complex management

------FOUR-WAY CROSS
- Often occurs in the poultry industry

Purebred A x Purebred B -----> F1a
Purebred C x Purebred D -----> F1b
F1a x F1b -----> hybrid commercial production

> Pros:
- Utilises individual, maternal, and paternal heterosis
- Utilises complementarity
> Cons:
- Only useful in production systems that have a high reproductive rate (short generation interval) because of the high management costs (of keeping 4 flocks for 1 lot of progeny)

12

What is the equation for calculating the amount of retained heterosis in a rotational cross?

(2^n - 2)/(2^n - 1)
where n = # breeds

13

Explain the equations:

alpha = a + d * (q - p)
and
2/A = 2*p*q*omega^2*A

alpha = the average effect of allele substitution

a = the additive effect of each allele in the trait of interest

d = the dominance effect of each allele in the trait of interest

q = frequency of minor allele

p = frequency of major allele

omega^2(sub)A = the additive genetic variance due to a major gene

If the trait has been lost or fixed in the population, i.e. q and p are close to 1, there will be little-to-no phenotypic variation in the trait of interest due to additive or dominant genetic effects. Therefore, any variation would be due to epistatic or environment interactions. However, as p and q approach 0.5, phenotypic variation increases until p=q and variation is maximised. This allelic frequency yields the greatest proportion of heterozygotes, while still displaying homozygous individuals for both alleles.

14

How would you calculate the accuracy of a genomic test if you were given the amount of genetic variation it accounted for?

square root it

e.g. test acc. for 49% of variation
accuracy = sqrt(0.49)
= 0.7

15

What traits respond well to crossbreeding?

Lowly heritable traits
e.g. fitness type traits (e.g. reproductive rate)

16

What is the equation for calculating the amount of retained heterosis in a composite cross?

(n-1)/n
n = number of breeds

17

Describe a rotational crossbreeding system and why it might be better than a single crossing system

> Breed A males are mated to Breed B females
> Their progeny are mated to Breed B males
> Their progeny are mated to Breed A males
> Their progeny are mated to Breed B males, etc

After ~ 7 generations, the genetic composition reaches an equilibrium where the progeny of Breed A sires will be 2/3A, 1//3 B, and the progeny of Breed B sires will be 2/3B, 1/3A

The retained heterosis is 2/3 of individual and maternal

In contrast, single crossing systems utilise 100% of the individual heterosis, but none of the maternal heterosis, where a significant proportion of the potential gains lie.

18

ANIMAL GENETIC RESOURCES
Describe the desired genetic structure of small populations (5 features)

> Ne ≥ 50 per generation
> delta F Constant Ne (avoid bottleneck)
> Long generation interval (to minimize homozygosity/genetic drift
> Spatially separated (but genetically linked) populations
- decr. risk of being wiped out by disease, natural disaster, etc

19

ANIMAL GENETIC RESOURCES
Name the 5 "The big five" most important species in animal production and give their chromosome numbers

Pigs - 38
Sheep - 54
Cattle - 60
Goats - 60
Chickens - 78

20

ANIMAL GENETIC RESOURCES
Explain 'genetic bottleneck' and 'genetic meltdown'

-----GENETIC BOTTLENECK
- A temporal (or temporary) severe reduction in effective population size
- Even though population sizes can recover after genetic bottlenecks, the genetic variation remains the same for 100s or 1000s of years

-----GENETIC MELTDOWN
- The accumulation of deleterious mutations that result in the inability to reproduce and survive

21

ANIMAL GENETIC RESOURCES
Name 4 different ways of germplasm conservation

> in situ (where it developed)
> ex situ (in a different environment)
> in vivo (i.e. live animals)
> in vitro (i.e. frozen gametes, embryos, etc)

22

ANIMAL GENETIC RESOURCES
List the 4 objectives of the global strategy for Domestic Animal Diversity (DAD)

1. Document existing animal genetic resources
2. Develop and improve their use in agriculture
3. Maintain those not currently of interest
4. Facilitate access to important resources

How do you convince someone that 3 is worth doing when they don't benefit from it but it costs them money? Very difficult!

23

ANIMAL GENETIC RESOURCES
Describe the "Weitzman approach" to conservation of genetic resources (3 major points)

Used as a way to allocate conservation funds based on economic value
Goal is to preserve the maximum amount of diversity
>
>
>

24

ANIMAL GENETIC RESOURCES
Explain Agenda 21 and how it relates to biodiversity and genetics

Agenda for the 21st century

Committed 118 countries to conservation of biodiversity and the sustainable use of those genetic resources (animals, plants, wildlife, farm animals, etc)

Conservation of animal genetic resources for socio-cultural value, adaption, disease resistance, biotechnology, etc.

If we don't have the resources, we can't utilise them in the future!

25

ANIMAL GENETIC RESOURCES
What are the reasons for the loss of genetic resources

> Introduction of exotic germplasm
> Poor agricultural policies
> Restriction of development to a few breeds
> Changing market requirements
> Degradation of ecosystems
> Natural disasters
> Political unrest and instability

26

ANIMAL GENETIC RESOURCES
Define "extinct"

No longer possible to recreate the breed population.
Becomes absolute when breeding animals, gametes (sperm, eggs), embryos, and cultured cells are no longer available

27

ANIMAL GENETIC RESOURCES
Define "critical"

# dams ≤ 100 or
# sires ≤ 5

OR

Overall population size ≤ 120 AND DECREASING, and the percentage of females bred to males of the same breed is ≤ 80%

28

ANIMAL GENETIC RESOURCES
Define "endangered"

# dams between 100 and 1000, or
# sires between 5 and 20

OR

Overall population size is between 80 and 100 AND INCREASING, and the percentage of females bred to males of the same breed is ≥ 80%

OR

Overall population size is between 1000 and 1200 AND DECREASING, and the percentage of females bred to males of the same breed is ≤ 80%

29

ANIMAL GENETIC RESOURCES
What does it mean when an animal is "critical-maintained" or "endangered-maintained"?

There are active conservation programs in place or populations are maintained by commercial companies or research institutions

30

ANIMAL GENETIC RESOURCES
T/F: To recover a population, you want to select the best individuals to take the breed forward

FALSE.
When recovering a population, you want to maintain as much genetic diversity (alleles) as possible, so there should be NO selection.

31

ANIMAL GENETIC RESOURCES
What are the 3 phases for any viable captive population?

1. Founder phase
- completely unrelated individuals

2. Growth phase
- build population size up to capacity as quickly as possible
- breed equally from all founders

3. Capacity phase
- maintain population size
- equalise sex ratio
- equalise family sizes
- manage inbreeding
- optimise founder representation
- increase generation interval

32

NON-MENDELIAN INHERITANCE
T/F: Mitochondrial DNA comes from your mother

TRUE

33

NON-MENDELIAN INHERITANCE
Define epigenetics

Processes that are on top of/additional to Mendelian genetics that influence gene expression and therefore phenotype

"Any gene-regulating modification or activity that doesn't involve changes to DNA and that can persist through one or more generations"

34

NON-MENDELIAN INHERITANCE
Contrast and explain the standard features and properties of the genome and epigenome (5 features/properties). What is the most important difference?

-----GENOME
- The genetic code (G, A, T, C) that people inherit from their parents and are born with
- Heritable
- Form genotype
- Genetic mutation
- in the form of insertions, deletions, substitutions, etc
- SNP

-----EPIGENOME
- Epigenetic code (modified C's, histone modifications, DNA binding proteins)
- Transiently heritable (can be erased and put back on)
- Forms epigenotype
- Epimutation
- in the form of changes to DNA methylation, histone modification, etc
- MVP

> If the genome is the hardware, the epigenome is the software that tells the hardware how to run

35

NON-MENDELIAN INHERITANCE
Describe the epigenetic reprogramming cycle

TWO STAGES
1. Rapid demethylation of paternal DNA
2. Passive, slow demethylation of maternal DNA

REMEMBER THE DIAGRAM
- Fertilisation/zygote in the middle
1. Paternal genome is rapidly demethylated, maternal genome is passively and continuously demethylated as cells divide
2. Both are remethylated

36

NON-MENDELIAN INHERITANCE
Explain genomic imprinting

> Gene expression based on the parent-of-origin of the allele.
> reversible in the next generation
> e.g. if the allele inherited from the sire is imprinted, only the allele from the mother will be expressed (i.e. the sire's allele will be silenced)

> caused by epigenetic modifications during gametogenesis and early embryonic development

37

NON-MENDELIAN INHERITANCE
What are the functions of epigenetic modifications?

> Correct temporal and spatial gene expression
- same DNA in almost every cell of the body, yet completely different functionality
- functionality created by epigenetically-controlled gene expression

> Silencing of transposons (genes that can move around the genome - retroviruses)

> X-Chromosome inactivation

> Genomic imprinting

38

GENOMIC QUESTIONS
Define gene mapping and what the requirements for doing it are

> Finding the specific location of genes, markers, and traits within a genome of a sp.

Requirements:
- Chromosome is known
- Approx position on the chromosome is known
- Distance between gene and other loci on the chromosome is known
- Order of the gene is known with respect to other loci

39

GENOMIC QUESTIONS
What are 3 types of markers (DNA variants)?

> Sequence changes (e.g. SNPs)
> Insertions/deletions
> Repeat number changes

40

GENOMIC QUESTIONS
Define 'haplotypes'

A set of closely linked genetic loci that are present on the same chromosome and which tend to be inherited together

41

GENOMIC QUESTIONS
T/F: More likely to get recombination of genes that are found closely together

FALSE. More likely to find with genes that are far apart (but on the same chromosome)

42

GENOMIC QUESTIONS
T/F: 1 cM = 10% recombination

FALSE. 1 cM = 1% recombination
= 1 map unit
= 1,000,000 bases (1 Mbase)

43

GENOMIC QUESTIONS
If markers A and B are inherited together 90% of the time, what is the map distance between them?

10 cM

(not inherited 10% of the time)

44

GENOMIC QUESTIONS
What is the point (in map units) at which two genes are unlikely to be inherited together?

≥ 50 cM = too far to be inherited together

(recombination)

45

GENOMIC QUESTIONS
How can genes be mapped?

Linkage analysis

Genome Wide Association Scan (GWAS)

Physical mapping

Essentially, find a marker (DNA variant, e.g. SNP or STR) that the gene is inherited with to use as a landmark (linkage mapping)

46

GENOMIC QUESTIONS
Define 'quantitative trait loci'

The region of a genome controlling a trait (genetic loci within the region affect the trait)

47

GENOMIC QUESTIONS
Explain what GWAS refers to

GWAS = Genome Wide Association Scan

Based on determining whether two loci (2 markers, 2 genes, 1 marker and 1 gene, 1 marker and 1 trait, etc) are associated more frequently than is expected in a given population

Called 'genome wide' because loci (usually thousands of random SNP markers) are used from all over the genome

Requires lots of tests and a large number of individuals in the population to test

Assumes that the gene(s) controlling a trait is in a *region*

High accuracy

48

GENOMIC QUESTIONS
What is physical mapping?

Finding what chromosome a loci is on, and in what region

49

GENOMIC QUESTIONS
What is meant by a 'major gene'?

One that has a big affect on phenotype

50

GENOMIC QUESTIONS
How can you make a linkage map more accurate?

> Use more markers
> Use (genotype) more animals
= More data

51

GENOMIC QUESTIONS
Explain the steps in shotgun genome sequencing

1. Sequence DNA fragments from entire genome
2. Clone
3. Computer aligns sequences into contigs (continuous pieces)
4. Assembly of contigs into large segments (scaffolds)

Essentially, by making lots of clones of the DNA fragments it means you can overlap them with eachother to help determine where they're located

52

GENOMIC QUESTIONS
What is comparative mapping and when would you use it?

Using physical gene maps of other species (preferably related) as a reference for a species with limited data

> Need alignment of genetic linkage and physical gene maps within the reference species first

> used when species of interest has insufficient genome data on its own

> based on the principle that gene order, location, and sequence is evolutionarily conserved (unless there's a large scale chromosome rearrangement during speciation)

53

GENOMIC QUESTIONS
What is a candidate gene?

A gene (loci) that we think might be controlling a trait

54

GENOMIC QUESTIONS
What is a virtual genome?

For species that have some sequence mapped but does not cover the entire genome and may have a large number of scaffolds that aren't connected.

Can build a virtual genome to locate segments and genes by comparing to a good genome map of a closely related species.

55

GENOMIC QUESTIONS
What is a 'causative variant'?

The one producing the phenotype

56

GENOMIC QUESTIONS
What is the best way of verifying a DNA variant in a gene controls a trait?

Perform association studies that determine whether the trait always segregates with the DNA variant