Animal Genetics Exam 3

Why do we care about animals genetic relationships? 4 things

1. Will help to predict breeding values of selection candidates (young animals) by utilizing performance of its relatives to improve accuracy of Estimated breeding values (2 Predicted transmitted Ability (PTA) and 2 expected progeny difference)

Best linear unbiased prediction (BLUP) method

2. To avoid the effect of high level of inbreeding

3. To explore heterosis, or hybrid vigor non-additive effects due to combo of gene alleles and genes

4. To optimize genetic diversity in small population

Polygenic effect/animals Effect: created using?

Factors affecting milk yield + a(animals effect) + error + micro = phenotypes

Animals effect created using genetic relationship model - form EBVs and additive genetic variance (o²A)

EBVs are predictions

Interbreeding: what is it? Consequences?

o The mating of relatives

o Matings individuals that are closer in genetic relationship than the average of relationships of the population

 Consequences

• Increases homozygosity,

• Increases expression of deleterious recessive alleles

• Inbreeding depression (i.e low performance)

Inbreeding coefficient (Fx): Measure of? Defined as? Range? F =?

• A measure of the level of inbreeding of an individual (e.g. x)

 Defined as the probability that both gene alleles (or a pair alleles of a gene) in an individual are identical by descent (IBD).

OR the probable proportion of an individual’s loci containing alleles that are identical by descent.

 Ranges from 0 (i.e. no inbreeding) to 1 (i.e. maximally inbred).

 F stands for fixation index, because of the increase in homozygosity, or fixing

Wright’s coefficient of relationship (Rxy): measure of? Defined as? Range? What does it mean if R=r

 a measure of the pedigree relationship

 Defined as the proportion of one individual’s Alleles (genes) that are identical by descent to Alleles(genes) of a second individual.

OR

It is the correlation between breeding values of two individuals due to pedigree relationship alone.

 Ranges from 0 (completely unrelated) to 1 (identical twin)

If R=r then there is noo genetic relationship and individual is not inbred

True or False: Wright coefficient is more accurate than numerator because it accounts for breeding values

True

3 methods of calculating interbreeding and relationship coefficients?

1) The Path Method (not much used)

2) The Tabular Method

3) Genomic relationship Matrix based on

DNA markers

The Tabular Method to calculate the numerator relationship between individuals X and Y Rules to calculate numerator relationship (1-4_

Steps: for calculating Animal relationship coefficients (1-8)

1. Order all animals by birth date, earliest to latest. Make sure no offspring comes before its parents.

2. Create a square table listing all animals in order across the top and again down the side

3. Write the parents of each animal above it at the top of the table. If the parent is unknown, write a blank ( _ ).

4. Proceed from left to right and fill in the first row of numerator relationships.

5. Copy the values in the first row of the table to the first column of the table

6. Fill in the next row of numerator relationships. Use rule 1 for off-diagonal elements and rules 2 and 3 for diagonal elements.

7. Copy the values from this row into the corresponding column

8. Repeat steps 6 and 7 until the table is complete

Tabular Method: Sort left to right by? fA=?, to calculate fA we must have __ and know ___

Sort from oldest to youngest, calculate r using youngest two parents

fA = 1/2(r two parents)

Conditions: must have 2 known parents and have genetic relationship between the parents

calculate Animal relationship coefficients Using Tabular Method

What is the level of inbreeding for B?

rrB - 1 = 0

What is the inbreeding coefficient and wrights coefficient of relationship

Calculate the inbreeding coefficient for A &C and wrights coeefeicnt of relationship between X and D

Genomic correlation based on DNA markers

A DNA genotype similarity matrix between animals can be used to measure

_______

A DNA genotype similarity matrix between animals can be used to measure

animals’ relationships matrix, (i.e. genomic relationship matrix)

What is this method of calculating genomic relationship matrix called?

GRM = ZZ’/ 2sum pi (1-pi)

Use __ to Calcutta genomic relationship matrix

VanRaden, genotypes

Wright coefficient of genetic relationship is more accurate than genetic relationship, true or flase and why

False, because genetic relationship accounts for interbreeding, lack errors that are found in pedgree and accounts for mendicant sampling

Which is more accurate the genomic relationship matrix or Wrights coefficient of relationship, why?

The genomic relationship matrix should be more accurate than Wright’s

coefficient of relationships as it captures the actual genotypes (Mendelian

sampling) while Wright’s coefficients is a pedigree average.

Genomics relationship matrix formula, what is Mendelian sampling?

• EBVoffspring = ½ EBV sire + ½ EBV dam + Mendelian Sampling

• Mendelian Sampling : the chance factor in distributing half the genetic material from each

parent to their offspring

Reasons to inbred

 To increase uniformity

 To allow for the creation of pure lines to increase hybrid vigor

 To identify deleterious recessive alleles and genotypes in a population for selection (i.e. test mating)

• Note: Relationship matrix can help designing of inbreeding

Does interbreeding cause immediate or longer term hybrid vigor

Long term

Consequences of interbreeding

Interbreeding depression (low performance) in diary cattle and low performance in sheep

Linebreeding

 The mating of individuals within a particular line;

 A mating system designed to maintain a substantial degree of relationship to a

highly regarded ancestor or group of ancestors without causing high levels of inbreeding.

 A slow form of inbreeding

 Planned inbreeding often breeding to one ‘line’

Line-breeding is a controlled mating system of inbreeding? Group of answer choices? True False

True

Outbreeding vs Outcrossing vs Crossbreeding vs linecrossing

Outbreeding:

The mating of unrelated individuals

• Matings farther away (i.e. lower than) than the average of the population

Outcrossing:

Mating unrelated animals within the same breed

Crossbreeding:

Crossing between two or more breeds

Linecrossing

• Crossing two inbred lines

Outbreeding: what are the consequences of outbreeding? What can help design outbreeding?

– Increases heterozygosity

– Masks the expression of deleterious recessive alleles with major effects

– Results in a gain in gene combination value (i.e. Hybrid vigor or Heterosis)

• when the performance of the offspring is greater than the average of the performance of the parents.

• Note: Relationship matrix can help designing of outbreeding

Three reasons of outbreeding?

1) To avoid the negative effects of inbreeding:

o Lethal or harmful recessive disorders

o Inbreeding depression

o Loss of genetic variance

2) To add hybrid vigor or Heterosis

– Improve Fertility, disease resistance and longevity by 10 – 30%

– % Heterosis = [(crossbred average - straightbred average) / straightbred average] x 100

• Example: Let 525 pounds be the average weaning weight of the F1 calves, 450 be the

average weaning weight of the Breed A population, and 550 be the average weaning

weight of the sire S population

• The pounds of heterosis would be: Pounds of heterosis = 525 - [(450 + 550) / 2] = 25

pounds

• The percent of heterosis would be: % heterosis = 25 / [(450 + 550) / 2] * 100 = 5%

3) To take advantage of breed complementarity

Breed Complementarity

Repeatability: formula? Ability? Correlation? Chance of? Proportion? Calculate using what models?

Repeatability

 Is the ability of the animal to repeat its records

 The correlation between animal’s records

 Repeatability is the chance of getting the same phenotype again from the same individual.

 The proportion of the phenotypic variance that is due to permanent effects unique to the individuals.

 we can calculate repeatability using ANOVA & linear models

Predicting Genetic Improvement Rate or Response to Selection Rate: Selection? Genetic or Genomic improvement using Selection

Selection: Process of identifying superior individuals to serve as parents

for the next generation.

Genetic or Genomic improvement using Selection

• Requirement for genetic improvement

program :

 The most important point is having “breeding goals

or objectives”

 Trait/s which have heritable genetic basis

 Genetic variation within the population of interest

Responses to Selection: Selection differential(S)? Response to selection (R)? Example 1:

• Average daily gain (ADG, kg/day) heritability (h²) = 0.36

• ADG for Charolais breed in is 1.66 kg/day

• Average of selected parents = 1.9 kg/day

Example 2:

• Average daily gain (ADG, kg/day) heritability (h²) = 0.36

• ADG for Charolais breed in is 1.66 kg/day

• Average of selected parents = 2.5 kg/day

Selection differential (S) = X selected parents - X population

S= average of selected parents deviated from the population mean

Response to selection (R) = X offspring - X population

R = deviation of progeny from original population average

= Selection differential (S) * Heritability (h²)

Example 1:

Selection differential, S = 1.9 – 1.66 = 0.24 kg/day

Expected genetic progress in next generation,

R = Sh²= (0.24) X (0.36) =0.0864 0.086 kg/day

Note:

 For constant h 2, R depends on S

 R & S units are the same as the phenotype

Example 2:

Selection differential, S = 2.5 – 1.66 = 0.84 kg/day

Expected genetic progress in next generation,

R = Sh 2 = (0.84) X (0.36) = 0.3024 kg/day

In Practice, How can we increase R?

Response to selection (R) = Sh²

⇒ How to increase S

o Select fewer individuals => watch out for

inbreeding

⇒ How to increase h 2

o Measure phenotype more precisely,

o Reduce environmental variances

o Use genomics information (e.g. genotypes

Rate of genetic change: How do we measure the effectiveness of selection? The rate of genetic change or the key equation?

What do the following symbol represent:

Delta G? BV? r? i? oBV? L? iop? oA?

(Delta 𝐺): the rate of change in the mean breeding value

(𝐵V) of a population caused by selection

 (r): Accuracy of selection - how well we rank animals?

 (i): Selection intensity - how picky?

 (𝜎BV): Standard deviation of genetic variation → genetic differences

 (L): Generation interval

iop: Standards deviation in phenotypic genetic variance

oA: Standard deviation of the additive genetic variance

End box: The selection intensity is not the proportion of the selective animals but it depends on the proportion of the selected animals as a parent

Genetic progress = __1__ x __2___ x __3___

1: how picky

2: how well we rank animals

3: natural genetic differences

The selection intensity is not the proportion of the selective animals but it depends on the proportion of the selected animals as a parent