3.

Aids to selection

Performance testing/ mass selection /individual

performance, Pedigree selection, family selection,
progeny testing
 Aids to selection
• Individual or mass selection/performance testing
• This is selection of an animal on the basis of his/her own
phenotype for a particular trait or traits.
• It is useful for traits of high heritability.
• All the animals in the population are measured for the trait.
 Individual or mass selection/performance testing
• The phenotypic merit of the individual for important economic
traits is determined by comparing the average of all individuals
within the population from which it is to be selected.
• For this to be effective there should be a controlled
environment, with other animals of nearly the same age and at
the same time.
• It is referred to as contemporary comparison.
 Individual or mass selection/performance testing
• Accurate records are required.
• Individual animals’ records will be of no value unless it shows
how the animals rank relative to other animals in the
population.
 Individual or mass selection/performance testing
• The estimated breeding value (EBV) of the individual is the
estimated genetic superiority of the individual over the
average of the group from which it was selected.
 Individual or mass selection/performance testing
• This performance testing is simple to apply and also there is no
need for information about the relatives to rank the animals.
• It also permits the evaluation of the animals at a much earlier
age compared to progeny testing for example.
• This means it reduces the generation interval.
• It also allows much greater selection intensity.
 Individual or mass selection/performance testing
• However, it also has its disadvantages.
• You cannot use it for sex-limited traits like milk yield in dairy
cattle.
• It is unsuitable for traits, which are not measurable in the live
animal or expressed late in life, like carcass traits and those
traits, which have low heritability.
 Pedigree selection
• The pedigree of an animal is the record of its ancestors related to it
genetically through its parents.
• Pedigree selection is based on fact that, the individual animal gets half
of its genes from each parent.
• Thus, the regression of an animal’s breeding value on the parents’
breeding value is half times the heritability.
• On grandparents it will be a quarter times the heritability.
• This means that, the ancestors that are more closely related to the
animal like the parents and grandparents should receive more
emphasis than others.
 Pedigree selection
• If the heritability is low, the more remote ancestors should be
emphasised.
• However, if the heritability is high then including them will
provide no new information.
• This is done by calculating the BV of the animal as shown:
 Pedigree selection
• Pedigree selection has the advantages that it is cheap to use.
• It can be used for traits that are expressed in one sex (sex-
limited) such as milk yield and litter size.
• Pedigree selection can be used to select animals before they can
express the trait(s).
• It is used to assess for genetic abnormalities and those traits that
are expressed late in life like carcass traits.
• Calculations show that genetic gain is higher per unit time when
using pedigree selection.
 Pedigree selection
• The disadvantages of the pedigree selection are that there has
been undue emphasis on ancestors particularly remote
ancestors and unwaranted favouritism towards the progeny of
certain presumed superior individuals.
• The performance records of the ancestors compared to their
contemporaries are lacking.
• The other disadvantage is that it provides no basis of selection
among individuals that are descendants of the same ancestors.
 Family selection
• An animal has direct relatives and collateral relatives.
• Direct relatives are the ancestors
• Whilst collateral relatives are those not directly related to that
animal.
• The collateral relatives include the animal’s brothers, sisters,
cousins, aunts and uncles.
 Family selection
• If the families are ranked with all members of the better
families selected and all members of the poorer families
rejected the system is called between family selection.
• If better individuals within each family are selected then we
have within family selection.
 Progeny testing
• When the selection is based on the information of the parent-
offspring, it is called progeny testing.
• In progeny testing the breeder decides to choose or cull a sire
or dam based on the average merit of their offspring as
compared to the average merit of the offspring of
contemporary sires or dams or reference sires.
 Progeny testing
• It is based on the principle that the parent gives a random half
sample of its genes to each offspring.
• Thus, the mean value of the progeny will give a good estimate
of the genotype of the parents.
• This is usually used to measure the sire’s estimated breeding
value since the sires can leave a large number of offspring
compared to the dams.
 Progeny Testing
• You can also mate a sire to a large number of females at a
given period, which is not possible for the dams.
• In a progeny testing, you mate each sire under test to a
random sample of females.
• Then you measure the progeny performance.
• You then select the sires on the basis of the progeny mean.
 Progeny Testing
• The selected sires are then mated with the best dams to
produce a second batch of parents.
• Then you do the above steps on the second batch.
• Sometime ago the dam’s contribution was taken to be the
same, now with the availability of computers this is no longer
the case.
 Progeny testing
• In running a progeny test you should ensure that each sire
produces a large number of progeny because the larger the
number the more accurate the results.
• Each sire should have at least 20 progeny.
• No selection among the progeny, each progeny of each sire
should be exposed to similar environments or each sire must
have progeny in each and every environment.
 Progeny testing
• The results of a progeny test are expressed in what is known as
the expected progeny difference (EPD) or simply progeny
difference (PD).
• The expected progeny difference is an estimate of how future
progeny of a sire are expected to perform relative to the
progeny of the average sire included when mated to
comparable dams and the progeny treated alike.
 Progeny testing
• Expected progeny difference estimates how future progeny of
an animal will compare with the progeny of other animals
within the breed.
• The expected progeny difference is expressed in the units of
the trait.
• The EPDs are comparable across herds and generations but
they cannot be used across breeds.
 Progeny testing
• Compared to all the other aids to selection progeny testing is
most accurate and powerful.
• It can be used for traits that are sex limited such as litter size and
milk yield.
• You can also use it for traits that are expressed late in life like
lean meat percentage in pigs.
• The major drawback of progeny testing is that you have to wait
until the progeny start to express the trait.
• It is very expensive as extensive resources are required.
 Progeny testing
• It is because of the last point that progeny testing cannot be run
by individuals but it has to be done as a national undertaking
with different farmers in different regions of the nation
participating.
• It also reduces the selection intensity as only a limited number
of animals can be tested at any one time but
• at the same time increasing selection accuracy.
• Progeny testing has not been done in most developing countries
because of the above reasons.
Selection on the basis of collateral relatives
• This is most useful when family size is large and when the traits
are highly heritable.
• It also works when there is a close genetic relationship between
members of family and the mean generation interval is short.
• It is obviously of more use in selecting for productive traits in
poultry and may be pigs than in cattle.
• It gives less accuracy than progeny testing because of small
numbers possible in collateral relatives.
Selection on the basis of collateral relatives
• Remember that the more closely the collateral relatives are
related to the individual to be selected the more valuable they
are for selection purposes.
• Information on collateral relatives, gives an indication of the
kinds of genes and combinations of genes the individual is
likely to have.
• Information can be obtained on sisters to use on the selection
for milk in dairy bulls, and for the cocks for egg production.
 Half sib Full sib tests
• One can use half sib or sub-sib test, where half sibs all have
one parent in common, whilst full-sibs have both parents
common.
• The accuracy of the full-sib test is lower than the half-sib test
because the full sibs have the similar environment from
conception to weaning and there are less numbers of animals
with full sibs compared to half sibs.
SELECTION METHODS
 1. Tandem selection
• This as the name suggests, involves selection for one trait for a
time until the level wanted is achieved.
• Then you change over to another trait for a further number of
generations until the desired level of the trait is achieved, then a
third and so on.
• Tandem selection is the simplest of the three methods.
• However, it is the least efficient.
• If the correlation between the traits is positive it would be
efficient.
PREDICTION OF BREEDING VALUES
PREDICTION OF EBV ON REPEATED PHENOTYPIC RECORDS OF THE ANIMAL, PREDICTION OF EBV
ON REPEATED PHENOTYPIC RECORDS OF THE ANIMAL, PREDICTION FROM PROGENY RECORDS,
BREEDING VALUE PREDICTION FROM PEDIGREE, BV PREDICTION FROM ONE TRAIT FROM
ANOTHER
 Introduction to the prediction of Breeding values

• Within animal breeding systems, we would like to rank and select

animals based on their true breeding values (TBV or “A”: additive
genetic value).
• Unfortunately we don't have this perfect knowledge - we cannot see
genes and breeding values, and so we must use observed phenotypes
to obtain estimated breeding values (EBV's or Â).
• Genetic change due to selection based on EBV will be lower than if
selection had been on true breeding value.
• The relative response is proportional to accuracy of EBV, and accuracy
is between 0 and 1.
 Introduction
• The most obvious piece of phenotypic information we can use to estimate an
animal’s breeding value is the animal’s own phenotype.
• But we can also use information from relatives, such as the sire, the dam,
siblings and progeny.
• Commercial genetic evaluation systems produce EBVs for each animal for all
traits of relevance.
• Such an evaluation is based on a statistical procedure leading to Best Linear
Unbiased Prediction (BLUP) of breeding values.
• Inclusion of information from relatives is automatically taken care of in the
BLUP method, provided such information is available in the database through
the knowledge of pedigree.
 Introduction
• First we present how phenotypic information is turned into an
EBV.
• The heritability of the trait is important here.
• Second, we discuss the accuracy of EBV, how it is calculated, and
why it is important.
• Basically, the higher the accuracy, the higher the response to
selection based on EBV.
• Closely related to accuracy are the variance of the EBV and the
Prediction Error Variance of EBV.
 Accuracy of breeding values
• The variance of the EBV indicates how much difference in EBV values we can
expect.
• This is relevant if we want to predict the EBV of a selected group of individuals.
• The Prediction Error Variance gives information about the uncertainty of an
EBV.
• It is used to predict how much an EBV can still change when more information
becomes available.
• The higher the accuracy of an index, the smaller the change when more
information comes in.
• This change has great practical importance, e.g. when determining the price
differences between top breeding animals based on EBV.
PRINCIPLE OF ESTIMATING BREEDING VALUES
 Components of Variation
• Breeding Values are estimated based on phenotypic differences between
animals.
• It is based on the notion that part of these phenotypic differences is due
to genetic components.
• Quantitative genetic theory is used here, and one of the key principles is
that phenotypic differences occur due to genetic as well as non-genetic
differences.
• Differences are measured as variance, and therefore, phenotypic variance
is the sum of genetic and non-genetic variance.
• Not all genetic differences between individuals are passed on to progeny.
 Additive genetic variance
• We are only interested in additive genetic variance as -
• it is the variance in breeding value, i.e.
• that part of the genetic differences that are passed on to
progeny –
• it can be more easily estimated, e.g.
• differences between progeny groups of different sires are a
reflection of additive genetic differences.
 Non-additive genetic effects
• The non-additive genetic effects are due to dominance effects as
well as (some) epistatic effects.
• These effects are not unimportant in real life, e.g. they could
explain why some sires make particularly good combinations
with certain cows (farmers call this ‘nicking’),
• but these effects are hard to estimate (because the same sire is
not often used to the same cow),
• they are relatively small and therefore non-additive effects are
hard to utilise in breeding.
 Residual effects
• Non-genetic effects are therefore put in the basket of ‘residual
effects’ together with non-genetic effects due to environmental
differences.
• Therefore
• Phenotypes are made up of breeding values and residual effects:
• P=A+E
• We use “E” for ‘environmental effect, although this is actually a
residual effect, also containing non-additive genetic effects.
 VP = VA + VE
• Phenotypic differences are due to differences in breeding
values plus differences in residual effects
• VP = VA + VE
• where: VP = Phenotypic Variance VA = Additive Genetic
Variance VE = Residual (or Environmental) Variance
 hypothetical scenario to show the importance of EBVs
Observed P A E
Phenotype Phenotypic Additive Residual Effect
(Yearling Deviation genetic Value
Weight)
314 +14 +3 +11
306 +6 +7 -1
302 +2 -3 +5
293 -7 +4 -11
289 -11 -7 -4
 Things illustrated by the figures in the Table
• Phenotypic differences are due to differences in both breeding value
(A) and residual effects (E)
• Differences in A and E are unrelated, i.e. animals with positive A do
not have more chance to have a positive (or negative) E.
• Differences in E are generally larger than differences in A
• Animals with the best phenotype do not necessarily have the best
breeding value, but…
• Selecting animals on phenotype will provide animals with on average
positive breeding values (there is a correlation between P and A)
• It is common that differences in E are larger than differences in A.
• A measure for difference is variance.
• Variance is formally calculated as the sum of the squared deviations.
• The mean values for P, A and E are zero.
• The variances and standard deviations in the example of table on slide 38 are
• VP = 101 SDP = 10
• VA = 32 SDA = 5.7
• VE = 71 SDE = 8.4
• Hence, about 30% of the observed phenotypic differences are due to breeding
value (A).
 The heritability
• This figure is called heritability.

• In the example, the exact heritability

 Distributions in animal breeding
• It is important in quantitative genetics to have a good understanding of distributions.
• Taking the table on slide 38 as an example: the phenotypic SD = 10.
• In a larger population we would expect the extremes to be about 3 SD deviating from
the mean, so ranging from about -30 to +30.
• Note 1: the example is only a small population so the extremes are closer to the mean.
• Note 2: In reality yearling weight has a larger SD: about 30Kg.
• If we sampled many animals, the range of values would be roughly between 200 and
400 Kg.
• The variance in true breeding value is smaller.
• If many were sampled we would expect values between -15 and +15.
 Estimating Breeding Value
• Without the knowledge of true genotypes, the only information
that can be used to estimate breeding value is the phenotype.
• For this purpose we use phenotypic differences between animals,
or more specifically, phenotypic deviations.
• The breeding value is now estimated as a proportion of this
deviation, being the proportion of total variation that is due to
variation in breeding value.
• This proportion is equal to heritability, i.e. in our example, the
proportion is equal to 0.32.
 Estimating Breeding Value
• Hence, when the information used is an animal’s own
phenotypic deviation, the breeding value is estimated as
• Where
– h2 is the symbol for heritability and
– P is the phenotypic deviation.
• The heritability is a population parameter, i.e. the value is
constant.
• It can only vary between traits or between the same trait in
distinctly different environments.
 Estimating Breeding Value
• The reason why we use h 2 rather than h is statistical.
• The correlation between breeding value and phenotype is equal to h.
• The proportion of variation explained by breeding value is h2.
• This notation is equivalent to statistical modeling, where we use r2
for the proportion of variance explained by the model, and r for the
correlation between observed values and predicted values.
• Notice that we don’t use the absolute phenotypic value, but we use
it as a deviation of a mean, since we are only interested in
differences between animals (variation).
 Estimating Breeding Value
• The larger the heritability of a trait, the more we believe that
observed phenotypic differences are due to breeding value.
• The principle of breeding value estimation is based on
regression
 Estimating Breeding Value
• We want to know differences in breeding value based on
observed differences in phenotype.
• The regression of breeding values on the phenotypic
observations,
• the slope of the regression line tells us how much difference
we have in breeding values per unit of difference in phenotype.
• This slope is equal to the heritability.
 Estimating Breeding Value
• This can be derived from quantitative genetic theory, since the
slope of a regression line is

• Recalling that
 Example
• In Table on slide 38, the best bull had a yearling weight of 314
kg. The mean of his contemporaries is 300 kg.
• The heritability of yearling weight is 0.32.
• What is the bull’s EBV?
 Example
Observed P A E EBV

Phenotype Phenotypic Additive genetic Residual

(Yearling Deviation Value Effect
Weight)
314 +14 +3 +11 +4.5
306 +6 +7 -1 +1.9
302 +2 -3 +5 +0.6
293 -7 +4 -11 -2.2
289 -11 -7 -4 -3.5
 Important aspects of EBVs
• The ranking based on EBV is not exactly the same as the ranking based
on true breeding value (A), but,
• Animals with the highest EBV have on average a higher true breeding
value
• There is a prediction error on each EBV (being the difference between A
and EBV).
• The estimation of EBV might seem very poor for individual animals, but
as a criterion for achieving genetic change the EBV is the most efficient.
• Also realise that with more information, especially information on
progeny, the EBV will be closer to A.
 Important aspects of EBVs
• In reality, we cannot see A, and therefore we will not know
prediction error.
• The expectation of prediction error is zero (meaning that they
are zero – on average).
• The size of the prediction error depends on the accuracy.
• With more information available the prediction error becomes
smaller, and the EBV will slowly move toward the true breeding
value.
• With an accuracy of 1, the prediction error will be zero.
 Important aspects of EBVs
• An important thing to note is that the animal with the best EBV
has no more chance to have a negative prediction error that
the animal with the worst EBV, i.e.
• each animal has just as much chance to change upward than
downward if more information becomes available.
 Correcting for Fixed Effects
• Estimation of breeding values has two aspects to it.
• This first is about deriving regression coefficients, i.e. how
much about a piece of information do we attribute to breeding
value.
• The other aspect is that breeding values should be based on
fair comparisons between individuals, i.e.
• they should not be biased by the fact that some animals had
more chance to realise a good phenotype than others.
Fixed effects
• Systematic effects that affect phenotypes are called fixed
effects, e.g. the effect of the animals’ sex, its herd (flock) or
management group, the season it was born in, whether it was
born as a single or twin, etc.
• For those fixed effects that are observable we can do a
correction.
• This is in contrast to the random environmental effects “E”
which we cannot observe, and cannot correct for.
 Fixed effects
• Correction for fixed effects will be discussed in more detail
when we discuss linear models and BLUP.
• However, the principle is that for a fair comparison among
animals,
• We need to consider their observed phenotype as a deviation
of an expected mean, i.e.
• As a deviation of a contemporary group mean.
 Fixed effects
Bull Phenotype Herd Average P EBV(h2=0.30)
Prefect 330 300 +30 +9
Lord 300 260 +40 +12
• So although Prefect is a bigger bull, its EBV is lower.
• He was bigger mainly because of being in a good herd.
• Correcting for fixed effects makes sense, and is the main reason why selecting on EBV is more
sensible than selecting on phenotype.
• However, at the same time this creates a lot of confusion as breeders might wonder why their best
looking animals do not have the best EBV.
• Note that it is possible that Prefect’s herd used better bulls, and in that case the correction would
be unfair.
• However, in the BLUP procedure, there is a joint correction for herds and bulls used in these herds,
and BLUP would take such a thing into account (this was one of the main reasons why BLUP was
introduced in dairy cattle evaluation in the 1970s).
 Fixed effects
• Besides correcting for fixed class effects, as above, we can also correct for
continuous effects such as age.
• In the example below, we use a correction for weight of 12 kg/month
(assume we have first estimated from data that growth per month is 12 kg).
• Each animal is adjusted to yearling weight, by adjusting their weight
according to age.
• For example, Frank was measured at 11 months, and we expect it would be
12 kg heavier if it had been measured at 12 months.
• Therefore, it gets 12 kg extra credit, and we put his corrected 12 month
weight at 302 kg.
Bull Phenotype Age(mo) Corrected Phenotype P EBV (h2 = 0.30)
Knox 290 11 302 +2 +0.6
Joe 305 13 293 +7 -2.1
 Accuracy of EBV
• The accuracy is defined as the correlation between true and
estimated breeding value.
• The symbol for accuracy is
• Since the EBV is often indicated as an Index (I), - the true breeding
value has symbol A and r is a common symbol for correlation.
• The accuracy is between 0 and 1 (or 0% and 100%).
• In the extreme case of no information, the accuracy of a breeding
value is 0, and with a very large amount of information, the
accuracy will approach 1.
 Accuracy of estimated breeding values
• Accuracy is higher when more information is used, e.g. from relatives and
progeny
• The accuracy is higher for traits with a higher heritability, but the effect of
heritability becomes smaller with more information used.
• The accuracy of parent average depends on the parent EBV accuracy and not on
heritability (but note that with low heritability it will be harder for a parent to
achieve a certain accuracy) •
• The accuracy of information from collateral relatives (i.e. siblings) is limited to
0.5 for HS and 0.71 for FS.
• A progeny test is required to obtain higher accuracies.
• Accuracies can be derived using selection index theory.
 Variance among EBV
• The variance among EBVs is of practical value because:
• it can give us an indication of the difference in EBV between the highest and
lowest animals •
• It is used to predict selection differential, e.g. the average EBV of the best
10% of animals
• In general:
• and
• where is the accuracy of the EBV.
• Hence, the variance of the EBV’s is equal to the accuracy-squared multiplied
by the variance of the true breeding values (additive genetic variance).
 Variance of estimated breeding values
• is generally smaller than
• becomes larger when accuracy is higher. i.e.
• the EBV of older animals will be more apart than those of
young animals.
• The same holds for EBV of intensely measured nucleus animals
compared to the EBV of base animals that have less
information and therefore EBVs closer to each other.
 Prediction Error Variance
• The Prediction Error Variance (PEV) gives insight into the
amount of error, and therefore the distribution of the true
breeding value.
• For this distribution we use the standard deviation, which is
the Standard Error of Prediction (SEP).
• This distribution can be used when assessing a change in an
EBV when more information becomes available –
• how much can they still change?
• The prediction error variance (PEV) is calculated as:
•
• And the Standard Error of Prediction (SEP) is
 Importance of PER
• The prediction error of an EBV is important as it gives us an indication of the
difference between the TBV and the EBV.
• This is important for example to answer questions like:
• how much could an EBV still change if we obtain more information on the
animal.
• Changes in EBV’s are not good for the industry’s confidence in the genetic
evaluation system.
• However, we have to realise that an EBV is never exact, unless the accuracy is
100%.
• We expect the TBV to be the same as the EBV, but there is a certain probability
that it will be a bit different.
 PREDICTION OF EBV ON ONE RECORD OF THE ANIMAL

• The EBV = ai for animal i can be calculated as:

• EBV =
• Whereis the phenotypic record for animal i for the trait.
• is the mean phenotypic performance of animals in the
same management group and it is assumed to be known.
• is the regression of the true BV on the phenotypic
performance.
 The ebv

• Therefore
• EBV = h2 (individual record – herd average)
•
• = h2( individual deviation form herd average).
Accuracy of prediction
• The correlation between the selection criterion in this case the phenotypic
value y and the true BV, ai of the animal i is called the accuracy of
prediction.
• The higher the correlation (accuracy) the better the criteria as a predictor
of the true BV.
• For a single record the accuracy
•
• The expected response to selection on the basis of a single record per
individual is (Falconer, 1989)
• R = ih2δy. and reliability equals h2
 Expected response with one record
• Expected response (R) to selection on the basis of a single
record per individual (Falconer and Mackay, 1996) is:

• where i, the intensity of selection, refers to the superiority of

selected individuals above population average expressed in
phenotypic standard deviation.
 Example
• Given that the yearling weight of a heifer is 320 kg in a herd
with a mean of 250 kg.
• Predict her breeding value and its accuracy if the heritability of
yearling weight is 0.45.
• From above : a ˆ = 0.45(320 − 250) = 31.50 kg and:
 Prediction with repeated records
• When multiple measurements on the same trait, such as milk
yield in successive lactations, are recorded on an animal, its BV
may be predicted from mean of records.
• with repeated measurements it is assumed that there is
additional resemblance between records of an individual due
to environmental factors or circumstances that affect the
records of the individual permanently.
• There is additional covariance between records of an individual
due to non-genetic permanent environmental effects.
• The between-individual variance is partly genetic and partly
environmental (permanent environmental effect).
• The within-individual variance is attributed to differences
between successive measurements of the individual arising from
temporary environmental variations from one record to another.

• Where var(g) = genetic variance that include additive and non-

additive
 The intra-class correlation
• Var(pe) = variance due to permanent environmental effect,
and
• Var(te) = variance due to random temporary environmental
effect.
• The intraclass correlation (t) is the ratio of the between –
individual variance to the phenotypic:
 Assumptions about this model
1. Assumed that the repeated records on the individual measure
the same trait:
• That is the genetic correlation of 1 between all pairs of records
2) Assumed that all records have equal variance
3) Assumed that the environmental correlations between all

• Let represent the mean of records on animal .

pairs of records are equal.
 The BV on repeated records
• The Bv is predicted as
•
• where
• Now = ( and
 Repeated records
• Expressing the quantities in t
•
• Therefore,

• Now b depends on heritability, repeatability and number of

records.
 Repeated records
• If the successive records are known to be affected by factors
that influence performance these must be corrected for.
• The accuracy of the EBV will be:
• =
• Compared to single records there is a gain in the accuracy of
prediction with repeated records which depends on the value
of repeatability and the number of records.
 Repeated records
• This gain is mainly from the reduction in temporary
environmental variance as the number of records increases.
• when t is low the gain is substantial as n increases.
• When t is high, there is little gain in accuracy with repeated
records compared with using only single records.
• In general, the rate of increase dropped rapidly as the number
of records exceeded 4 and it is seldom necessary to record
more than 4 measurements.
 Example of repeated records
• Assume that a cow has a mean yield of 8000 kg of milk for first and second
lactations.
• If the phenotypic standard deviation and heritability of milk yield in the first two
lactations are 600 kg and 0.30, respectively, and
• The correlation between first and second lactation yields is 0.5.
• Predict the breeding value of the cow for milk yield in the first two lactations and
its accuracy.
• Assume that the herd mean for first and second lactations is 6000 kg.
• From with:

• Therefore: = 0.4(8000 − 6000) = 800 kg and: = = 0.632

 Breeding Value Prediction from Progeny Records
• For traits where records can be obtained only on females, the
prediction of breeding values for sires is usually based on the
mean of their progeny.
• This is typical of the dairy cattle situation, where bulls are
evaluated on the basis of their daughters.
• Let be the mean of single records of progeny of sire and
assume that the progeny are only related through the sire
(paternal half-sibs),
 EBV prediction from progeny
• and so the breeding value of sire is:
• where:
•
• Now:=
• where is the sire breeding value and represents the breeding
value for the dams.
 Prediction of BV from progeny
• Therefore
• After some mathematics we find that (see Mrode page 7)
•
• with
 Prediction of BV from progeny
• is constant for any assumed heritability.
• The weight is depends on heritability and number of progeny
and approaches 2 as number of daughters increases.
• The accuracy of
• This approaches 1 as the number of daughters becomes large.
• The accuracy of the predicted BV is which half of the accuracy
of the predicted BV of the sire.
 Breeding value estimation from pedigree
• When an animal has no record, its breeding value can be
predicted from the evaluations of its sire (s) and dam (d).
• Each parent contributes half of its genes to their progeny, and
so the predicted breeding value of progeny (o) is:
 BV prediction from one trait from another
• The BV for one trait may be estimated from the observation on another trait
if traits are genetically correlated.
• If is the observation on animal from one trait, its BV for another trait is
• Where

• the genetic correlation between trait and is

• therefore
• = r axy σaxσay
•
 BV estimation from correlated traits
• If the additive standard deviations for x and y are expressed in
as products of the square root of their individual heritabilities
and phenotypic variances then

• Thus the weight depends on the genetic correlation between the two
traits, their heritabilities and phenotypic standard deviations.
• The accuracy
• It depends on the genetic correlation between the two traits and
heritability of the recorded trait
 Tandem selection
• In cases where there is very little or negative correlation, the
selection for one trait may nullify or reverse the progress made
in the first trait.
• It also involves a very long time such that the breeder might
change her goals too often or become discouraged and stop.
• This method is rarely used today.
 2. Independent culling level
• It involves setting independent minimum or maximum levels for
two or more traits.
• And animals not meeting any one of those levels in one trait will
be culled regardless of its performance in the other traits.
• In this method selection is practised for more than one trait
simultaneously which is one advantage over the tandem
method.
• One can adjust the relative importance for each trait by
modifying the culling levels for each trait.
 Independent culling level
• This flexibility is to some extent determined by the proportion
of animals to be saved.
• Independent culling method does not involve complicated
calculations.
• It also involves a short time between taking of the
measurements and the results.
• One of its major disadvantages is that it is possible to cull some
genetically very superior animals when this method is used.
 Independent culling levels
• Use the pig example to illustrate.
 3. Selection Index
• This method involves selecting for all traits simultaneously by
using an index of net merit.
• The selection index is constructed by adding into one figure the
credits and penalties given each animal according to the
degree of its superiority or inferiority in each trait.
• It is the most efficient and accurate of the three methods.
• The calculation of the index is not simple.
 Selection index
• We can only do it with the aid of computers. The index is
calculated as

• Where I is the selection index

• bi is the phenotypic weight of the trait
• Xi is the value of the ith trait
 Selection index
• An example of an index in beef cattle is given below:
• I = (0.58 x weaning mass) + (18.64 x rate of gain in feedlot) –
(0.73 x Number of days to bring animal to a low choice
slaughter grade) – (5.87 x Amount of feed per kg mass gained)
or
• I = 0.58 W + 18.64 R – 0.73 F – 5.87E
The major disadvantages of the selection Index
• The records have to be pre-adjusted for fixed or environmental
factors.
• These are assumed to be known, which is not the case in most
of the time.
• Solutions to the index equations require the inverse of the
covariance matrix for observations and this may not be
computationally feasible for large data sets.
 Best linear unbiased prediction (BLUP)
• Developed by Henderson in 1949 which simultaneously
estimated both the fixed effects and breeding values.
• Has properties similar to those of a selection index.
• The methodology reduce s to selection indices when no
adjustments for environmental factors are needed.
 Properties of BLUP
• The properties are more or less contained in the name.
• Best – means it maximizes the correlation between true and
predicted breeding value or minimizes prediction error variance
(PEV)
• Linear – predictors are linear functions of observations.
• Unbiased – estimation of realized values for a random variable
such as animal breeding values, and of estimable functions of
fixed effects are unbiased .
• Prediction – involves prediction of true breeding value.
 Widespread use of BLUP
• BLUP has found widespread usage in genetic evaluation of
domestic animals because of its desirable statistical properties.
• This has been enhanced by the steady increase in computing
power and has evolved in terms of its application to simple
models, such as the sire model, in its early years, to more
complex models such as the animal, maternal, multivariate and
random regression models, in recent years.
 Software for BLUP
• Several general purpose computer packages for BLUP
evaluations such as
• PEST (Groeneveld et al., 1990),
• BREEDPLAN, Mix 99 (Lidauer et al., 2011) and a host of others
have been written and made available.
• AIREML.
 Theoretical background of BLUP
• Consider the following equation for a mixed linear model:
• equation 1
• where:
• vector of observations;
• number of records
• vector of fixed effects;
• number of levels for fixed effects
• 1 vector of random animal effects;
• number of levels for random effects
• 1 vector of random residual effects
• design matrix of order , which relates records to fixed effects
• design matrix of order , which relates records to random animal effects
 Some assumptions
• Both X and Z are termed incidence matrices.
• It is assumed that the expectations (E) of the variables are:
• and
• it is assumed that residual effects, which include random environmental
and non-additive genetic effects, are independently distributed with
variance ;
• therefore, and
• ,
• where A is the numerator relationship matrix.
 Theoretical background
• Then:

• Since
• then:
 Theoretical background
• and:
 The linear functions
• The general problem with respect to Equation 1 is to predict a
linear function of and , that is, (predictand),
• using a linear function of , say (predictor), given that is
estimable.
• The predictor is chosen such that it is unbiased (i.e. its
expected value is equal to the expected value of the
predictand) and PEV is minimized.
 Linear functions
• This minimization leads to the BLUP of a (Henderson, 1973) as:
• equation 2
and:
• where
• where = (X′V−1X)X′V−1y
• the generalized least square solution (GLS) for b, and k′ is the
best linear unbiased estimator (BLUE) of k′b,
• given that k′b is estimable.
 Linear functions- the BLUE
• BLUE is similar in meaning and properties to BLUP but relates to
estimates of linear functions of fixed effects.
• It is an estimator of the estimable functions of fixed effects that has
minimum sampling variance, is unbiased and is based on the linear
function of the data (Henderson, 1984).
• BLUP is equivalent to the selection index with the GLS of substituted
for b.
• Alternatively this could be illustrated by considering the index to
compute BVs for a group of individuals with relationship matrix A,
which have records with known mean.
• The relevant matrices are
• and
• With :
• or
• Hence

• Which is similar to the BLUP assuming fixed effects are absent

and with
• The solutions for a and b in Equation 2 require , which is not
always computationally feasible.
 Solutions for and
• However, Henderson (1950) presented the mixed model
equations (MME) to estimate
• solutions (fixed effects solutions) and predict
• solutions for random effects simultaneously without the need
for computing.
• The MME for

• assuming that R and G are non-singular.

• Since is an identity matrix from the earlier definition of R,
• it can be factored out from both sides of the equation to give:

• Note that the MME may not be of full rank, usually due to
dependency in the coefficient matrix for fixed environmental effects.
• It may be necessary to set certain levels of fixed effects to zero when
there is dependency to obtain solutions to the MME.
• However, the equations for equation 2 are usually of full rank since
is usually positive definite and is invariant to the choice of
constraint.
• The solutions to the MME give the BLUE and BLUP of under
certain assumptions, especially when data span several
generations and may be subject to selection.
• These assumptions are:
• 1. Distributions of and are assumed to be multivariate normal,
implying that traits are determined by many additive genes of
infinitesimal effects at many infinitely unlinked loci
(infinitesimal model.
• With the infinitesimal model, changes in genetic variance
resulting from selection, such as gametic disequilibrium
(negative covariance between frequencies of genes at different
loci), or
• from inbreeding and genetic drift, are accounted for in the
MME through the inclusion of the relationship matrix
(Sorensen and Kennedy, 1983),
• as well as assortative mating (Kemp, 1985).
• 2. The variances and covariances (R and G) for the base
population are assumed to be known or at least known to
proportionality.
• In practice, variances and covariances of the base population
are never known exactly but, assuming the infinitesimal model,
these can be estimated by restricted (or residual) maximum
likelihood (REML) if data include information on which
selection is based.
• 3. The MME can account for selection if based on a linear
function of (Henderson, 1975) and
• there is no selection on information not included in the data.
• The use of these MME for the prediction of breeding values
and estimation of fixed effects under an animal model is
presented in the next section.
 Sire model
• The application of a sire model implies that only sires are being evaluated
using progeny records.
• Most early applications of BLUP for the prediction of breeding values,
especially in dairy cattle, were based on a sire model.
• The main advantage with a sire model is that the number of equations is
reduced compared with an animal model since only sires are evaluated.
• However, with a sire model, the genetic merit of the mate (dam of
progeny) is not accounted for.
• It is assumed that all mates are of similar genetic merit and this can result
in bias in the predicted breeding values if there is preferential mating.
 Reduced animal model
• The BLUP of breeding value for the animal model involved setting up equations for
every animal, that is, all parents and progeny.
• Thus the order of the animal equations was equal to the number of animals being
evaluated.
• If equations were set up only for parents, this would greatly reduce the number of
equations to be solved, especially since the number of parents is usually less than the
number of progeny in most data sets.
• Breeding values of progeny can be obtained by back-solving from the predicted parental
breeding values.
• Quaas and Pollak (1980) developed the reduced animal model (RAM), which allowed
equations to be set up only for parents in the MME, and breeding values of progeny are
obtained by back-solving from the predicted parental breeding values.
 Reduced animal model
• The application of a RAM involves setting up animal equations
for parents only and representing the breeding values of non-
parents in terms of parental breeding value.
 Animal Model with Groups
• In prediction the BVs, there were animals in the pedigree with
unknown parents, usually called base population animals.
• The use of the relationship matrix in animal model evaluation
assumes that these animals were sampled from a single
population with average breeding value of zero and common
variance .
 Animal model with groups
• The breeding values of animals in subsequent generations are
usually expressed relative to those of the base animals.
• However, if it is known that base animals were actually from
populations that differ in genetic means, for instance, sires
from different countries, this must then be accounted for in the
model.
• In the dairy cattle situation, due to differences in selection
intensity, the genetic means for sires of bulls, sires of cows,
dams of bulls and dams of cows may all be different.
 Animal model with groups
• These various sub-population structures should be accounted for in the
model to avoid bias in the prediction of breeding values.
• This can be achieved through a proper grouping of base animals using
available information.
• Westell and Van Vleck (1987) presented a procedure for grouping, which
has generally been adopted.
• For instance, if sires have been imported from several countries over a
period of time and their ancestors are unknown, these sires could be
assigned to groups on the basis of the expected year of birth of the
ancestors and the country of origin.
 Animal model with groups
• The sires born within a similar time period in a particular
foreign country are assumed to come from ancestors of similar
genetic merit.
• Thus each sire with one or both parents unknown is initially
assigned phantom parents.
• Phantom parents are assumed to have had only one progeny
each. Within each of the foreign countries, the phantom
parents are grouped by the year of birth of their progeny and
any other factor, such as sex of progeny.
 Animal model with groups
• In addition, for the dairy cattle situation, the four selection
paths –
• sire of sires,
• sire of dams,
• dam of sires and
• dam of dams –
• are usually assumed to be of different genetic merit and this is
accounted for in the grouping strategy.
 Animal model with groups
• The animal proofs above are generally lower than those from,
the model without groups.
• In addition, the ranking for animals is also different.
 MODEL WITH COMMON ENVRIONEMETAL EFFECTS
• Apart from the resemblance between records of an individual
due to permanent environmental circumstances can also
contribute to the resemblance between relatives.
• When members of a family are reared together, such as litters
of pigs, they share a common environment and this
contributes to the similarity between members of the family.
• Thus there is an additional covariance between members of a
family due to the common environment they share and this
increases the variance between different families.
 MODEL WITH COMMON ENVRIONEMETAL EFFECTS
• The environmental variance may be partitioned therefore into
the between-family or group component (, usually termed the
common environment, which causes resemblance between
members of a family, and the within-family or within-group
variance (
• Sources of common environmental variance between families
may be due to factors such as nutrition and/or climatic
conditions.
 MODEL WITH COMMON ENVRIONEMETAL EFFECTS
• All sorts of relatives are subject to an environmental source of
resemblance, but most analyses concerned with this type of
variation in animal breeding tend to account for the common
environment effects associated with full-sibs or maternal half-sibs,
especially in pig and chicken studies
• The environmental covariance among full-sibs or maternal half-
sibs might be due to influences from the dam (mothering ability or
maternal effect); therefore, differences in mothering ability among
dams would cause environmental variance between families.
 MODEL WITH COMMON ENVRIONEMETAL EFFECTS
• For instance, resemblance among progeny of the same dam in body weight could be
due to the fact they share the same milk supply and variation in milk yield among
dams would result in differences between families in body weight.
• This variation in mothering ability of dams has a genetic basis and, to some degree, is
due to genetic variation in some character of the dams.
• Some dams has the highest breeding value among the dams and would therefore be
the first dam of choice,
• whether selection is for dams of the next generation on the basis of breeding value
only or
• selection is for future performance of the dams in the same herd, which will be based
on some combination of breeding value and estimate of common environmental
effect.
 MBLUP
• Selection of livestock is usually based on a combination of several traits of
economic importance that may be phenotypically and genetically related.
• Such traits may be combined into an index on which animals are ranked.
• A multiple trait evaluation is the optimum methodology to evaluate animals
on these traits because it accounts for the relationship between them.
• A multiple trait analysis involves the simultaneous evaluation of animals for
two or more traits and makes use of the phenotypic and genetic
correlations between the traits.
• The first application of best linear unbiased prediction (BLUP) for multiple
trait evaluation was by Henderson and Quaas (1976).
 Advantage of MBLUP
• One of the main advantages of multivariate best linear
unbiased prediction (MBLUP) is that it increases the accuracy
of evaluations.
• The gain in accuracy is dependent on the absolute difference
between the genetic and residual correlations between the
traits.
• The larger the differences in these correlations, the greater the
gain in accuracy of evaluations (Schaeffer, 1984; Thompson and
Meyer, 1986).
 Advantages of MBLUP
• When the heritability, genetic and environmental correlations
for two traits are equal, multivariate predictions are equivalent
essentially to those from univariate analysis for each trait.
• Moreover, traits with lower heritabilities benefit more when
analysed with traits with higher heritabilities in a multivariate
analysis.
• Also, there is an additional increase in accuracy with multivariate
analysis resulting from better connections in the data due to
residual covariance between traits (Thompson and Meyer, 1986)
 Maternal trait Models
• The phenotypic expression of some traits in the progeny, such as
weaning weight in beef cattle, is influenced by the ability of the dam
to provide a suitable environment in the form of better nourishment.
• Thus the dam contributes to the performance of the progeny in two
ways: first, through her direct genetic effects passed to the progeny
and second, through her ability to provide a suitable environment,
for instance in producing milk.
• Traits such as birth and weaning weights in beef cattle fall into this
category and are termed maternally influenced traits.
 Maternal trait Models
• The ability of the dam to provide a suitable environment for the expression
of such traits in her progeny is partly genetic and partly environmental.
• Similar to the genetic component of an individual, the maternal genetic
component can be partitioned into additive, dominance and epistatic
effects (Willham, 1963).
• The environmental part may be partitioned into permanent and temporary
environmental components.
• It is the maternal additive genetic component of the dam that is passed on
to all her offspring, but it is expressed only when the female offspring have
progeny of their own.
 Maternal trait Models
• In the usual mixed linear model for maternally influenced traits, the
phenotype is partitioned into:
• 1. Additive genetic effects from the sire and the dam, usually termed the
direct genetic effect.
• 2. Additive genetic ability of the dam to provide a suitable environment,
usually termed the indirect or maternal genetic effect.
• 3. Permanent environmental effects, which include permanent
environmental influences on the dam’s mothering ability and the maternal
non-additive genetic effects of the dam.
• 4. Other random environmental effects, termed residual effects.
 Maternal trait Models
• The application of BLUP to models with maternal effects was
first presented by Quaas and Pollak (1980).
• When repeated measurements for maternally influenced traits
are available over a range of ages (for instance, body weight
from birth to 630 days), a random regression model might be
more appropriate to analyse such a trait.
• These can be selected for in a population and the choice
depends on whether the selection is for direct or indirect
maternal effects.
 Marker Assisted Selection (MAS)

• An Overview
• The addition of genomic information to phenotypic information to increase the
selection response to the traditional method is known as Marker-Assisted
Selection (MAS).
• The concept of Marker Assisted Selection (MAS) utilizing the information of
polymorphic loci as an aid to selection was introduced as early as in 1900 .
• The method where marker genes used to indicate the presence of desirable
genes is called as marker assisted selection .
• Marker assisted selection (MAS) is indirect selection process where a trait of
interest is selected not based on the trait itself but on a marker linked to it.
 Overview
• The purpose is to combine all genetic information at markers and
QTL with the phenotypic information to improve genetic evaluation
and selection.
• The advantage of using MAS is that the effect of genes on
production is directly measured on the genetic makeup of the
animal and not estimated from the phenotype.
• The integration of two selection methods, i.e., traditional or
conventional selection methods with molecular genetics methods
beneficial to the selection response.
• Multiple estimated QTL effects and multiple trait selection could help
to make better decisions regarding the use of MAS in animal
improvement
Marker assisted selection and quantitative trait loci (QTL)

• MAS only can increase the rate of genetic gain when there is a
continuous identification of new QTL,
• The extra genetic gain due to the MAS decreases very quickly with the
number of generations of selection for a same QTL also the rate of
identification of new QTL is difficult to predict, the gain due to MAS for a
certain QTL is higher when the characteristic like fertility and carcass is
measured after the selection.
• The aim of MAS is improving selection response.
• For a successful implementation of such QTL within selection programs,
the identification of specific polymorphisms which are responsible for
the observed effect is needed.
 MAS &QTL
• The effectiveness of MAS by both recombination
between the marker and the actual QTL and by
mutation elsewhere in the genome .
• The continued development of genome maps and QTL
analysis will eventually remove the recombination
problem, as the genes and even the specific
polymorphic alleles that generate QTL are identified.
• Genetic gains from MAS equal to 10-20%, depending
on the size of the QTL.
 MAS &QTL 1
• When MAS is used in a population, the frequency of the
favorable QTL allele is quickly increased during the first
generations compared to conventional selection based on
BLUP (Best linear unbiased prediction).
• Selection of an animal for genotyping should be related to the
linkage of marker loci and the QTL.
• Use of information from the detected QTL in the selection
requires developing selection criteria to connect this molecular
information with phenotypic information.
 MAS &QTL 2
• The optimum selection should identify outstanding individuals as the
parents of the next generation.
• For traits regulated by a QTL with large effects and for which
phenotypic selection is expensive, MAS can be efficiently used.
• However, use of MAS requires linkage disequilibrium
which could be used in dairy cattle as MAS within family.
• One problem of MAS within family is the large number of
offspring required from each half-sib family in order to
estimate unbiased effects.
 MAS&QTL 3
• The selection schemes using marker information for dairy cattle
were largely based on information from within families [7].
• The use of linkage disequilibrium (LD) information to locate QTL
has increased [8].
• The next step after fine-mapping of QTL is to use them in
prediction of breeding values.
• There are several examples in dairy cattle with LD markers
used for pre-selection of candidates [9].
• Using DNA-information in a population with LD can enhance the
accuracy of identifying superior animals.
 Advantages of marker assisted selection
• Analysis of the genes helps in identification of the
traits an individual will pass on to the next generation,
regardless of the environmental conditions.
• Selection based on traits when the phenotype is not easy to evaluate
such as for disease resistance genes.
• Selection is possible for recessive genes and mutants.
• Faster selection process because an individual’s phenotype can be
predicted at a very early stage.
 ADVANTAGES OF MAS
• MAS is profitable than conventional selection for sex-limited traits (milk yield,
egg production), low heritability traits or traits that are a poor predictor of
breeding value (litter size, fertility)
• and a corresponding lack of selection response and genetic gain in
conventional selection and breeding programs,
• carcass traits as they cannot be measured on breeding animals(meat quality),
• difficulty or expensive to measure (disease resistance),
• traits that are genetically correlated milk production and protein content of
milk
• traits that are expressed late in life, that are controlled by a few pairs of alleles
and
• large genotype by environment interactions and progeny testing scheme
where long generation interval, lengthy and costly step.
 ADVANTAGES OF MAS 1
• MAS are used as a tool to reduce generation interval through
early selection, even before maturity and to select those
traits which are observed in only one sex.
• MAS could be particularly useful in crossbreeding
programmes where, desirable genotypes are introgressed
into productive local breeds with overall better breeding
values.
• The disease resistance genes of local breeds are specifically
targeted in upgrading programmes with imported stock with
higher productivity breeds being crossed to local breeds.
 ADVANTAGES OF MAS 2
• Reproduction traits as well as maternal behavior, mothering ability
and ewe survival are also good MAS targets as they are sex limited
and are only expressed after the first stage of reproduction.
• Disease resistance traits are generally hard to measure under
uniform conditions and would also greatly benefit from MAS.
• MAS would be expected to have limited benefit for wool production
traits because of their high heritability and the ability to measure
the traits before the age of first selection.
• Feed efficiency and maternal efficiency are important determinants
of pastoral production systems and genetic improvement would
benefit from MAS because of the cost of their measurement.
 ADVANTAGES OF MAS 3
• As the reproductive rate is a trait of high economic value and due
to the availability of a test for the actual gene mutation, Booroola
gene used for MAS and marker-assisted introgression (MAI)
programmes.
• MAS gave an additional gain of 24% when half of the selected
candidates were slaughtered to measure phenotypes on carcasses.
• When the non-selected halves were slaughtered, the marker-
phenotype information could be used to select in the next
generation, giving 64% additional gain.
• The use of Marker Assisted Selection (MAS) has the potential if the
markers are highly correlated with the desired phenotype to
enhance the power of the present-day breeding strategy.
 ADVANTAGES OF MAS 4
• Many genetic markers linked with QTL affecting traits
of economic importance in livestock, including milk
production, conformation and health have been
identified and mapped during the past decade [16].
• Pongpisantham (1994) found that the inclusion of
markers could increase up to 15% the genetic response
to selection for growth rate in a population of chickens,
compared with selection based on family selection.
• MAS can increase the reliability of breeding values
[17,18].
DISADVANTAGES OF MARKER-ASSISTED SELECTION
• Increased cost involved in sample collection for genotyping and
complete genotype information in MAS is a major limitation in a
breeding scheme.
• Genotyping the whole population is also difficult in commercial dairy
cattle populations.
• To decrease genotyping costs by identifying the most informative
individuals based on phenotypic information , segregation analysis or
combining the phenotypic and genotypic information, limited number of
genes of importance fully characterized and also lack of confidence of
users, low accuracy of QTL detection.
 DISADVANTAGES OF MAS
• In most situations, there is not complete genotype information
in the population used in MAS schemes, lack of markers,
Selecting on marker information is not fully reliable due to
possible overestimation of QTL effects and error in QTL
position.
• A common problem related with QTL estimates is
inconsistency, which means that a QTL effect is not expressed
similarly in several years or when is used in a different
population.
 CONCLUSION ON MAS
• The use genetic markers with the phenotypes in a process called marker-assisted selection.
• Combined with traditional selection techniques, MAS has become a valuable tool in selecting
organisms for desirable traits.
• MAS is expected to increase genetic gain compared to traditional breeding programs and reduce the
cost of progeny testing by early selection of the potential young bulls.
• The application of MAS in breeding programmes depends on the knowledge of breeders about
variable marker information from animal to animal and the different effects on multiple traits and his
ability to spend in genotypic information that helps in improve their commercial breeding activities.
• MAS also provide an apparently possible approach to selection for genetic disease resistance
animals.
• In the future to make MAS effective in large breeding populations, the availability of large-scale
genotyping methods and infrastructure that allows the generation of hundreds of thousands of
molecular data at a reasonable cost will be necessary.
 GENOMIC SELECTION
• The future for faster genetic improvement in livestock
 Conventional selection
• – Based on individual records, pedigree or progeny
performance or family performance.
Progeny testing –Bulls evaluated on the basis of daughters
performance
 History of geneomics

 1911-The gene map of Drosphila by Alfred Sturtevant.

 1930s-Molecular Biology begins.

 1965-Margaret Dayhoff's Atlas of Protein Sequences

 1970-Sequencing techniques by Fredirick Sanger

 Three disciplines Genetics, Molecular biology and Bioinformatics

converged in 1980s and 1990s -Genomics
• In the 1990s starts QTL analysis in in farm animals
Marker Assisted Selection (MAS)

1-Detect one or several QTLs

2-Fine mapping
3-Find the gene responsible
4-Introgression
 Limitations of MAS

1-The effect of individual Quantitative trait loci (QTL) on

polygenic traits, such as milk yield, are likely to be small

2-Number of QTL required is quite large to sufficiently explain

the genetic variation in these traits
 Genomic Breeding
In 1990 Human Genome project started and in 2003 human
genome was published. This was followed by sequencing of
farm animal genomes
Species Year
Dog (Canis Familiaris) 2003
Chicken (Gallus Gallus) 2004
Cat (Felis sylvestris) 2006
Sheep (Ovis Aries) 2008
Cattle (Bos taurus) 2009
Horse (Equus caballus) 2009
Pig (Sus Scrofa) 2009
 Sequencing revolutionised development of large panels of
SNPs in domestic animals
 Genomic Selection was actually first introduced by Haley
and Visscher at Armidale WCGALP in 1998
 But the methodology for Genomic Selection was first
presented by Meuwissen et. al.in 2001
 Genomic selection
• “Genomic Selection is defined as a technology for increasing the
accuracy with which the genetic merit of young potential breeding
animals can be determined". Wickham et al. ,2012

• Two step process:

• Estimate the effects of markers in a reference (training) populations
(phenotyped and genotyped)
• This information utilized to predict the breeding value of candidates to
selection in a testing (evaluation) population (genotyped)
Methodology

Eggen,2012
 Differences with MAS

 MAS concentrates on few QTLs having association with markers

 Genomic selection uses a genome-wide panel of dense markers
 Advantages
Animals at an early age because breeding values can be
predicted with an accuracy of 0.8 for selection candidates at
birth
Higher rate of gain as compared to Progeny
testing
Lower rate of Inbreeding per generation
Genomic selection for future uses:
-Mitigation of effects of climatic change-select for lower GHG
(green-house gas) emissions in species: "Eco friendly
cattle”(Hayes et. al. , 2013)

Genomic selection is especially useful for

 Traits with low heritability(fitness traits)
 Traits difficult/expensive to measure(like wool quality in sheep
 Disease susceptibility/resistance traits
 Traits that take a lifetime to measure(longevity)
 High-density SNP Chips available for

 Cattle
 Sheep
 Goat
 Pigs
 Horses
 Dogs
 Chicken
 Salmon
 Human
 Countries following Genomic Selection

 USA & Canada (In Collaboration)

 New Zealand
 Netherlands
 Australia
 Denmark & Sweden
 Brazil
 Limitations

 Genotyping requires sufficiently large set of

animals for accurate marker estimates
 For Low heritable traits more records are needed
 Between breed accuracy low-High Density chip
 Marker estimates must be estimated in
population where they have to be used