WAP 214 PRINCIPLES OF ANIMAL BREEDING
Office hours: 0900hrs-1645hrs (Mon-Fri)
Textbooks:
Richard M. Bourdon. 1997. Understanding animal breeding,Dr S.M.
Makuza.Animal Breeding.ZOU Module.
Prerequsite:AGRO101 -Principles of Genetics
COURSE OBJECTIVES: The course is designed to enhance your understanding of genetic
principles and their applications on genetic improvement of livestock populations. During the first
part of the course we will review concepts of classical (Mendelian) inheritance and population
genetics. Then, we’ll learn how to calculate and interpret basic statistics used to describe a given
population and on genetic evaluation. We’ll then discuss selection principles for short and long term
responses on herd improvement. We’ll focus on interpretation of performance records and estimated
genetic values, including information produced by national genetic evaluation programs, such as
breed association sire summaries.
STUDENT OUTCOMES:
After attending the course, the students will able to:
1.
Use statistics to describe the genetic and phenotypic variation of a given population.
2.
Explain the use of phenotypic information from the animal and its relatives in
estimating transmitting ability.
3.
Understand the information generated on a genetic evaluation program and how to
apply this information on animal breeding.
4.
Understand concepts of breeding goal, selection index, heritability, repeatability,
correlation, accuracy, selection intensity, generation interval and their effects in making
genetic change.
5.
Relate the Hardy-Weinberg Law to forces that causes changes on genetic and
genotypic frequencies.
6.
Design breeding programs using the concepts listed above to achieve defined
breeding goals.
7.
Calculate relationship coefficient and inbreeding and understand its effects at the
application level.
8.
Infer relationships between reproductive rate, longevity on selection intensity and
generation interval.
9.
Characterize heterozygosis and heterosis and how to explore it through systematic
crossbreeding
10.
Understand the role of molecular genetics and new technologies on genetic
improvement.
11.
Understand the biological and biochemical basis for genetic variability and
heritability
12.
Understand advantages and limitation of multiple trait selection.
13.
Explain the impact of new technologies on livestock improvement.
GRADING:Coursework-30% 2 assignments (10%)+ 1 mid-semester test (20%)exam-70%
Final
COURSE OUTLINE:
I. Introduction, History of Animal Breeding & Genetics (Chapters 1 and 2)-Description of various
domestic livestock species, breeds, their origin, productive & adaptive characteristics.
II. Review of Basic Principles of Mendelian Inheritance
1. Cellular aspects of genetics
2. Mendel's laws of Inheritance.
3. Functional aspects of Dominance and Co-dominance (Gene Action).
4. Testing for genetic abnormalities, Pleiotropic effects, variable expressivity,Incomplete
Penetrance.
III. Population Genetics
1. Gene and genotypic frequencies
2. Hardy-Weinberg Law
3. Forces that change gene frequency
a) Mutation
b) Migration
c) Selection
d) Random drift
e) Mating Systems
The importance of changing gene/genotype frequencies in livestock improvement.
IV. Principles of selection-influence of selection, selection response,
1.Basic statistics for animal breeding
a) Mean
b) Variance and standard deviation
c) Regression and correlation
d) Normal distribution, statistical significance and confidence limits.
2. Relationships and inbreeding.
3.Quantitative traits-the quantitaive traits model, phenotypic and genetic variation in animals
(causes and estimation). Genotype value, breeding value, additive genetic value, dominace genetic
value, epistatic genetic value.
4.Genetic parameters- Heritability and repeatability
V.Heredity and environment-Genotype*Environmental interaction,environmental effects, maternal
effects, phenotypic corrrelation,environmental corrrelations, genetic correlations.
Cattle breeds in Zimbabwe
Bos taurus
Bos indicus
-polled/short horned
-hairy and rough, diificult control of external
parasites.
-insignificant humps
The above are the phyical traits, below are
the production traits.
-low disease resistance in Zim.
-Highly selective-demand good quality feed.Not
browsers.
-low meat to bone ratio.
-low fertility in Zim.
Examples of breeds
-Charolais, Sussex, Simmental (Dual purpose).
-Hereford, Limousine, Gelbviah,Belgian blue,
Aberdeen Angus, Blonde Aquatine, Marchigiana
(Beef).
-Composite breeds-Beefmaster, Bonsmara,Santa
Gertrudis, Charbrays, Simbras,Brahford.
-Dairy breeds-Jersey, Red Dane, Holstein,
Aryshire, Guernsey, Dexter, Milk Shorthorn.
Students to have an appreciation of the
physical and production characteristics of
each breed.
-big horned
-smooth shiny coats
-pronounced humps.
-high disease resistance.
-non-selective, good browsers, survive in
drought periods.
- high meat to bone ratio.
- average fertility.
-Brahaman (white/red), Tuli (9 colors), Nguni
(red/back with white spots),Mashona
(red/black), Afrikander(big huge horns),Boran
(like the Brahman but short legs-fron Kenya
prevalent in the Mvurwi area.), Sahiwal (kenya),
Angoni (Zambia very short and very small150kg).
Composite Breeds.
Defn: A breed made up of two / more component breeds and designed to benefit from hybrid vigour
without crossing with other breeds.
Examples,
1. Beefmaster-Brahman*Hereford=F1*Dairy shorthorn
2. Bonsmara-Afrikander*Hereford=F1*Dairy shorthorn.
3. Santa Gertrudis-Brahman*Sussex.
Students to explore other different types of livestock and their breeds, ( sheep, goats, poultry,
pigs).
Review of basic principles Of Mendelian Inheritance.
Key words; Gene, DNA, chromosome, locus, allele, genotype, honozygous, heterozygous,
segregation, germ cell, meiosis, independent assortment, linkage, crossing over, Punnet square,
Mendelian Sampling,Dominance, no dominance, partial dominance, complete dominance,
overdominance, epistasis.
Defination of terms:
Gene-basic unit of inheritance, can also be described as a segment of DNA at a specific location on
a chromosome.
DNA- a complex molecule that forms the genetic code.
Chromosome- a strand of DNA and associated proteins present in the nucleus of every cell of a
living organism.
Locus- the specific location of a gene on a chromosome. Plural loci.They are two genes at each
locus, one partenaland one martenal.
Allele- an alternative form of a gene.
Genotype- a combination of genes at a single locus or a number of locus.
Homozygous Genotype- a one locus genotype consisting of functionally identical genes.
Heterozygous Genotype-a one locus genotype consisting of functionally different genes.
Segregation- the separation of paired genes during germ cell formation.
Germ cell- sex cell (sperm/egg).
Meiosis- process of germ cell formation.P
Punnet Square- a two dimensioal grid used to determine the possibe zygotes obtainable from a
mating.
Mendelian Sampling-the random sampling of parental genes caused by segregation and independent
assortment of genes during germ cell formation and by random selection of gametes in the
formation of the embryo.
Dominance- an interaction of genes at a single locus such that in the heterozygous one allele has
more effect than the other. The one that is masked is said to be recessive.
Complete Dominance- A form of dominace in which the expression of the heterozygote is idebtical
to the expression of the homozygous dominat genotype.
Partial Domiance-A form of dominace in which the expression of the heterozygote is intermediate
to the expression of the homozygous genotypes and closely resembles the homozygous dominant
genotype (which can be recessive as well).
No dominace-A form of dominance in which the expression of the heterozygote s exactly midway
between the expression of the homozygous genotypes.
Overdominance- a form of dominace in which the expression of the heterozygote is outside the
range defined by the expressions of the homozygous genotypes and most closely resembles the
expressions of the dominant genotype.
Epistatis- An interaction among genes at different loci such that the expression of genes at one locus
depends on the alleles present at one or more loci.
Pleiotropy-a genetic situation in which one gene /sing;e allele affects more than one distinct
qualitative/ quantative trait of an individual animal.
Variabile expressivity- similar individuals genetically either show up/ are supressed due to
environmental variations.
Incomplete penetrance-the genotype of a trait is not expresssed in the phenotype at all.
Mendel's Laws of Inheritance.
1. Law of Segreagation-In the formation of a germ cell (meiosis) the two genes at a locus
in the parent cell are separated, only one gene being incorporated into each germ cell.
2. Law of Independent Assortment-genes assort independently during meiosis if all
possible gametes are formed in equal proportions. (A given gene from one locus must
have an equal probability of being present in the same germ cell with either of the two
genes from some other locus).Segregation at one locus does not influence segreagation at
another.
Assupmtions of the law:
1. There is no linkage i.e. The loci dnt occur on the same chromosome if they do then some
genes will occur at a higher frequencies than others.
2. There is no crossing over i.e no exhange of chromosomal segemts between homologs, if it
happens then the genes will be rearranged and there will be differences in their frequencies.
3. Some genes are lethal, some genes are affected by the environment (phenocopies),
Illustrations of Mendel's laws:
Parental Genotype: JJBB
JJBb
JjBb
Possible gametes:
JB
JB
Jb
JB
Jb
jB
jb
Example above show 2 locus genotype (with homozygous and heterozygous genotyepes).
For law 1, each gamete contains only one gene from each locus. NB: the original 2 locus genotype
contains 4 genes altogether, the resultant germ cell contains, as a Rule, germ cells contain half the
number of chromosomes and therefore half the number of genes of normal body cells.
For law 2, the homozygous genotype (JJBB) can produce 1 gamete, , the partial heterozyguos can
produce two and the completely heterozygous can produce 4 gametes. For the latter if all four
gametes occur in equal proportions then the genes have assorted independently unless otherwise
there is linkage and crossing over.
Gamete Selection: The Punnet square
When two individuals mate all possible gametes have an equal chance of contributing to a zygote.
This is a random process.
The Punnet square is a commonly used device for determining the possible zygotes from the mating
of two parental genotypes.
f
JB
Jb
jB
jb
JJBB------1
JJBb----------2
JjBB--------3
JjBb----------4
JB
horizontal: female, vertical male
(punnet square showing the possible gametes from mating two animals of the same 2 locus genotype
JjBb). There are 9 possible unique genotypes.
It is possible therefore to determine the likelihood of any particular offspring genotype, and if
you know the phenotype associated with each genotype (for simply inhertaed traits not
plygenic traits) u can also determine the expected proportions of offspring phenotypes.
A gud example is coat color in Shorthorn cattle ( red, white or roan).The colors are controledd by
the white locus RR=red, Rr= roan, rr=white. Using the Punnet square u can mate 2 roans
(illustrate), the results show three offspring genotypes and phenotypes in the ratio 1:2:1 (red, roan
and white).NB this is an expectation. We cannot control the outcome of matings as there is random
sampling of parental genes and random selection of gametes during the formation of an embryo
(Mendelian Sampling). This leads to genetiv variation through segreagation and recombination.
Number of unique gametes an indv can produce=2 raised to the power n, where n is the number of
loci at which the individual is heterozygous. (some examples- how many gametes can be produced
by an indv, with the foll genotype AaBbCc Ans=8) show working. If the indv (AaBBCcDdee) is
mated to a female with the following genotype AABbCcDdEe, the number of unique zygotes =
3^n* 2^m where n is the number of loci at which both parents are heterozygous and m is the
number of loci at which one parent is heterozygous.
How many unique gametes can the sire produce=Ans (8)
How many unique gametes can the dam produce=Ans (16)
How many unique gametes can be produced from this mating=Ans( 72). show working.
Examples of diffeernt types of Gene Expressions (Gene Action)
Complete domiance- common in a number of simply inherited traits e.g polledness P (polledness) is
dominant over p (horned). Traits have more than one genotype for a phenotype ( Polled cattle can
be PP/Pp. e.g purebred Angus (PP&BB -black) * purebred Hereford ( horned&bb). F1 is
heterozyguos polled black animals. Show Punnet square. Crosing the F1 gen, results in 39polled
(black) and one horned (red)., 3 black horned, 3 polled red.show working.
J'J'
JJ
JJ'
Partial domiance- hyperkalemic periodic paraylsis HYPP in horses. Causes muscle tremors
resulting in heavy shaking and collapse in horses but also leads to heavy muscling in horess
necessary for increased speed in horses hence it has peroetuated coz Breeders unknowingly select
for it.
J'J'
JJ'
JJ
JJ' is more closer to JJ hence J is the dominant allele.
b)
J'J'
JJ'
JJ
in this case J' is the domiant allele as exemplified by the HYPP syndrome in horses. Another
xample is the bull dog (short legs and compavct bodies) condition in Dexter cattle (the trait is
dominant over the normal).Partail domiance can also be used to explain the phenomenon of additive
gene actio and non-additive gene action.This is for the former two alleles may be equal in power so
that the phenotype of the heterozygote is midway between trhe homozygotes.It is used with ref to
quantitative traits;milk production, weaning weight and backfat thickness in pigs.In non-additive
gene action the heterozygot does not lie between the homozygotes.
No dominance- resistance to tuberculosis, res gene (T^r) animals survive 100% of the tym,
susceptible gene animals survive 40% of the tym. Heterozygous gene animals survive 70% of the
tym hence there is no dominace in the locus.
JJ
JJ'
JJ
Overdominance- survivabiltiy of wild rats, both homozygoytes not affected by the poison warfarin,
rats without the resistant gene succumb to warfarin, the warfarin gene displays overdominance.
The phenomenon can be expressed in 2 ways,
a)
b)
J'J'
JJ'
JJ
J'J'
JJ'
JJ
Epistatis (non-additive gene action)
Epistasis affects the kinds and proportion of phenotypes we can expect from matingsin simply
inherited traits.It is also a source of hybrid vigour and inbreeding depression in polygenic traits.
Examples of epistasis, explain, the case of an albino (recessive epistasis) where color is infuence d
at the B-extension locus. Dominace epistasis-coat color in sheep, white dominant.
Apllication of Gene Action in Livestock Improvement
Dominace,Epistasis are implicated in theories which explain hybrid/heterosis.
Additive gene action is exploited by breeders in selection and culling programmes.
Testing for careers with recesive alleles.
This is done so as to eliminate the recessive genes which are usually lethal.3 methods are used.
 Mating the suspect male to the known heterozygos female. If the male is a career, ¼ of the
f1 will be recessive and exhibit the condition.
 Mating a sire to its own daughters.The expected frequency is 7 heterozygos and 1
defective.the test requires 17 progeny to have a 10% chance of success.
 Mating with affected females (homozygos), 1 affected offspring show that the male is a
career.
Pleiotropic Effects
Usually common in traits which are postively corelated e.g. Weaning weight and birth weight they
have genes whic are common. Also they are associated with the lethal effects of the bull dog
condition in Dexter cattle.The product of a single gene will affect more than one trait.
Variable Expressivity
A G*E interaction. e.gs include mulefootedness in pigs (dominant) and cattle (recessive), Porcine
Stress Syndrome (PSS)- affects well muscled pigs (labored breathing which can be fatal).
Incomplete Penetrance
The animal appears normal though it is affected, e.g polydactylty in fowl and humans. The indv has
an extra digit on the foot/finger.The gene for plydactylty is domiant over that of the normal but fails
to express iself in the phenotype.
PRINCIPLES OF POPULATION GENETICS
The goal of animal breeding is to change populations and not individuals therefore we are
concerned about programms that have have the capacity to change gene and genotype frequencies
in populations.
Keywords and concepts: Gene and genotype frequency, H-W law, mutation, migration, selection,
mating systems, inbreeding, outbreeding, relationships,
Defiantio of terms:
Population genetics- the study of factors affecting gene and genotype frequencies in a population.
(usually limited to simply -inherited traits).
Gene/allelic frequency- the relative frequency of a particular allele in a population. How common is
the allele relative to other alleles in a population..
Genotypic frequency- relative frequency of a particular one locus genotype in a population.
Mating System- is a set of rules for mating ( Inbreeding, random mating,assortative mating,
outbreeding).
Relationship-full-sib (full brothers/sisters), half sibs, parent-offspring.
Hardy-Weinberg law- a state of constant gene and genotype frequencies occuring in a population in
the absence of forces that bchange those frequencies.
Mutation- the process that alters DNA to create new alleles.
Migration- the movement of indv into or out of a population.Se
Selection- the process that determines which individuals become parents, how many offspring they
may produce, and how long they remain in the breeding population.
Inbreding-the mating of relatives.
Outbreeding-the mating of unrelated individuals.
Relative frequency-ranges from 0-1.
The frequency of the dominant allele is represented by the lowercase letter p.
The frequency of the recessive allele is represented by the lowercase letter q.
Homozygous dominant=P heterozygous =H homozygous recessive=Q
P=p^2 H=2pq Q=q^2.
Number of p genes=P+1/2H number of q genes= Q+1/2H p+q=1
Calculations
A flock of 100 Andalusians consists of 36 black (BB), 44 blue (Bb) and 20 white (bb).
Calucate the gene and genotype frequencies.
Total number of genes=100*2 genes for each individual i.e 200.
p= 36+1/2(44)=58*2=116 black genes.
q=20+1/2(44)=42*2=84 white genes.
f(p)= 116/200=0.58 f(q)=84/200=0.42
f(P)=36/100=0.36 F(Q)= 20/100=0.2 f(H)= 44/100=0.44
NB: P+Q+H=1
FACTORS THAT AFFECT GENE AND GENOTYPE FREQUENCIES IN A POPULATION.
These apply to both quantative (polygenic) and qualitative traits (simply-inherited).
Examples of Qualitative traits-affected by few loci.
 Polledness and coat color.
Examples of Quantative traits-affected by many loci.
 Growth rate, carcasse composition, milk yield, weaning weight, backfat thickness, egg
production, feed efficiency, yearling weight, fat percentage , protein yield.
1.Selection- Selection increases the gene frequency (immediate action-genotype fequencies
take time )of favorable alleles in a population.We select for animals with a high breeding value (
better sets of genes) so that the next gen may have an improved breeding value. Show this on a
diagram.Read more about selectio-natural versus artifial selection ( replacement selection, culling,
phenotypic selection-for those traits that are highly heritable, pedigree and progeny selection,
collateral selection-use of contemporaries, performance testing-use of sire summaries).
2. Mating Systems ( Random mating, assortative mating, outbreeding and inbreeding-explain
this)- this has an effect when combined with selection.The more common use of mating
systems is to change genotypic frequencies by increasing the number of homozygous
/heterozygous gene combinations.Gene frequencies may/ may not change as a result.
Breeders use mating systems to achieve the following-- a) to produce offspring with extreme
breeding value to increase rate of genetic change, b) to make use of complementarity c) to
obtain hybrid vigour.
We have two catergories for the purposes of this discussion: Inbreeding and Oubreeding.
 Inbreeding – increases the frequency of homozygous genotypes.
Types of relationships: Full sib, half sib, common ancestor (pedigree). Show relationship diagram
and explain inbreeding.Inbreeding can be used to create the breeds within species or lines within
breeds that when crossed produce hybrid vigour.
 Oubreeding (Crossbreeding)- increases hybrid vigour by ncreasing heterozygosity.Example
there are two unrelated populations.
P1=0.8 , q1=0.2 & p2=0.1 q2=0.9 the differences in the frequencies
reveal that indeed the populations are unrelated.
Crosing the two populations (Bb* Bb) will result in F1, BB= 0.08 Bb=0.74 bb =0.18 (from
punnet square). NB: The increase in heterozygosity and the decrease in homozygousity.
f(p)=( P+ 1/2H)*2 divided by the total number of genes= 0.45 f(q)=0.55.
Mating F1, will result in BB=0.2025 Bb=0.495 bb=0.3025 NB; An increase in homozygosity as
this is now a form of inbreeding. However on calcultion of the gene frequencies, they dnt change
p=0.45 and q=0.55. i.e pF2=Pf2+1/2Hf2 =0.45 and qf2=Qf2+1/2Hf2=0.55. The chi-square
goodnes of fit test is used to test whether a population is in H-W equilbrium.
This phenomenon is known as the H-W law of equilbrium (1908)The frequencies will only change
under conditions of selection, mutation and migration.
Futher Assumptions of the law.
1. Large populations.
2. Migrations can be negligible.
3. Random mating-only one generation is needed to reach equilibrium.
4. There is no selection.
5. There is no mutation.
6. There is normal gene segregation.
7. There is equal fertility of parents anf equal ferilising capacity of gametes and reproduction is
sexual
8. There is equal viability and equal gene frequencies in male and female parents.
9. The generations are non overlapping.
10. The gene frequency is the same in parents and offspring.
If gene frequencies are the sane in both sexes a population reaches H-W after one generation, if not
H-W is reached after two generations.With sex-linked loci this may take several generations. Why?
Example- In a population of 1000 Hampshire pigs 910 are belted and 90 are solid colored. What is
the frequency of the genotypes.
Ans F(recesive)=90/1000 Q=q^2 Q= 0.09 hence q=square root of Q= 0.3 and therefore p=0.7
p^2=P P=0.49 H=2pq= 0.42
number of heterozygosites= 0.42*1000=420 numbr of homozygosites dominant=0.49*1000=490.
Note that this is a case of coimplete domiance.
3) Mutation- explain how it changes genotype frequencies.Use examples.
-Mutatios are very slow.
-Mutations may occur in any direction, the major role is to present new genetic
material(desirable/undesirable) into the population.Selection then increases the frequency of
the desirable mutation e.g polledness.
-Mutation has a minimum impact on quantative traits aand is not useful in domestic animals.
4) Migrations-use examples to explain.(imports of exotic breeds).
This can be a rapid way of changing gene frequency, the rate of change will howver depend on
the following.
 Frequencies of the gene (s) in the immigrants must be high i.e. The differences btwn imm
and natives.
 The number of immigrants introduced in2 the native population.
5) Random Genetic Drift (Effect of chance)
This is a chance change in gene frequency outside any influence, it is most likely in small
popualtions.This is largely due to chance sampling of parents which affects the offspring.e.g the
appearance of horned cattle in a herd selected for polledness.horned Holstein cattle in Zim.
The importance of changing gene and genotype frequencies in livestock
1.
Selection increases gene frequency and in turn incrreases performance.
2.
Changing gene frequency is the only way to make a long term improvement e.g im milk
production, eggs, higher grwoth rates.
3.
Changing gene frequency is a permanent change buit we cannot change gene action.
4.
Long term change in gene action is the central issue in selection.
5.
Mating systems can change genotypic frequencies but one can lose wht he/she has gained.