Resemblance Between Relatives

Objectives
• Utilize population genetic concepts as a foundation to understand
coefficients of inbreeding, parentage and relationship.
• Calculate coefficients of parentage and inbreeding.
Introduction – explanation
• Plant breeding populations, by definition, employ methods
that force populations into states of disequilibrium.
• Use of small numbers of parents – drift
• They select the parents that will be used in matings, thus selection,
linkage and pleiotropy affect the population structure.
• Introduction of new lines from external breeding projects
Introduction – Background

• Herein inbreeding and parentage will be

introduced as deviations (disequilibrium)
from Hardy Weinberg Equilibrium.
• In other words the calculation of all of
these measures are based on a reference
Sewall Wright Gustave Malécot
population and the reference population
Coefficients of Identity by descent must be defined or else the calculated
relationships and
inbreeding
values have no meaning.
The Concept of Inbreeding and Relationship
• Inbreeding results when two related indivudals are mated.

• The level of inbreeding is therefore defined relative to some base

population in which all the individuals are assumed unrelated.

• So far we have not made any distinction among alleles according to thier
origion.

• The concept of inbreeding and relationship are based on the origin of

alleles rather than on the physical state of alleles.
• Remember the concept of identity by discent and identity state from chapter 02
The Concept of Inbreeding and Relationship
• Suppose
  an individual (I-1 in Fig 1) is
mated to unrelated individuals that carry I-1: A1A1
the allele.
• Assume that the two alleles in I-1 are not
identical by descent.
• Individuals II-1 and II-2 receive copies of
the same allele found in I-1, whereas II-3 II-1: A1A2 II-2: A1A2 II-3: A1A2
receives a copy of the other allele found in
I-1.
• The copies of the allele in II-1 and II-2 are
not only alike in state but are also III-1: A1A1 III-2: A1A1
identical by descent.
• In contrast, the copy of the allele found in
Figure 1. Identity by descent of alleles
II-3 is alike in state, but not identical by Source: R. Bernardo 2010
descent, with the copies of the allele in II-1
and II-2.
Coefficient of Inbreeding
Coefficient of Inbreeding
•  The coefficient of inbreeding, denoted by F, can be defined in
two ways:
1. The probability that, at a single locus, the two alleles in the
same individual are identical by descent (IBD).
• indicates no inbreeding, whereas indicates complete inbreeding.
• Coefficient of inbreeding measures IBD within an individual,
• Coefficeint of coancestry measures IBD either within an individual (i.e.,
fxx) or between two individuals (i.e., fxy).
2. The increase in homozygosity due to IBD.
• Alleles that are IBD within an individual are always in homozygous form.
• The F coefficient is equal to the proportion by which heterozygosity is
reduced upon inbreeding relative to a population in Hardy-Weinburg
equilibrium.
Coefficient of Inbreeding - Definition
• Let’s
  consider a random mating diploid population consisting of N
individuals: Because there are 2N gametes the probability that two
mating gametes are identical by descent is Therefore,
• The remaining proportion of zygotes carry genes that are independent in
origin from generation 1.
• Therefore the probability of identical homozygotes in generation 2 is:

• Where F1 and F2 are the inbreeding coefficients of generations 1 and 2. The

same arguments apply to future generations, so we can write the
recurrence equation:

• The inbreeding of any generation is composed of two components:

1. New inbreeding, which arises from self-fertilization and
2. the “old” that was already there.
General Principle of Selfing
• Rather
  than considering a random mating population, let’s consider a population
that is experiencing a systematic inbreeding process.
• In this case F refers to the proportionate reduction in heterozygosity (relative to a
population that is in HWE) through inbreeding processes.
• For example, consider an population with genotype frequencies of
37.5% A1A1;
• 25% A1A1; Selfing F2 leads to F3 25% A1A2; and
37.5% A2A2
• 50% of A1A2; and
• 25% of A2A2.
• The coefficient of inbreeding among F3 plants is equal to
• The increase in the F coefficient is halved upon each additional generation of
selfing. In a cross between inbreds, the coefficient of inbreeding among indivual
plants in the Fn generation (n >1) is

• F is the proportionate decrease in heterozygosity due to an inbreeding process

General Principle of selfing…
• 
• This equation assumes that the population is non-inbred, which is true if the two
inbreds crossed to form the are unrelated (i.e., ).

• If the relationship between parents X and Y is considered (i.e., ), the coefficient of

inbreeding in the generation of selfing increases to

• The above equation indicates that, assumptions aside, the actual level of inbreeding is higher with
related parents than with unrelated parents – compare the time taken to get fixed inbred lines from
pops developed from related and unrelated parents.
Coefficient of Parentage
Coefficient of coancestry (or parentage)
•  The probability, that two alleles are identical by descent can be
deduced from
1. System of mating or
2. Pedigree structure.
• The coefficient of coancestry (also known as the coefficient of
parentage) between individuals X and Y is the probability that, at a
single locus, a random allele from X and a random allele from Y are
identical by descent.
• A coefficient of coancestary of indicates no relationship.
• A coefficient of coancestary of at a given locus indicates that the two
individuals are homozygous for copies of the same allele found in an ancestor.
• A coefficient of coancestry of across all loci indicates that the two individuals
are fully inbred and genetically identical – What is the implication for hybrid
breeding?
Identity by Descent in pedigree
• 
• The definition of F as the relative loss of heterozygosity is most
meaningful if the population has a well-defined family structure.

• But when pedigrees are irregular, relatedness and inbreeding are

easier to intrepret when defined as the probability of identity by
descent.

• First let us formulate in mathematical terms and consider the

relationship between and F.

• Then we will illustrate the calcuation of from general pedigree

Probability of identity by descent
••  Suppose the alleles in individual :
• Alleles in X are arbitrarily designated as and ,

• Alleles in Y are arbitrarily designated as and (Fig).

• These designations have no bearing on the physical state of the

actual alleles:
• and both represent allele if X has the genotype, where as

• represents allele A1 and represents allele (or vice versa) if X has the
genotype.

• An allele, denoted by x, is chosen at random from individual X. An

allele, denoted by y, is likewise chosen at random from individual Y.

• The coefficient of coancestry (parentage) between individuals X

and Y is the probability that alleles x and y are identical by descent:
where the sign indicates identity by descent.
Probability of identity by descent
•  Allele x and y become identical by descent through four events.
1. Allele is chosen as x; allele is chosen as y; and alleles and are identical by
descent.
2. Allele is chosen as x; allele is chosen as y; and alleles and are identical by
descent.
3. Allele is chosen as x; allele is chosen as y; and alleles and are identical by
descent.
4. Allele is chosen as x; allele is chosen as y; and alleles and are identical by
descent.
• The probability that alleles x and y are identical by descent is obtained
by summing up the probabilities of these four events:

• In diploid, the probabilities are all equal to ½. The coefficient of coancestry

between X and Y therefore reduces to
Probability of identity by descent
•  How is an individual related to itself?
• Suppose individual X has a coefficient of inbreeding of . The coefficient of
coancestary of X with itself is obtained by substituting
• for and
• for in the equation on the previous page

• The coefficient of coancestry of an individual with itself is therefore

• , if the individual is not inbred
• , if the individual is fully inbred
The relation of F of offspring & fxy parents
 •
Now suppose X and Y are the parents of individual Z in Fig. The
alleles in Z are arbitrarily designated as and .
• For convenience, we assume that allele is inherited from X whereas
allele is inherited from Y. The coefficient of inbreeding of Z is
• 

𝒀
𝑭𝒁= 𝒇 𝑿
• The F coefficient of an offspring is equal to the
between the parents.

 
Calculation of coancestry from pedigree
  • There are two ways of calculating from pedigrees.
1. The first method is based on the relationships
among the four parents of two individuals.
• Suppose individual A and B are the parents of X, whereas C
and D are the parents of Y (Fig). Alleles in X and Y become
identical by descent through four events:
i. Alleles in A and C are identical by descent, and the
identical alleles are transmitted from A to X and from
C to Y.
ii. Alleles in A and D are identical by descent, and the
identical alleles are transmittd from A to X and from
D to Y.
iii. Alleles in B and C are identical by descent, and the
identical alleles are transmitted from B to X and from
C to Y.
iv. Alleles in B and D are identical by descent, and the
identical alleles are transmitted from B to X and from
D to Y.
Calculation of coancestry from pedigree…
•  The coefficient of coancestry between X and Y is obtained by summing
up the probabilities of these four events. The probability that random
alleles in A and C are identical by descent is
• The probability that a given allele is transmitted from A to X is ½; the
probability that a give allele is transmitted from C to Y is likewise ½.
• The probability of each of the four events is then equal to the respective
coefficient of coancestry multiplied by ¼. Therefore,

• In other words, the coefficient of coancestry between two progeny is

equal to the average of the coefficients of coancestry between their
parents.
Calculation of coancestry from pedigree…
•   The second method for calculating is based on the
2.
relationship between an individual and another
individual‘s parents.
• Suppose individual A and B are the parents of X, whereas Y is
any individual that is not a descendant of X (Fig).
• Alleles in X and Y become identical by descent through two
events:
i. An allele in A is identical by descent to an allele in Y, and is
transmitted from A to X
ii. An allele in B is identical by descent to an allele in Y, and is
transmitted from B to X.
• The coefficient of coancestry between X and Y is obtained
by summing up the probabilities of these two events:

• The coefficient of coancestry is therefore equal to the

average coefficient of coancestry between an individual
and the other individual‘s parents.
• An important condition is that Y is not a descendant of X.
Calculation of coancestry from pedigree…
•  Consider individual Z, which is a
descendant of X. The coefficient of
coancestry between X and Z is not equal
to the average coefficient of coancestry
between Z and the parents of X:

• Instead, is equal to the average coefficient

of coancestry between X and the parents
Z:
Coancestry between a parent and ist offspring
•  The between a parent and its offspring is .
• If X is non inbred and X and Y are unrelated, the
coefficient of coancestry between a parent and its
offspring (PO) is

• With fully inbred parents

• The coefficient of coancestry between either of

two unrelated inbreds and their progeny is
therefore
Coancestry between full sibs
•• The
  between full sibs is .
• Individuals X and Y are full sibs if they both have the same parents, A and B. By substituting
1. A for C and
2. B for D in the equation abov, the between full sibs (FS) is

• The value of is if the parents are non-inbred ( and = 0) and unrelated ( =0).
• With fully inbred parents ( and = 1), the coefficient of coancestry between full sibs is

• This coefficient is equal to ½ if inbreds A and B are unrelated, and it is greater than ½ if they
are related.
Coancestry between half sibs
••  The between half sibs is .

• Individuals X and Y are half sibs (HS) if they have one common parents,
e.g., A and B are the parents of X, whereas A and D are the parents of Y.
By substituting A for C in our our equation, the between halfsibs is

• If the three parents are unrelated, the above equation reduces to

• This coefficient is equal to 1/8 if A is not inbred and ¼ if A is fully

inbred.
Summary
• Write three new things you have learned from this session, and
explain how some of these are related to your work