Breeding Values and Inbreeding. Breeding Values and Inbreeding

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1 Breeding Values and Inbreeding

2 Genotypic Values For the bi-allelic single locus case, we previously defined the mean genotypic (or equivalently the mean phenotypic values) to be a if genotype is A 2 A 2 G ij = d if genotype is A 1 A 2 a if genotype is A 1 A 1 and µ G = a(p q) + d(2pq). The additive genetic values are G A ij = µ G + 2α 2 if genotype is A 2 A 2 µ G + α 1 + α 2 if genotype is A 1 A 2 µ G + 2α 1 if genotype is A 1 A 1 where the additive effects α i were defined by Fisher to be the least-squares regression coefficients of genotypic values on allele counts at a locus.

3 Breeding Values For the bi-allelic case, we showed that additive effects are α 1 = q[a + d(q p)] and α 2 = p[a + d(q p)], where p and q be the allele frequencies of the A 1 and A 2 allele, respectively, in the population. The usefulness of the concept of additive effects arises from the fact that parents pass on their alleles and not their genotypes to their progeny, as previously mentioned. The value of an individual, as judged the the mean value of the individual s progeny, is called the individuals breeding value. The breeding value for an individual at a locus is defined to be the sum of the additive effects of the alleles at the locus. For a single locus trait with two alleles, the breeding values are 2α 1 for homozygous genotype A 1 A 1, α 1 + α 2 for heterozygous genotype A 1 A 2, and 2α 2 for homozygotes genotype A 2 A 2.

4 Breeding Values Consider the expected genotypic values of progeny produced by the parental genotypes. If an individual with the A 1 A 1 genotype is mated to a number of individuals taken at random from the population, what would be the mean genotypic value of the progeny? What is the deviation of the expected progeny mean from the population mean? Similarly, what is the mean genotypic progeny values and the deviation of the expected progeny values from the population mean for individuals with the A 1 A 2 and A 2 A 2 genotypes?

5 Mean Progeny Breeding Values E[progeny genotypic value one parent is A 1 A 1 ] = a P(progeny has genotype A 1 A 1 one parent is A 1 A 1 ) +d P(progeny has genotype A 1 A 2 one parent is A 1 A 1 ) = pa+qd The mean deviation of the progeny from the population mean is pa + qd µ G = pa + qd [a(p q) + 2dpq] = q[a + d(1 2p)] = q[a + d(q p)] = α 1 A parent with a breeding value of 2α 1 has progeny with an average deviation from the population mean equal to α 1!

6 Mean Progeny Breeding Values E[progeny genotypic value one parent is A 2 A 2 ] a P(progeny has genotype A 2 A 2 one parent is A 2 A 2 ) +d P(progeny has genotype A 1 A 2 one parent is A 2 A 2 ) = qa + pd The mean deviation of the progeny from the population mean is qa + pd µ G = qa + pd [a(p q) + 2dpq] = p[a + d(1 2p)] = p[a + d(q p)] = α 2 So a parent with a breeding value of 2α 2 has progeny with an average deviation from the population mean equal to α 2!

7 Mean Progeny Breeding Values E[progeny genotypic value one parent is A 1 A 2 ] a P(progeny has genotype A 1 A 1 one parent is A 1 A 2 ) +d P(progeny has genotype A 1 A 2 one parent is A 1 A 2 ) a P(progeny has genotype A 2 A 2 one parent is A 1 A 2 ) = pa 2 + d 2 qa 2 The mean deviation of the progeny from the population mean is pa 2 + d 2 qa 2 µ G = 1 2 (pa + qd µ G ) ( qa + pd µ G ) = α 1 + α 2 2 So a parent with a breeding value of α 1 + α 2 has progeny with average deviation from population mean equal to α 1+α 2 2!

8 Mean Progeny Breeding Values So, when mating is random, the breeding value of a genotype for an individual is equivalent to twice the expected deviation if its offspring mean phenotype from the population mean. The deviation is multiplied by two since only of one the two parental genes is passed on to each offspring (which is why the average allelic effect is so important!) Thus, we can estimate the breeding value of an individual by mating it to randomly chosen individuals from the population and taking twice the deviation of its offspring mean from the population mean These types of experiments are often performed in animal genetics

9 Kinship Coefficients and Inbreeding Two alleles that are inherited copies of a common ancestral allele are said to be identical by descent (IBD). The term IBD is generally used for referring to recent, rather than ancient, common ancestry. Two individuals that have IBD alleles are said to be related.

10 Kinship Coefficients and Inbreeding If two parents are related, then the probability that two parents transmit IBD alleles to a child is the inbreeding coefficient F of the child. The probability that an allele taken at random from one individual is IBD to an allele taken at random from another individual is the kinship coefficient or coancestry coefficient, φ of those two individuals. The inbreeding coefficient of an individual is the coancestry of its parents. What is the inbreeding coefficient for an offspring that is a product of a mating between siblings?

11 Genotype Frequencies for Inbred Individuals Consider once again a bi-allelic genetic marker with alleles A 1 and A 2. Let p be the frequency of allele A 1 and q = 1 p the frequency of allele A 2 in the population. Consider an individual with inbreeding coefficient F. What are the genotype frequencies for this individual at the marker? Genotype A 1 A 1 A 1 A 2 A 2 A 2 Frequency

12 Genotype Frequencies for Inbred Individuals We have that P(A 1 A 1 F ) = P(A 1 A 1 and alleles are IBD F ) +P(A 1 A 1 and alleles are not IBD F ) = P(A 1 A 1 alleles are IBD, F )P(alleles are IBD F ) +P(A 1 A 1 alleles are not IBD, F )P(alleles are not IBD F ) = pf + p 2 (1 F ) = p 2 + Fp(1 p)

13 Generalized Hardy-Weinberg Deviations The table below gives genotype frequencies at a marker for an inbred individual with inbreeding coefficient F Genotype A 1 A 1 A 1 A 2 A 2 A 2 Frequency p 2 + Fp(1 p) 2pq(1 F ) q 2 + Fq(1 q) where q = 1 p F = 0 corresponds to outbred populations and with genotype frequencies in HWE. The parameters p and F are sufficient to describe the genotype frequencies at a single locus for an inbreed individual.

14 General Expression for Quantitative Traits for Multi-allelic Locus We will now focus on the mean genetic values in populations with inbreeding. For an arbitrary number of alleles at a locus, the genetic value for genotype A i A j can be written as G ij = µ G + α i + α j + δ ij and values assigned to the coefficients are: µ G = i p i p j G ij = G.. j α i = j p j G ij µ G = G i. G.. δ ij = G ij µ G α i α j = G ij G i. G j. + G.. These imply that i p iα i = 0 and i p iδ ij = 0

15 Mean Trait Value in Inbred Populations Finding the first two moments (the means and variances) for quantitative trait values proceeds by tracing the relevant genes back to genes in a reference (or founder) population. For a single-locus trait this requires the inbreeding coefficient. For a random member of a population inbred to an extent F relative to the reference population, the genotype frequencies are P ii = p 2 i + Fp i (1 p i ) P ij = 2p i p j (1 F )

16 Mean Trait Value in Inbred Populations The expected trait value for an individual with inbreeding coefficient F is µ GF = i P ij (µ G + α i + α j + δ ij ) j = i [p 2 i + Fp i (1 p i )](µ G + 2α i + δ ii ) + i j [p i p j (1 F )](µ G + α i + α j + δ ij ) = i [p 2 i (1 F ) + Fp i ](µ G + 2α i + δ ii ) + [p i p j (1 F )](µ G + α i + α j + δ ij ) i j

17 Mean Trait Value in Inbred Populations = F p i (µ G + 2α i + δ ii ) i +(1 F ) p i p j (µ G + α i + α j + δ ij ) i j = F (µ G + p i δ ii ) + (1 F )(µ G ) i = µ G + FH where H = i p iδ ii and the δ ij terms are the same as in the non-inbreeding case. So the mean trait value in an inbred population is µ GF = µ G + FH, and µ GF mean changes with the degree of inbreeding in the population and the degree of dominance for the trait.

18 Inbreeding Depression Inbred individuals are almost always less fit than progeny of nonrelatives The decline in the mean phenotype with increasing homozygosity within populations is known as inbreeding depression Next week we will obtain genotypic variance components in populations with inbreeding.

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