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Lecture 7: Inbreeding and Crossbreeding

Lecture 7: Inbreeding and Crossbreeding. Inbreeding. Inbreeding = mating of related individuals Often results in a change in the mean of a trait Inbreeding is intentionally practiced to: create genetic uniformity of laboratory stocks produce stocks for crossing (animal and plant breeding)

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Lecture 7: Inbreeding and Crossbreeding

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  1. Lecture 7:Inbreeding and Crossbreeding

  2. Inbreeding • Inbreeding = mating of related individuals • Often results in a change in the mean of a trait • Inbreeding is intentionally practiced to: • create genetic uniformity of laboratory stocks • produce stocks for crossing (animal and plant breeding) • Inbreeding is unintentionally generated: • by keeping small populations (such as is found at zoos) • during selection

  3. Genotype frequencies under inbreeding • The inbreeding coefficient, F • F = Prob(the two alleles within an individual are IBD) -- identical by descent • Hence, with probability F both alleles in an individual are identical, and hence a homozygote • With probability 1-F, the alleles are combined at random

  4. Random mating Alleles IBD

  5. Genotypes A1A1 A1A2 A2A2 0 a+d 2a freq(A1) = p, freq(A2) = q Changes in the mean under inbreeding Using the genotypic frequencies under inbreeding, the population mean mF under a level of inbreeding F is related to the mean m0 under random mating by mF = m0 - 2Fpqd

  6. Here B is the reduction in mean under complete inbreeding (F=1) , where For k loci, the change in mean is • There will be a change of mean value dominance is present (d not zero) • For a single locus, if d > 0, inbreeding will decrease the mean value of the trait. If d < 0, inbreeding will increase the mean • For multiple loci, a decrease (inbreeding depression) requires directional dominance --- dominance effects di tending to be positive. • The magnitude of the change of mean on inbreeding depends on gene frequency, and is greatest when p = q = 0.5

  7. Break for Problem 1

  8. Inbred Outbred Inbreeding Depression and Fitness traits

  9. Define ID = 1-mF/m0 = 1-(m0-B)/m0 = B/m0

  10. Why do traits associated with fitness show inbreeding depression? • Two competing hypotheses: • Overdominance Hypothesis: Genetic variance for fitness is caused by loci at which heterozygotes are more fit than both homozygotes. Inbreeding decreases the frequency of heterozygotes, increases the frequency of homozygotes, so fitness is reduced. • Dominance Hypothesis: Genetic variance for fitness is caused by rare deleterious alleles that are recessive or partly recessive; such alleles persist in populations because of recurrent mutation. Most copies of deleterious alleles in the base population are in heterozygotes. Inbreeding increases the frequency of homozygotes for deleterious alleles, so fitness is reduced.

  11. mF m0 - B F m0 0 1 In many cases, lines cannot be completely inbred due to either time constraints and/or because in many species lines near complete inbreeding are nonviable Estimating B In such cases, estimate B from the regression of mF on F, mF = m0 - BF If epistasis is present, this regression is non-linear, with CkFk for k-th order epistasis

  12. Minimizing the Rate of Inbreeding • Avoid mating of relatives • Maximum effective population size Ne • Ne maximized with equal representation • Contribution (number of sibs) from each parent as equal as possible • Sex ratio as close to 1:1 as possible • When sex ratio skewed (r dams/sires ),every male should contribute (exactly) one son and r daughters, while every female should leave one daughter and also with probability 1/r contribute a son

  13. F = 1/4 F = 0 F = 1 F = 3/4 Variance Changes Under Inbreeding Inbreeding reduces variation within each population Inbreeding increases the variation between populations (i.e., variation in the means of the populations)

  14. Variance Changes Under Inbreeding

  15. Line Crosses: Heterosis When inbred lines are crossed, the progeny show an increase in mean for characters that previously suffered a reduction from inbreeding. This increase in the mean over the average value of the parents is called hybrid vigor or heterosis A cross is said to show heterosis if H > 0, so that the F1 mean is average than the average of both parents.

  16. The expected amount of heterosis becomes Expected levels of heterosis If pi denotes the frequency of Qi in line 1, let pi + di denote the frequency of Qi in line 2. • Heterosis depends on dominance: d = 0 = no inbreeding depression and no. heterosis as with inbreeding depression, directional dominance is required for heterosis. • H is proportional to the square of the difference in gene frequency Between populations. H is greatest when alleles are fixed in one population and lost in the other (so that | di| = 1). H = 0 if d = 0. • H is specific to each particular cross. H must be determined empirically, since we do not know the relevant loci nor their gene frequencies.

  17. Heterosis declines in the F2 In the F1, all offspring are heterozygotes. In the F2, Random mating has occurred, reducing the frequency of heterozygotes. As a result, there is a reduction of the amount of heterosis in the F2 relative to the F1, Since random mating occurs in the F2 and subsequent generations, the level of heterosis stays at the F2 level.

  18. Agricultural importance of heterosis Crosses often show high-parent heterosis, wherein the F1 not only beats the average of the two parents (mid-parent heterosis), it exceeds the best parent.

  19. Break for Problem 2

  20. Crossbreeding in Animals Individual heterosis: Enhanced performance in a hybrid individual Maternal heterosis: Enhanced maternal performance, e.g., increased litter size and higher survival rates of offspring Maternal heterosis is often comparable, and can be greater than, individual heterosis

  21. Maternal and individual heterosis effects can be combined by using crossbred (hybrid) dams. For example, for total weight of lambs rear per mated ewe has an 18% individual heterotic advantage in a crossbred offspring and an addition 18% advantage (from maternal heterosis) when crossbred ewes are used in place of purebred ewes. This combining of maternal and individual heterotic effects is one reason why three-way crosses are common in animal breeding, generally by crossing a male from line A with a hybrid female (from a B x C cross). This strategy exploits maternal heterosis in the female, with the sire line often chosen for its contribution to some production trait.

  22. Synthetics and Rotational Crossbreeding To maximally exploit heterosis, we ideally would use only F1 individuals, as the heterotic advantage decreases in the F2 Problem: In (most) large farm animals, the number of offspring is on order of the number of dams. Thus, to produce n triple cross hybrid offspring requires on the order of 2n dams (the granddam to produce the B x C dam, and the dam herself in the A X (B X C) cross).

  23. ( ) Average of the founding lines Mean of the F1 from all pairwise crosses One partial solution around this problem: Synthetics: n parental lines are chosen and a random-mating population formed by first making all n(n-1)/2 pairwise intercrosses between the lines This is equivalent to The larger n (number of founding lines), smaller decrease in H

  24. cross dam back to A sire dam dam cross dam back to B sire cross dam back to A sire dam Second Solution: Rotational Crossbreeding A x B (A x B)x A ((A x B)x A)x B And so on ….

  25. Key: Heterosis advantage divided by 3, not by 2 as in F2 1/7th of heterosis is lost Mean of all six pair-wise crosses 1/15 of heterosis is lost Mean of crosses of nonadjacent lines The expected mean value under a two-way rotation: The expected mean value under a three-way rotation: Under a 4-way rotation, the order matters:

  26. Note that F1 > R > S > P For a 2-way rotation: For weaning weight For the 2-breed synthetic,

  27. Break for Problem 3

  28. Grandmaternal genetic effect (BV) Individual genetic effect (BV) Maternal genetic effect (BV) Estimating the Amount of Heterosis in Maternal Effects Contributions to mean value of line A

  29. Maternal and grandmaternal effects from the B mothers Contribution from (individual) heterosis Individual genetic value is the average of both parental lines Individual genetic and heterotic effects as in A x B cross Maternal and grandmaternal genetic effects for B line Consider the offspring of an A sire and a B dam Now consider the offspring of an B sire and a A dam

  30. Likewise, an estimate of maternal/grandmaternal effects is given by ( ) ( ) Hence, an estimate of individual heteroic effects is How about estimation of maternal heteroic effects?

  31. Average individual genetic value (average of the line BV’s) Maternal genetic heteroic effect New individual heterosis of C x AB cross Genetic maternal effect (average of maternal BV for both lines) Grandmaternal genetic effect “Recombinational loss” --- decay of the F1 heterosis in The F2 . The mean of offspring from a sire in line C crossed to a dam from a A X B cross (B = granddam, AB = dam) One estimate (confounded) of maternal heterosis

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