Lecture 19. Long Term Selection: Topics Selection limits. Avoidance of inbreeding New Mutations

Transcription

1 Lecture 19 Long Term Selection: Topics Selection limits Avoidance of inbreeding New Mutations 1

2 Roberson (1960) Limits of Selection For a single gene selective advantage s, the chance of fixation is a function only of Ns, where N is the effective population size. In artificial selection based on the individual measurements, the expected limit is a function of Ni i is the selection intensity Lecture 19 2

3 Verification Lecture 19 3

4 Verification Lecture 19 4

5 Effect of Selection Intensity on N, the effective population size As Selection Intensity Increases Number of breeders decreases For the same total number of breeders Effective population size is less for Randomly Selected parents than directionally selected If the heritability is greater than 0, then relatives are more similar for that trait than non-relatives Directional Selection tends to select relatives because they have similar performance Lecture 19 5

6 Roberson (1960) Limits of Selection In a selection program of individual selection of equal intensity in both sexes, the furthest limit should be attained when half the population is selected each generation. This is especially true if additive variance predominates and within family selection is utilized, i.e. the best male and female in each family is chosen. In which case the limit may be increased by almost 50% above that of simple mass selection saving the best 50% (Dempfle, 1975) Lecture 19 6

7 Selection Limits as a function of Percent Saved Gen N=2048 u=.0001 Lecture 19 7

8 Selection Limits as a function of Percent Saved Generations N=2048 u=.0001 N=2048 u=.0001 Lecture 19 8

9 Selection Limits as a function of Percent Saved Generations N=2048 u=.0001 N=2048 u=.0001 Lecture 19 9

10 Roberson (1960) Limits of Selection The use of information on relatives is always a sacrifice on the eventual limit for the sake of immediate gain in the early generation. The loss may be small in large populations Lecture 19 10

11 Experimental Evidence Theoretical Advantages of Index (family) Selection Over Mass Selection Not Attained Kinney Et Al., 1970 Doolittle, Et Al Garwood and Lowe, 1979; Garwood Et Al., 1980 Wilson, 1974; Campo and Tagarro, 1977 Perez and Toro 1992 Lecture 19 11

12 Experimental Results (Wilson, 1974) I=individual I=individual Mass Selection Mass Selection Lecture 19 12

13 Experimental Results (Wilson, 1974) I=individual Mass Selection Lecture 19 13

14 Wilson (1974) Concluded There Is No Obvious Explanation for the Discrepancies That Exist Between These Experimental Results and the Theoretical Expectations. 14

15 Possible Explanation Inbreeding 15

16 80 70 BLUP Selection Additive Effects 60 RESPONSE % 20% 50% GENERATIONS INT 5 7 Lecture

17 60 50 BLUP Selection Dominance Effects RESPONSE % 20 5% % GENERATIONS Lecture INT

18 Selection Intensity and Inbreeding with BLUP % INBREEDING % % GENERATIONS INT Lecture 19 18

19 Inbreeding Impacts Random Genetic Drift With Additive Systems Inbreeding Causes Loss of Favorable Alleles Lowers Selection Limits Effects Seen in the Long Term Directional Dominance Causes a Further Depression in The Mean Due to Loss of Heterozygosity Effect Seen in the Short Term Lecture 19 19

20 Comparison Between BLUP and MASS Same Selection Intensity 20

21 80 70 Additive Effects 60 BLUP 50 MASS 20% RESPONSE % 50% GENERATIONS Lecture LINE

22 60 50 BLUP Dominance Effects 20% 40 MASS RESPONSE % 5% % GENERATIONS Lecture LINE

23 Experimental Results (Wilson, 1974) Lecture 19 23

24 Avoid Inbreeding Selection Program Maximize Selection Intensity Minimize Inbreeding Cannot do both Optimal Breeding Program Depends on Time Horizon Short term-maximize selection intensity Long Term-select upper 50% and equal number of males and females Within Family Selection Lecture 19 24

25 Methods to Control Inbreeding and Maximize Response: Fixed Generations Meuwissen (1997) Maximizing the response of selection with a predefined rate of inbreeding J ANIM SCI 75 (4): maximizes genetic gain constraining their average coancestry to a predefined value. At equal rates of inbreeding, genetic gains were 21 to 60% greater than that with selection just for BLUP-EBV Lecture 19 25

26 Methods to Control Inbreeding and Maximize Response: Overlapping Generations Meuwissen and Sonesson AK (1998). Maximizing the response of selection with a predefined rate of inbreeding: Overlapping generations. J ANIM SCI. 76 : dynamic selection rule developed maximizes selection response in populations with overlapping generations. At the same rates of inbreeding, the dynamic selection rule obtained up to 44% more genetic gain than direct selection for BLUP breeding values. advantage of the dynamic rule over pure BLUP selection decreased with increasing population sizes Lecture 19 26

27 Long Term Selection Limits Causes New Mutations 27

28 Case Study Tribolium castaneum:the red flour beetle Lecture 19 28

29 Tribolium Life History Lecture 19 29

30 Large Lines Replications I and II (Large I and II) Initiated heterogeneous randomly mated populations (Purdue +) Rep III initiated in 1961 Purdue + foundation Lecture 19 30

31 Initiated in 1963 Small Lines Used Same Line as Large (Purdue +) Lecture 19 31

32 Procedure Large I, II, III and Small Closed Populations Selection Pupae Weight (100/400) 200 Pupa Of Each Sex Were Weighed Largest or Smallest 50 of Each Sex Chosen Randomly Mated in Mass Lecture 19 32

33 Relaxed Selection Varying Periods Of Length Combat The Loss Of Reproductive Fitness Lecture 19 33

34 Results 30 years and 360 Generations Later About 150 Generations of Selection 34

35 Large and Small Adults Lecture 19 35

36 Large and Small Pupae Lecture 19 36

37 Large I Over All Fit b=11.85 mg/gen b=1.28 dug/gen b=4.74 dug/gen Lecture 19 37

38 Large I Gen b=1.28 dug/gen b=4.74 dug/gen Lecture 19 38

39 Large II Overall Fit b=1.70 dug/gen b=9.26 dug/gen Lecture 19 39

40 Large II Generations b=1.70 dug/gen b=9.26 dug/gen Lecture 19 40

41 Large III Overall Fit b=1.6 dug/gen b=11.6 dug/gen Lecture 19 41

42 Large III Generations b=1.6 dug/gen Lecture 19 42

43 Small: Overall Fit b= dug/gen b= dug/gen b= dug/gen Lecture 19 43

44 Small: Generations b= dug/gen b= dug/gen Lecture 19 44

45 Possible Causes Plateaus Loss of Genetic Variability Physiological Limits Loss of Selection Differential Loss of Fitness Lecture 19 45

46 Test of Alternative Hypothesis Loss of Genetic Variability Reverse Selection Observe Response Physiological Limit Loss of Selection Differential Examine Change In Selection Differential Loss of Fitness Measure Fitness Related Traits in Direct and Reverse Selected Lines Lecture 19 46

47 Loss of Genetic Variability? Reverse Selection Applied Generations Same Selection Intensity As In The Positive Selection Measured Response Lecture 19 47

48 Up-Down Selection Large Line b=0.09 dug/gen (ns) b= dug/gen (p <.01) Lecture 19 48

49 Up-Down Selection Small Line b= 0.41 dug/gen (ns) b= dug/gen (ns) Lecture 19 49

50 Up-Down Selection Control Line b=13.8 dug/gen (p <.01) b= -9.2 dug/gen (p <.01) Lecture 19 50

51 Conclusions Plateau in Small Line Due to Loss of Genetic Variability Plateau in Small Line May Also Be Due to Physiological Limit Plateau in Large Line Due to Physiological Limit Lecture 19 51

52 Physiological Limit Loss of Selection Differential Examine Change In Selection Differential As Selection Advances Selection Differentials Measured Generations Generations of Sustained Selection Lecture 19 52

53 Selection Differential b= 0.39 dug/gen b= dug/gen Lecture 19 53

54 Relative Selection Differential RSD=100xSD/Generation Mean b= -0.01%/gen (ns) b= %/gen (ns) Lecture 19 54

55 Conclusion Selection Differential Unaffected by Selection Not Cause For Limit Lecture 19 55

56 Physiological Limit Loss of Fitness In Direction of Selection? 56

57 Physiological Limits Last Generation (360) Large I and Small Assortatively Mated 1,200 Single Pairs Measured Parental Pupae Weight Offspring Pupae Weight Offspring Pupae Number Regressed Offspring Number on Parental Weight (Genetic Regression) Lecture 19 57

58 Relationship Between Pupae Number and Parental Weight b=+21 Pupae/mg b= -4.4 Pupae/mg Lecture 19 58

59 Fitness Conclusion Positively Correlated With Pupae Wt In Small Line Negatively Correlated With Pupae Wt In Large Line Effective Selection Differential Diminishes in Direction of Selection Physiological Limits Constrain Further Progress in Either Line Lecture 19 59

60 Conclusion Causes For Selection Limit Loss of Effective Selection Differential Due to Negative Correlation with Fitness In Both Lines Loss of Genetic Variability in Small Line Verified via DNA Finger Prints No Variability Lecture 19 60

61 Remaining Questions 1. True Physiological Limit? Refuted by Goliath Single Gene Mutation For Large Homozygote Same Size as Large Cross With Large Additive Effect Doubles Body Size Is Fertile Lecture 19 61

62 Remaining Questions 2. Mechanism For Relationship Between Pupae Number and Parental Weight Unknown 3. Mutations What Happened To Mutational Heritability Particularly w.r.t. Small Line Possibility Rate of Inbreeding? F > 85% by Termination of Experiment But Same as For Large Line Lecture 19 62

63 Nature of Selection Limits in Other Laboratory Experiments (WL( ch16) Lecture 19 63

64 Nature of Selection Limits in Other Laboratory Experiments (WL( ch16) Lecture 19 64

65 New Mutations and Selection Limits 50% of population selected Only helpful if population size large Lecture 19 65

66 Lab Problem Chose one of the commodity groups below Design an optimal breeding program What traits to select on What method of selection would you utilize How many animals be utilized How many breeders would be chosen (How many of each sex would you save) What mating system would be employed (how would you determine who mates to whom and how many offspring would be kept per mating? Lecture 19 66