1. DaDa work 2001-2003 Efficient long-term cycling strategy

2. Contents of 1 h Introduction and our studies (5 min.) Main finding (2 min) Testing strategy: optimization and timing (50 min): Single-stage strategies compared, Two-stage strategies compared, Amplified case: Progeny testing versus Pheno/Progeny. Main finding separately for pine and spruce (5 min.)

3. 4: BP size optimised 3: Ph/Prog amplified (pine), effect of J-M. Seminar 2004.03.02 1-2: Best testing strategy The Road to this semianr Breeding cycler Hungry shark

4. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Main findings: cloning is the best strategy

5. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Main findings Clonal test is superior (use for spruce)Clonal test is superior (use for spruce) Progeny testing not efficientProgeny testing not efficient For Pine, use 2 stage Pheno/ProgenyFor Pine, use 2 stage Pheno/Progeny Pine flowers not needed before age ~ 10- 15Pine flowers not needed before age ~ 10- 15

6. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 General M&M

7. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Basic advantage of our approach Gain per time Cost Diversity Is a complete comparison as it simultaneously considers: Other things, e.g. to well see the road

8. The long-term program Recurrent cycles of mating, testing and balanced selection Adaptive environment Testing Within family selection Mating We consider one such breeding population Breeding population

9. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Benefit = Group Merit/Year Gain Diversity Time Diversity loss was set to be as important as gain

10. Main inputs and scenarios While testing an alternative parameter value, the other parameters were at main scenario values Low lower reasonable bound Genetic parameters Time components Cost components Main typical for Pine or spruce High higher reasonable bound

11. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Cost per test plant = 1 ’cost unit’, all the other costs expressed as ratio of this 1. Cost per test plant = 1 ’cost unit’, all the other costs expressed as ratio of this 1. Such expression also helped to set the budget constraint corresponding to the present-day budget Such expression also helped to set the budget constraint corresponding to the present-day budget The time and cost explained Established in 5 years after seed harvest Field trial Establishment, maintenance and assessments Cutting of ramets Rooting of ramets (1 year) Transportation Crossing Recombination cost=20, Time=4 Plant dependent cost=1 (per ramet) Genotype depend. cost=2 (per ortet) Nursery Production of sibs (4 years) Mating time Time before Testing time Lag

12. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 All these costs should fit to a present-day budget Budget estimate is taken from pine and spruce breeding plan ~ test size expressed per year and BP member. ~ 10 ’cost units’ for pine, 20- for spruce. Budget constraint

13. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Why budget constraint per BP member and year? Because costs expressed per BP member = easier to handle Because costs expressed per BP member = easier to handle Gain efficiency should be assessed per unit of time Gain efficiency should be assessed per unit of time Optimization= optimum combination of testing time and testing size to obtain max GM/Year and to satisfy the budget constraint (use Solver) Optimization= optimum combination of testing time and testing size to obtain max GM/Year and to satisfy the budget constraint (use Solver)

14. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 The Relativity theory holds for the Cycler as well… It optimizes “your case” What if budget is such What if costs are such What if we reduce them What if heritably is such What if J-M correlation is So, interpretation should consider that everything is relative to each other

15. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Single-stage testing strategies

16. Objective: compare strategies based on phenotype, clone or progeny testing (…n) Phenotype testing N=50 (…n), (…m) and selection age were optimized Clone or progeny testing N=50 (…n) (…m) OBS: Further result on numbers and costs- for one of these families

17. Parameters- for reference ParametersMain scenarioAlternative scenarios Additive variance  A 2 ) 1 Dominance variance, % of the additive variance in BP  D 2 ) 250; 100 Narrow-sense heritability (h 2 ) (obtained by changing  E 2 ) 0.10.05; 0.5 Additive standard deviation at mature age (  Am ), % 105; 20 Diversity loss per cycle, % 0.50.25;1 Rotation age, years 6010; 120 Time before establishment of the selection test (T BEFORE ), years 1 (phenotype)3; 5 (phenotype) 5 (clone)3; 7 (clone) 17 (progeny)5; 7 (progeny) Recombination cost (C RECOMB ), $ 3015; 50 Cost per genotype (Cg), $ 0.1 (clone),1; 5 (clone), 1 (progeny)0.1; 5 (progeny) Cost per plant (Cp), $ 10.5; 3 Cost per year and parent (constraint) 105; 20 Group Merit Gain per year (GMG/Y) To be maximized

18. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 CVa at mature age CV a =14 % is based on pine tests in south Sweden Jansson et al (1998), CV a =14 % is based on pine tests in south Sweden Jansson et al (1998), 1/2 of additive var in pop is within full sib families, 1/2 of additive var in pop is within full sib families, Our program is balanced= gain only from within full-sib selection, Our program is balanced= gain only from within full-sib selection, Thus, CV a within fam= CVa in pop divided by the square root of 2, thus a CV = 10%, which we use here (even if not quite correct). Thus, CV a within fam= CVa in pop divided by the square root of 2, thus a CV = 10%, which we use here (even if not quite correct). CVa within = sqrt(  2 /2) = sqrt(  2 )/sqrt(2)=  2 /sqrt(2)

19. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Results-clonal best, progeny worst At all the scenarios, Clonal was superior, except high h 2. Test 26 clones with 21 ramet (18/15  budget), select at age 20 Test 182 phenotypes; select at age 15, (  budget: 86, for 17 years) (second best) Test 11 female parents with 47 progeny each; select at age 34 (  budget: 8/34, 40 years) Annual Group Merit, % 0.0 0.1 0.2 0.3 0.4 0.5 0.6 00.10.20.30.40.50.6 Narrow-sense heritability Phenotype Clone Progeny

20. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 GM/Y digits after comma are important If for Clone GM/Y=0.25%; cycle= 30 years then If for Clone GM/Y=0.25%; cycle= 30 years then Cycle GM=8 % (gain 8.5 - 0.5 div loss) Cycle GM=8 % (gain 8.5 - 0.5 div loss) Thus GM/Y reduction by 0.03 (10%) = Cycle gain reduction by 1% Thus GM/Y reduction by 0.03 (10%) = Cycle gain reduction by 1% Loss of Cycle gain by 1% = important loss Loss of Cycle gain by 1% = important loss

21. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 0.10 0.15 0.20 0.25 0.30 4(59)10(25)15(18)20(14)30(10)40(8) Clone no (ramets per clone) Annual Group Merit, % How flat are the optima (clone)? Clone number (ramet per clone) = 12(22)-24 (14) Less ramets at optimum clone number is sensitive: no > than 5, (not shown) If problems with cloning, better-> clones with clones with < ramets If h 2 is higher, see next GM/Y by Pheno h 2 =0.1, lower budget, at optimum testing time Optimum 18(15) 17 18 20 22 23 25 Test time

22. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 If not enough cuttings, better more clones with less ramets, rather than to reduce ramet number at optimum clone number GM/Y by Phenotype=0,275 12 12 12 12 12 13 13 13 14 14 15 15 15 15 17 testing time

23. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Higher h 2 = more clones and less ramets Spruce plan 40/15 Ola’s thesis, paper I, Fig. 9= 40 cl with 7 ram at test size 280 0.00 0.10 0.20 0.30 0.40 0.50 00.10.20.30.40.5 Narrow-sense heritability GM/Y, % 13/23 18/15 28/9 46/5 Clone no/ramet no Optimum then is between 18/15 and 30/10 Budget= 10

24. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Clone strategy 0.00 0.05 0.10 0.15 0.20 0.25 0.30 1516171819202122232425 Testing time, years Annual Group Merit, % The optimal testing time 18-20 No effect to test longer than 18-20 years These 18-20 years with conservative J-M function (Lambeth 1980) With Lambeth 2001, about 15-17 years Figure with optimum at main scenario parameters (budget=10) clones/ramets 18/15

25. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 How realistic are the optima? Optima depends on budget, h 2, J-M correlation- how realistic are they? Optima depends on budget, h 2, J-M correlation- how realistic are they? 1. Budget is the present-day allocation. Increase will result in more gain. But we test how to optimise the resources we have. 2. h 2 =0,1 seems to be reasonable 3. J-M functions taken from southerly pines, it affects the timing with stand. error of 2 years (7-10-12).

26. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Why Phenotype ≥Progeny ? Drawbacks of Progeny: long time and high cost (important to consider for improvement) Drawbacks of Progeny: long time and high cost (important to consider for improvement) Phenotype generates less gain but this is compensated by cheaper and faster cycles. Phenotype generates less gain but this is compensated by cheaper and faster cycles.

27. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Dominance seems to matter little Annual Group Merit, % Dominance would not markedly affect superior performance of clonal testing 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0255075100125 Dominance variance (% of additive) Clone Progeny Phenotype

28. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 On Genotype cost Tbefore 0.05 0.10 0.15 0.20 0.25 0.30 0123456 Cost per genotype 0.05 0.10 0.15 0.20 0.25 0.30 0369121518 Delay before establishment of selection test (years) Expensive genotypes are of interest only if it would markedly shorten T before for Progeny or improve cloning Clone Progeny Phenotype Clone Progeny

29. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Recombinatin cost and total budget Clone Progeny Phenotype 0.0 0.1 0.2 0.3 0510152025 Budget per year and parent 0.05 0.10 0.15 0.20 0.25 0.30 102030405060 Recombination cost Clone Progeny Phenotype Important factors; what happens if they fluctuate? Phenotype get more attractive at low budget, strategy choice not depending on recombination cost Annual Group Merit, %

30. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Conclusions Clonal testing is the best breeding strategy Phenotype 2nd best, except very low h 2 or high budget Superiority of the Phenotype over Progeny is minor = additional considerations may be important (idea of a two-stage strategy).

31. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Let’s do it in 2 stages?

32. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Stage 2:.Sexual propagation of pre-selected individuals Reselection based on performance of the progeny Mating Testing of the progeny Stage 2:.Sexual propagation of pre-selected individuals Reselection based on performance of the progeny Mating Stage1: Phenotype test and pre-selection Testing of the progeny Phenotype/Progeny strategy

33. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Values- study 2

34. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 arrows show main scenario 0.10 0.15 0.20 0.25 0.30 1357911131517 Delay before establishment of selection test (years) Phenotype/ProgenyIf Progeny initiated early, may~ Phenotype/Progeny = need for a amplification Phenotype/Progeny is shown with a restriction for Phenotype selection age > 15 Clone = Phenotype/Clone = no need for 2 stages.Clone = Phenotype/Clone = no need for 2 stages. Phenotype/Progeny is 2nd best = best for PinePhenotype/Progeny is 2nd best = best for Pine Clone Progeny Phenotype Pheno/Progeny Results: two-stage 2nd best

35. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Budget cuts = switching to Phenotype tests in Pine If budget is cut by half = simple Phenotype test 0.1 0.2 0.3 05101520 Budget per year and parent (%) Annual Group Merit, % Clone Progeny Phenotype Pheno/Progeny

36. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Budget cuts for Pheno/Progeny Budget  = resources reallocated on cheaper Phenotype test Testing time 10 (stage 1) and 14 (stage 2) little affected by the budget 2 3 4 5 Budget=10Budget=5 Genetic gain, % Stage 1 Phenotype Stage 2 Progeny 17 32 5(44)5(72)

37. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Why Pheno/Progeny was so good? It generated extra gain by taking advantage of the time before the candidates reach their sexual maturity It generated extra gain by taking advantage of the time before the candidates reach their sexual maturity This was more beneficial than single-stage Progeny test at a very early age This was more beneficial than single-stage Progeny test at a very early age Question for the next study: is there any feasible case where Progeny can be better? Question for the next study: is there any feasible case where Progeny can be better?

38. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Progeny test with and without phenotypic pre-selection Is there any realistic situation where Progeny testing is superior over Pheno/Progeny (reasonable interactions and scenarios) What and how flat is the optimum age of pre-selection for Pheno/Progeny? (when do we will need flowers?) Phenotype test Pre-selection age? Progeny test

39. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Simply- where best to invest? Phenotype- based pre- selection Early flowering induction

40. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Time and cost components C Per CYCLE = C recomb + n (C G + m C P ), T cycle = T recomb + T MATING + T LAG + T progtest T LAG is crossing lag for progeny test (polycross, seed maturation, seedling production) T MATING age of sufficient flowering capacity to initiate progeny test (for 2-stage strategy it corresponds to the age of phenotypic pre-selection

41. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Parameters study 3

42. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 J-M correlation functions Lambeth (1980)= phenotypic fam mean corrs from many trials of 3 temperate conifers 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 0.00.10.20.30.40.50.60.70.80.91.0 Ratio selection/rotation age (Q) J-M genetic correlation coefficient Lambeth (1980) Lambeth & Dill (2001) Gwaze et al. (2000) Gwaze et al. (2000)= genetic correlations from 19 trials with 190 fams of P taeda western USA. Lambeth (2001) Main = genetic corrs in 4 series (15 trials) P taeda (296 fams)

43. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Results: 2 stage is better 2 stage strategy was better under most reasonable values 2 stage strategy was better under most reasonable values Main scenario 0.0 0.3 0.6 0510152025 Annual Group Merit (%) Age of mating for progeny test (years) No marked loss would occur if mating is postponed to age 15No marked loss would occur if mating is postponed to age 15 Pheno/Progeny Progeny

44. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 J-M correlation affects pre-selection age Optimum selection age depends on efficiency of Phenotype to generate enough gain to motivate prolongation of testing for an unit of time.Optimum selection age depends on efficiency of Phenotype to generate enough gain to motivate prolongation of testing for an unit of time. 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 0.00.10.20.30.40.50.60.70.80.91.0 Ratio selection/rotation age (Q) J-M genetic correlation coefficient Do we have J-M estimates for spruce and pine? Gwaze et al. (2000) 7 Lambeth & Dill (2001) 10 Lambeth (1980) 12 Gain increases fast by time Gain would increase faster if switching to progeny test The gain generating efficiency mainly depends on slope of J-M correlation function.The gain generating efficiency mainly depends on slope of J-M correlation function.

45. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 When the loss from optimum is important? Rotation age = 20 0.0 0.3 0.6 0510152025 When early testing is advantageous h 2 is high but then Phenotype alone is better 0.0 0.3 0.6 0510152025 Plant cost= 0.1 0.0 0.3 0.6 0510152025 Rotation is short Plants are cheap h 2 = 0.5 0.0 0.2 0.4 0.6 0.8 0510152025 Pheno/Progeny Progeny Annual Group Merit (%) Age of mating for progeny test (years)

46. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Better crossings are motivated Crossing lag and genotype costs had no marked effect = the crosses can be made over a longer time to simultaneously test all pre-selected individuals and their flowering may be induced at a higher cost. Crossing lag= 5 0.23 0.0 0.1 0.2 0.3 0.4 0.5 0510152025 10 ; 0.26 Crossing lag= 8 0.22 0.0 0.1 0.2 0.3 0.4 0.5 0510152025 10; 0.25 Pheno/Progeny Progeny Annual Group Merit (%) Age of mating for progeny test (years)

47. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 These are as for our interactive scenario: low heritability (0,01), long rotation (80 y)= less J-M at pre-selection, weak J-M correlation (L1980) Progeny is motivated when conditions disfavour Phenotype But the optima flat and scenario unrealistic Pheno/Progeny Progeny Interactive scenario 0.00 0.03 0.06 0510152025 Annual Group Merit (%) Age of mating for progeny test (years)

48. Optimum test time and size for pine (for one of the 50 full sib fams) Long-term breeding Stage 2. Progeny- test each of those 5 with 30 offspring Stage 1: Test 70 full-sibs Mating 2-4 years, at a high cost if feasible Lag- 3-4 years Cycle time~ 27 Gain=8 % GM/Y= 0,27% Select back the best of 5 when progeny- test age is 10 Select 5 at age 10

49. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 What if no pine flowers until age 25? Pheno/Progeny is still leading Phenotype with selection age of 25 is better Progeny is the last Budget cuts, high h 2 will favour Phenotype This means, singe stage Phenotype cycle time > 25 years and For the two-stage, pre-selection not at its optimum age (10 years) Main (h=0.1, budget=10), Flowers at age 25 0.179 0.135 0.140 0.00 0.05 0.10 0.15 0.20 Progeny Phenotype Pheno/ Progeny Annual Group Merit, %

50. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 May be 2 cycles of Phenotype instead of Pheno/Progeny? Cycle, years GM/year, % GM/cycle 2 cycle s of Pheno Phenotype200,1523,046,08 Pheno/Prog 400,1817,26 Answer is No: 7,26 is > 6,08

51. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Conclusions Under all realistic values, Pheno/Progeny better than Progeny Sufficient flowering of pine at age 10 is desirable, but the disadvantage to wait until the age of 15 years was minor, If rotation short, h 2 high, testing cheap, delays from optimum age could be important

52. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Our main findings

53. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Main findings - spruce (18) (15)(15)(15) (15)(15) (15)(15)(15)(15) (15)(15) Clonal test by far the best Select at age 15 (20) depending on J-M correlation If higher h 2 more clones less ramets Present plans: size 40/15, selection age: 10 years With L(2001), Cycle time~ 21 Gain=8.2 % GM/Y= 0,34%

54. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Main findings- P ine (70) Use 2 stage Pheno/Progeny strategy Stage 1 Phenotype select at age 10 (15 only 3% GM lost) Stage 2 Progeny test select at ca 10 (30) With L(2001), Cycle time~ 27 Gain=8 % GM/Y= 0,27%

55. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Research needs- Faster cloning

56. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Research needs (a PhD thesis) Faster, better cloning: embryogenesis, rooting, C-effects (especially for pine)Faster, better cloning: embryogenesis, rooting, C-effects (especially for pine) Sufficient flowering at age 10 (15) for pineSufficient flowering at age 10 (15) for pine Documentation of flowering in breeding stockDocumentation of flowering in breeding stock How sexual maturation, flowering abundance are related to breeding value?How sexual maturation, flowering abundance are related to breeding value?

57. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 In breeding, thanks to Dag there may be less risk to enter a wrong way...

58. The end