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Efficient long-term cycling strategy DaDa work 2001-2003 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.) The Road to this semianr Seminar 2004.03.02 4: BP size optimised 3: Ph/Prog amplified (pine), effect of J-M. Hungry shark 1-2: Best testing strategy Breeding cycler Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Main findings: cloning is the best strategy Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Main findings •Clonal test is superior (use for spruce) •Progeny testing not efficient •For Pine, use 2 stage Pheno/Progeny •Pine flowers not needed before age ~ 1015 Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 General M&M Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Basic advantage of our approach Is a complete comparison as it simultaneously considers: Cost Gain per time Diversity Other things, e.g. to well see the road The long-term program Recurrent cycles of mating, testing and balanced selection Adaptive Mating environment Within family selection Breeding population Testing We consider one such breeding population Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Benefit = Group Merit/Year Diversity loss was set to be as important as gain Gain Diversity Time Main inputs and scenarios Low Main High Genetic parameters lower typical for higher Time components reasonable Pine or reasonable bound spruce bound Cost components While testing an alternative parameter value, the other parameters were at main scenario values Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 The time and cost explained •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 Production of Cutting of sibs (4 years) ramets Crossing Genotype Recombination depend. cost=2 cost=20, (per ortet) Time=4 Mating time Established in 5 years after seed harvest Rooting of ramets (1 year) Transportation Nursery Establishment, maintenance and assessments Field trial Plant dependent cost=1 (per ramet) Time before Testing time Lag 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. ng of Rooti year) s (1 ramet of tting f Cu mets o n o i ra d u ct Pro rs) 4 yea sibs ( type sing Geno st=0.1 Cros ation epend. co t) mbin d o rt e Reco 20-50, (per cost= =3 Time time g n i t Ma Field p or Trans ery Nurs ent, lishm Estab ance and en maint sments asses in lished Estab s after r 5 yea rvest ha d e e s d Plant e befor e m i T tation epen e r ra t=1 (p s o c t den trial met) e Lag m i t ng Testi 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 • 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) 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 Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Single-stage testing strategies Objective: compare strategies based on phenotype, clone or progeny testing Clone or progeny testing Phenotype testing N=50 N=50 (…n) (…n) (…n) OBS: Further result on numbers and costs- for one of these families (…n) (…m)(…m)(…m) (…m)(…m)(…m) (…n), (…m) and selection age were optimized Parameters- for reference Parameters Main scenario Alternative scenarios Additive variance (sA2 ) 1 Dominance variance, % of the additive variance in BP (sD2) 25 0; 100 Narrow-sense heritability (h2) (obtained by changing sE2) 0.1 0.05; 0.5 Additive standard deviation at mature age (sAm), % 10 5; 20 Diversity loss per cycle, % 0.5 0.25;1 Rotation age, years 60 10; 120 1 (phenotype) 3; 5 (phenotype) 5 (clone) 3; 7 (clone) 17 (progeny) 5; 7 (progeny) 30 15; 50 0.1 (clone), 1; 5 (clone), 1 (progeny) 0.1; 5 (progeny) Cost per plant (Cp), $ 1 0.5; 3 Cost per year and parent (constraint) 10 5; 20 Time before establishment of the selection test (TBEFORE), years Recombination cost (CRECOMB), $ Cost per genotype (Cg), $ Group Merit Gain per year (GMG/Y) To be maximized Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 CVa at mature age • CVa=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, • Our program is balanced= gain only from within full-sib selection, • Thus, CVa 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(s /2)= sqrt(s )/sqrt(2)= s /sqrt(2) 2 2 2 Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 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, % Results-clonal best, progeny worst 0.6 0.5 0.4 0.3 0.2 0.1 0.0 Clone Phenotype Progeny 0 0.1 0.2 0.3 0.4 0.5 0.6 Narrow-sense heritability At all the scenarios, Clonal was superior, except high h2. 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 • Cycle GM=8 % (gain 8.5 - 0.5 div loss) • Thus GM/Y reduction by 0.03 (10%) = Cycle gain reduction by 1% • Loss of Cycle gain by 1% = important loss Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 How flat are the optima (clone)? h2=0.1, lower budget, at optimum testing time Less ramets at optimum clone number is sensitive: no > than 5, (not shown) If problems with cloning, better-> clones with < ramets 0.30 Optimum 18(15) Annual Group Merit , % Clone number (ramet per clone) = 12(22)-24 (14) 0.25 0.20 GM/Y by Pheno 0.15 0.10 4(59) 10(25) 15(18) 20(14) 30(10) 40(8) If h2 is higher , see next Clone no (ramets per clone) Test time 17 18 20 22 23 25 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 testing time 70(5) 57(6) 50(7) 45(8) 39(9) 32(11) 30(12) 28(13) 26(14) 24(15) 22(16) 21(18) 20(18) 19(19) 0.450 0.440 0.436 0.430 0.420 0.410 This line marks loss of GM/Y > 0,03 0.400 0.390 0.380 GM/Y by Phenotype=0,275 0.370 0.360 0.350 Variation in these outlined numbers will 0.340 not cause marked loss of benefit 0.330 36(10) Budget=20, h2=0.1, Cycling cost=20, time 4, Tbefore=5, Cg=2, J-M corr by L(2001), c=100 Optimum for clone number (ramet no per clone) 12 12 12 12 12 13 13 13 14 14 15 15 15 15 17 Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Higher 2 h = more clones and less ramets Clone no/ramet no 0.50 0.40 GM/Y, % Optimum then is between 18/15 and 30/10 46/5 18/15 0.30 0.20 Spruce plan 40/15 0.10 Ola’s thesis, paper I, Fig. 9= 40 cl with 7 ram at test size 280 0.00 28/9 13/23 0 0.1 0.2 0.3 0.4 0.5 Narrow-sense heritability Budget= 10 Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 The optimal testing time 18-20 •These 18-20 years with conservative J-M function (Lambeth 1980) •With Lambeth 2001, about 15-17 years 0.30 Annual Group Merit, % •No effect to test longer than 18-20 years Clone strategy 0.25 0.20 0.15 0.10 0.05 0.00 15 16 17 18 19 20 21 22 23 24 25 Testing time, years Figure with optimum at main scenario parameters (budget=10) clones/ramets 18/15 Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 How realistic are the optima? • Optima depends on budget, h2, 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. h2 =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). 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) • Phenotype generates less gain but this is compensated by cheaper and faster cycles. Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Dominance would not markedly affect superior performance of clonal testing Annual Group Merit, % Dominance seems to matter little 0.6 0.5 0.4 0.3 0.2 0.1 0.0 Clone Phenotype Progeny 0 25 50 75 100 125 Dominance variance (% of additive) Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 0.30 0.25 0.30 0.25 Tbefore On Genotype cost Clone 0.20 0.20 0.15 Clone Progeny 0.15 Progeny 0.10 0.10 Phenotype 0.05 0.05 0 1 2 3 4 5 Cost per genotype 6 0 3 6 9 12 15 18 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 Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Recombinatin cost and total budget Annual Group Merit , % 0.3 0.30 Clone Clone 0.25 Phenotype 0.2 0.20 Phenotype 0.15 0.1 Progeny Progeny 0.10 0.0 0.05 0 5 10 15 20 Budget per year and parent 25 10 20 30 40 50 60 Recombination cost Important factors; what happens if they fluctuate? Phenotype get more attractive at low budget, strategy choice not depending on recombination cost 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 h2 or high budget • Superiority of the Phenotype over Progeny is minor = additional considerations may be important (idea of a two-stage strategy). Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Let’s do it in 2 stages? Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Phenotype/Progeny strategy Mating Stage1: Phenotype test and pre-selection Reselection based on performance of the progeny Stage 2:.Sexual propagation of pre-selected individuals Testing of the progeny Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Values- study 2 Parameters Main scenario Additive variance (sA2 ) Dominance variance, % of the additive variance in 2 BP (sD ) Environmental variance, % of total variance s ( E2 ) Additive standard deviation at mature age(sAm), % Diversity loss per cycle, % Rotation age, years 1 Alternative scenarios - 25 0; 100 Time before establishment of the selection test (TBEFORE), years Recombination cost (CRECOMB ), $ Cost per genotype (Cg), $ Cost per plant (Cp), $ Budget per year and parent (the constraint) Group Merit Gain per year (GMG/Y) 88 0; 38; 94 10 5; 20 0.5 0.25;1; 5 60 10; 20; 120 1 (phenotype) 3; 5 (phenotype) 5 (clone; 3; 7 (clone; phenotype/clone) phenotype/clone) 17 (progeny; 5; 7 (progeny; phenotype/progeny) phenotype/progeny) 30 0.1 (clone), 1; 5 (clone), 1 (progeny) 0.1; 5 (progeny) 1 0.5; 3 10 5; 20; 50 To be maximized Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Results: two-stage 2nd best •Clone = Phenotype/Clone = no need for 2 stages. 0.30 Clone 0.25 •Phenotype/Progeny is 2nd 0.20 best = best for Pine •If Progeny initiated early, may~ Phenotype/Progeny = need for a amplification •Phenotype/Progeny is shown with a restriction for Phenotype selection age > 15 Pheno/Progeny 0.15 Phenotype Progeny 0.10 1 3 5 7 9 11 13 15 17 Delay before establishment of selection test (years) arrows show main scenario Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 If budget is cut by half = simple Phenotype test Annual Group Merit, % Budget cuts = switching to Phenotype tests in Pine 0.3 Clone Pheno/Progeny 0.2 Phenotype Progeny 0.1 0 5 10 15 20 Budget per year and parent (%) Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Budget cuts for Pheno/Progeny Genetic gain, % Budget = resources reallocated on cheaper Phenotype test 5 32 Stage 2 Progeny 4 17 3 5(44) Stage 1 5(72) Phenotype 2 Budget=10 Budget=5 Testing time 10 (stage 1) and 14 (stage 2) little affected by the budget 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 • 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? 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 Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Simply- where best to invest? Phenotypebased preselection Early flowering induction Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Time and cost components CPer CYCLE = Crecomb + n (CG + m CP), Tcycle = Trecomb + TMATING + TLAG + Tprogtest TMATING age of sufficient flowering capacity to initiate progeny test (for 2-stage strategy it corresponds to the age of phenotypic pre-selection TLAG is crossing lag for progeny test (polycross, seed maturation, seedling production) Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Parameters study 3 Main scenario values Alternative scenario values* Interactive scenario values Additive variance (sA2 ) 1 - - Dominance variance, % of the additive variance (sD2) 25 0; 100 - Narrow-sense heritability (h2) (obtained by changing sE2) 0.1 0.01; 0.5 0.01 Additive standard deviation at mature age % 10 - - Diversity loss per cycle, % 0.5 - - L (2001) L(1980); G(2000) L(1980) 3 to 25 by 1 - - Crossing lag for progeny test (crossing; seed maturation, seedling production),years 3 5; 8 - Rotation age (RA), years 50 20; 30; 80 80 Recombination cost (CRECOMB), $ 30 0; 100 - Cost per genotype (Cg), $ 1 0.1; 10 - Cost per plant (Cp), $ 1 0.1; 2 - Budget per year and parent, $ (the constraint) 10 5; 20 - Parameters J-M genetic correlation function Age of mating for progeny test (age of sufficient flowering capacity for progeny testing), years Annual progress in Group Merit (GM/Y) 1 To be maximized Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 J-M correlation functions • •Gwaze et al. (2000)= genetic correlations from 19 trials with 190 fams of P taeda western USA. •Lambeth (1980)= phenotypic fam mean corrs from many trials of 3 temperate conifers J-M genetic correlation coefficient •Lambeth (2001) Main = genetic corrs in 4 series (15 trials) P taeda (296 fams) 1.0 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 Lambeth (1980) Lambeth & Dill (2001) Gwaze et al. (2000) 0.0 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 Ratio selection/rotation age (Q) Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 • 2 stage strategy was better under most reasonable values •No marked loss would occur if mating is postponed to age 15 Annual Group Merit (%) Results: 2 stage is better Main scenario 0.6 Pheno/Progeny 0.3 Progeny 0.0 0 5 10 15 20 25 Age of mating for progeny test (years) Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 J-M correlation affects pre-selection age •The gain generating efficiency mainly depends on slope of J-M correlation function. • 1.0 J-M genetic correlation coefficient •Optimum selection age depends on efficiency of Phenotype to generate enough gain to motivate prolongation of testing for an unit of time. 0.9 0.8 10 0.7 0.6 0.5 0.4 0.3 0.2 0.1 7 Gain would increase faster if switching to 12 progeny test Gain increases fast by time Lambeth (1980) Lambeth & Dill (2001) Gwaze et al. (2000) 0.0 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 Ratio selection/rotation age (Q) Do we have J-M estimates for spruce and pine? Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 When the loss from optimum is important? Annual Group Merit (%) When early testing is advantageous Rotation age = 20 0.6 2 0.8 h = 0.5 Plant cost= 0.1 0.6 Pheno/Progeny 0.6 0.4 0.3 0.3 0.0 0.0 Progeny 0.2 0.0 0 5 10 15 20 25 0 5 10 15 20 25 0 5 10 15 20 25 Age of mating for progeny test (years) h2 is high but then Phenotype alone is better Rotation is short Plants are cheap Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Annual Group Merit (%) Better crossings are motivated Crossing lag= 5 0.5 0.4 0.4 Pheno/Progeny 10; 0.26 0.3 0.2 0.23 Progeny 0.3 0.1 0.0 0.0 5 10 15 20 25 10; 0.25 0.22 0.2 0.1 0 Crossing lag= 8 0.5 0 5 10 15 20 25 Age of mating for progeny test (years) 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. 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) Annual Group Merit (%) Progeny is motivated when conditions disfavour Phenotype Interactive scenario 0.06 Pheno/Progeny Progeny 0.03 0.00 0 5 10 15 20 25 Age of mating for progeny test (years) But the optima flat and scenario unrealistic Optimum test time and size for pine (for one of the 50 full sib fams) Cycle time~ 27 Gain=8 % GM/Y= 0,27% Select back the best of 5 when progeny- test age is 10 Stage 2. Progenytest each of those 5 with 30 offspring 2-4 years, at a high cost if feasible Mating Long-term breeding Lag- 3-4 years Stage 1: Test 70 full-sibs Select 5 at age 10 Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 What if no pine flowers until age 25? •Progeny is the last •Budget cuts, high h2 will favour Phenotype 0.15 0.179 0.135 0.140 Phenotype •Phenotype with selection age of 25 is better 0.20 Progeny •Pheno/Progeny is still leading Annual Group Merit, % This means, singe stage Phenotype cycle time > 25 years and For the two-stage, pre-selection not at its Main (h=0.1, budget=10), Flowers at age 25 optimum age (10 years) 0.10 0.05 0.00 Pheno/ Progeny Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 May be 2 cycles of Phenotype instead of Pheno/Progeny? Phenotype Cycle, GM/year, GM/cycle 2 cycle s years % of Pheno 20 0,152 3,04 6,08 Pheno/Prog 40 0,181 Answer is No: 7,26 is > 6,08 7,26 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, h2 high, testing cheap, delays from optimum age could be important Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Our main findings Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Main findings- spruce Clonal test by far the best If higher h2 more clones less ramets Present plans: size 40/15, selection age: 10 years (18) (18) Select at age 15 (20) depending on J-M correlation (15) (15) (15) (15) (15) (15) With L(2001), Cycle time~ 21 Gain=8.2 % GM/Y= 0,34% Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Main findings- Pine Use 2 stage Pheno/Progeny strategy (70) (70) (30) (30)(30)(30)(30) (30) (30)(30)(30)(30) Stage 1 Phenotype select at age 10 (15 only 3% GM lost) Stage 2 Progeny test select at ca 10 With L(2001), Cycle time~ 27 Gain=8 % GM/Y= 0,27% Clonal- best; progeny- worst; Pine- phenotype pre-selection and progeny; flowers at age 15 Research needs- Faster cloning 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) •Sufficient flowering at age 10 (15) for pine •Documentation of flowering in breeding stock •How sexual maturation, flowering abundance are related to breeding value? 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 ... The end