Size of breeding Size of breeding populationpopulation

Dag Lindgren and Darius DanuseviciusDag Lindgren and Darius Danusevicius

DaDaDaDa

March 2004March 2004For some reason all slides are not visible from my portable, but from other computers

Start with two other mattersStart with two other matters

The Swedish long-term breeding is still The Swedish long-term breeding is still rather open as most of it has not really rather open as most of it has not really started yet, thus easy to reconsider.started yet, thus easy to reconsider.

A number of possible limitations on breeding A number of possible limitations on breeding cycler has to be mentioned and discussedcycler has to be mentioned and discussed

Swedish long-term breeding - Swedish long-term breeding - IntentionsIntentions

20+ subpopulations with BP=50+ (Gpop 20+ subpopulations with BP=50+ (Gpop and Tpop) for spruce and pineand Tpop) for spruce and pine

Norway spruceNorway spruce Karlsson & Rosvall (1993) suggest 40*14 Karlsson & Rosvall (1993) suggest 40*14

ramets per parent in a 20 year cycleramets per parent in a 20 year cycle

Scots pineScots pine Wilhelmsson & Andersson (1993) made a Wilhelmsson & Andersson (1993) made a

suggestion, which depends on the success suggestion, which depends on the success of progeny-testing F1 uncertain cycling time of progeny-testing F1 uncertain cycling time

Swedish spruce breeding status 2002 per Swedish spruce breeding status 2002 per subpopulation subpopulation

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F1 incomplete Complete F1 in frig Part of F1 in clone tests

0 2 12 15 25 Year

50 P

, dpm

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F1C

andi

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s

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ion pc

20.0

00 F

2pr

ogen

y tr

ials

eval

uatio

n F2

sele

ctio

n50

F1,

dpm

Standard pine strategy

Picture stolen from Bengt Andersson 2001http://www.metla.fi/tapahtumat/2001/nordicgenetics/Bengt_Andersson.ppt

Swedish Scots pine breeding status 2002 per Swedish Scots pine breeding status 2002 per subpopulation subpopulation

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F1 incomplete Complete F1 in frig F1 in field test Part of F1 in field test

Scots pine - additionScots pine - additionTpop 11 has run a whole cycle to F2, seems “phenotypic” in DaDa language.

•Tpop 17; OP seeds have been collected from 20 year old F1; 8 progeny tests with 25000 plants. If cycle length is 25 and BP=50, 25000/(50*25)=20 +, so if that was typical annual cost for pine would be >20 trees per BP parent and year, seems “phen/prog” in DaDa language

•I could find only a single case (Tpop17) of major progeny-testing F1 initiated. Things take time….

That long-term breeding takes much time is no surprise. Thanks to the current good documentation (Annual status rapports are available), we will better grasp the time-line and avoid delays.

Long-term breeding has not proceeded far for most Swedish populations, thus the methods of long term breeding are not well-established or based on much experience, but open for discussion.

It has been thought that methods to force early flowering to get progeny-test initiated really early on pine should become important. This has not yet been done for a single Tpop. Our calculations indicate that this line of breeding is less efficient than progeny-testing of field-tested F1 genotypes.

Alternative pine strategy (cheap)

Graft archive (5*30)

Progeny test 20*5*40 PC + 30*5*20 OP = 7000

Year (approx)

0 2 12 18 30

Top grafts (5*20)

Field test 5000 F1 (50*100)

Planting

Ne

xt Cycle

BP

DP

M

Select 5 best in 20 best

fam.s

BP N=50

Top grafting Polycross

Select 5 in worse 30

fam.s

Planting

Grafting

DP

M

pollen

Phenotypic vs progenyPhenotypic vs progenyIn future seed orchards tested clones will probably In future seed orchards tested clones will probably be preferrable to somewhat better - but untested - be preferrable to somewhat better - but untested - fresh 15 year old phenotypic selections fresh 15 year old phenotypic selections

Progeny offers options which phenotype does not Progeny offers options which phenotype does not (like observations on survival, estimates of genetic (like observations on survival, estimates of genetic correlations and other parameters).correlations and other parameters).

Constraints and limitations of Constraints and limitations of breeding cyclerbreeding cycler

Shit in – shit out, entries must be chosen with care. Shit in – shit out, entries must be chosen with care. Sometimes they are not important but sometimes Sometimes they are not important but sometimes they arethey are

The input values may need some adjustment from The input values may need some adjustment from the most evident for considering factors not the most evident for considering factors not considered in the mathconsidered in the math

Breeding heads for an area and gets information Breeding heads for an area and gets information from a limited number of sites with limited materials, from a limited number of sites with limited materials, this can be considered by a reduction of CVAmthis can be considered by a reduction of CVAm

The test environments may not be considered a The test environments may not be considered a sample of future forest environments, this can also sample of future forest environments, this can also be considered by a reduction of CVAm.be considered by a reduction of CVAm.

Constraints and limitations of Constraints and limitations of breeding cycler –continued 1breeding cycler –continued 1

If ever leading for the details for Sweden (or elsewhere) I If ever leading for the details for Sweden (or elsewhere) I recommend breeding cycler to be rerun after a more recommend breeding cycler to be rerun after a more engaged debate about the inputs. We are willing to do the engaged debate about the inputs. We are willing to do the reruns. reruns.

Any decision support tool may need modifications for Any decision support tool may need modifications for conciderations beyond the model.conciderations beyond the model.

Breeding heads for improvement in many characters, we Breeding heads for improvement in many characters, we set the goal as one character “value for forestry” and the set the goal as one character “value for forestry” and the observed character can be seen as an index with as high observed character can be seen as an index with as high correlation as possible to the goal.correlation as possible to the goal.

The “observation” is an index of observations, and J*M is The “observation” is an index of observations, and J*M is thought of as time development of observed vs goal. thought of as time development of observed vs goal.

Constraints and limitations of Constraints and limitations of breeding cycler – continued2breeding cycler – continued2

Plant cost is seen as independent of age of evaluation. This can Plant cost is seen as independent of age of evaluation. This can cause problems for some type of comparisons (e.g. expensive cause problems for some type of comparisons (e.g. expensive flowering induction). This difficulty can be overcome by inserting flowering induction). This difficulty can be overcome by inserting different costs for different compared alternatives.different costs for different compared alternatives.

It is easy to add many types of considerations to the EXCEL sheet, It is easy to add many types of considerations to the EXCEL sheet, but it makes it difficult and complex for the user and journal papers. but it makes it difficult and complex for the user and journal papers. Those who want a special feature can often rather easy program it Those who want a special feature can often rather easy program it into the existing breeding cycler or even I can do it if you ask.into the existing breeding cycler or even I can do it if you ask.

Phenotypic preselection reduces the genetic variance somewhat in Phenotypic preselection reduces the genetic variance somewhat in our pheno/progeny calculations, quantitatively the effect is our pheno/progeny calculations, quantitatively the effect is negliable (3%) in our main scenario.negliable (3%) in our main scenario.

The gain by within family phenotypic selection may be slightly The gain by within family phenotypic selection may be slightly overexegarated with large families. This effect is probably small overexegarated with large families. This effect is probably small and very depending on as well the experimental lay-out as the and very depending on as well the experimental lay-out as the evaluation method.evaluation method.

Constraints and limitations of Constraints and limitations of breeding cycler – continued 3breeding cycler – continued 3

The optimal breeding strategy is too chaotic The optimal breeding strategy is too chaotic to be found by formulas, stochastic to be found by formulas, stochastic simulation is needed instead of breeding simulation is needed instead of breeding cycler.cycler.

Constraints and limitations of Constraints and limitations of breeding cycler – continued 4breeding cycler – continued 4

Breeding cycler does not specifically link to Breeding cycler does not specifically link to seed orchards. To cream off seed orchards seed orchards. To cream off seed orchards with sufficient diversity and little inbreeding is with sufficient diversity and little inbreeding is the most important reason for tree breeding! the most important reason for tree breeding! But this is taken care of by the choice of the But this is taken care of by the choice of the diversity coeff (penalty).diversity coeff (penalty).

Constraints and limitations of Constraints and limitations of breeding cycler – continued 5breeding cycler – continued 5

Genetic correlation are likely to change over Genetic correlation are likely to change over generationsgenerations

Breeding cycler considers the first cycle, the Breeding cycler considers the first cycle, the cumulative effect of some cycles can be cumulative effect of some cycles can be assumed to be additive, but after a number assumed to be additive, but after a number of cycles this oversimplifications become of cycles this oversimplifications become unrealistic.unrealistic.

Swedish Norway spruce breedingSwedish Norway spruce breeding

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0 1 2 3 4 5 6 7 8 9 10 11

Generation

breeding pop

10 clone seed orchard

10 clone clonal mixture

Rosvall, Lindgren & Mullin 1998

Conclusions:Accumulative progress for many generationsOrchard progress follows breeding pop progress

Inbreeding follows group coancestryInbreeding follows group coancestrySimulation of Swedish Norway spruce breeding program by POPSIM,

BP=48, DPM, equal representation (2/parent)

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bab

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Rosvall, Lindgren & Mullin 1999

Conclusions:Accumulative change over many cycles

Cycling will accumulate gain. Cycling will accumulate gain. Where is the limit?Where is the limit?

Balanced long-term breedingBalanced long-term breeding

Some unbalance is favourableSome unbalance is favourable

The inoptimality loss seem to be small; it is The inoptimality loss seem to be small; it is tricky to utilize unbalance, and the balance tricky to utilize unbalance, and the balance is unlikely to affect recommendations is unlikely to affect recommendations much.much.

Imbalance at initiation of breedingImbalance at initiation of breeding

At initiation of breeding there is no “balance”. At initiation of breeding there is no “balance”.

Truncating tested plus trees to long term breeding Truncating tested plus trees to long term breeding has sometimes been done with inoptimal has sometimes been done with inoptimal imbalance. imbalance.

I believe it is more optimal to sacrify the gene I believe it is more optimal to sacrify the gene diversity in the initial selections slower. diversity in the initial selections slower.

This has been discussed i förädlingsrådet 1999 This has been discussed i förädlingsrådet 1999 (see link on seminar page), and one argument is in (see link on seminar page), and one argument is in Routsalainen’s thesis (2002).Routsalainen’s thesis (2002).

Sweden started imbalancedSweden started imbalanced

Swedish recently decided to decrease Swedish recently decided to decrease the breeding population drastically (= the breeding population drastically (= veryvery low Ne first generation), low Ne first generation),

6000 plus trees 6000 plus trees 1000 founders 1000 founders

Flowering – when?Flowering – when?•We assume flowering in phenotypes of conifers at ages around 11. That may work with top-grafting. To make progeny-testing with open pollination possible may take 20 years.

•It is important that hard data on flowering time and flowering variations in modern progeny trials are collected and well documented.

•In our current figures we probably have discounted early flowering assuming pollen collection, hormone injections and top grafting whenever possible. It is also important to document and systematize how efficient such actions are.

More constraints on breeding More constraints on breeding population numberpopulation number

An unpublished manus, which was An unpublished manus, which was produced during a hectic month in the produced during a hectic month in the autumn 2003, is not autumn 2003, is not muchmuch fuel fuel

Results are contraintuitive to me, before Results are contraintuitive to me, before the study I thought the study would the study I thought the study would suggest larger population sizesuggest larger population size

Decrease of breeding population is Decrease of breeding population is something one should be very something one should be very conservative aboutconservative about

No immediate reason to go downward!No immediate reason to go downward!

Earlier considerations on Earlier considerations on breeding population numberbreeding population number

•Most considerations (including Swedish) is to choose the lowest number, which ensures sustainability and conservation and assurance against loss of alleles, not optimal trade-off with gain.

•It has not been well investigated if the optimal number could be higher than applied.

Genetic progress as function of NeGenetic progress as function of NeExpected gain after 1, 5, 10, and infinite () generations of selection for different values of Ne in a model population (Baker and Curnow 1969 from Johnson et al 2001 http://www.fs.fed.us/pnw/pubs/journals/Johnson_StClair_Lipow_2001.pdf).

Generation

Ne 1 5 10

4 3.3 12.4 19.5 28.4

16 3.3 16.0 31.4 114.5

32 3.3 16.8 34.6 177.5

64 3.3 17.2 36.4 220.9

256 3.3 17.5 37.8 240.0

3.3 17.6 38.0 240.0

Ne > 50 in one subpop and much larger in the metapop, so we may not constrain future genetic progress

E globulus CELBI -Portugal 300APM - Australia 300

E grandis ARACRUZ – Brazil 400

E nitens APM – Australia 300New Zealand 270

E. regnans APM – Australia 300New Zealand 300

E. Urophylla ARACRUZ – Brazil 400

Picea abies Sweden >1000

Picea glauca Nova Scotia 450

P mariana New Brunswick 400

Pinus elliottii CFGRP - USA 900

WGFTIP - USA 800

Pinus radiata STBA - Australia 300

FRI – New Zealand

550

Pinus taeda NCSU- USA 160

WGGTIP 800

Pseudots. Menziesii

BC - Canada 450

NWTIC - USA 404

Tsuga heterophylla

HEMTIC CAN-USA

150

Note sometimes values refer to what is available for a zone but mostly a meta-population for a larger area

Pinus banksiana

Lake states - USA 400

Manitoba -Canada 116

Pinus caribea QFS - Australia 200-300

BP sizes reported in tree improvement programsBP sizes reported in tree improvement programs

from Johnson et al 2001from Johnson et al 2001http://www.fs.fed.us/pnw/pubs/journals/Johnson_StClair_Liphttp://www.fs.fed.us/pnw/pubs/journals/Johnson_StClair_Lipow_2001.pdf).ow_2001.pdf).

Comment: The Swedish breeding population seems unusually large (this may be justified by the ecological amplitude covered by the Swedish breeding program)

The current Swedish breeding program is sustainable for more than 10 generations.Ten generations downstream will offer new unknown options. There is gene banking and natural resources besides breeders activities. The current breeders responsibility do not stretch longer.Question 1: Can it be made more narrow to save money or to boost gain without loosing sustainability?Question 2: Are there gains to be made by enlarging BP

How many are needed and desired?How many are needed and desired?

SummarySummary

Census number 50 per subpopulation and 1000+ in meta-population for pine and spruce is OK to continue in the coming decades.

Optimal breeding population sizeOptimal breeding population size

•What is more beneficial at a fixed budget: larger Breeding population (diversity) and smaller testing pop (test precision) or vice versa?

•Find the breeding population size which maximizes the annual progress in group merit under the annual budget

How optimally allocate the resourcesHow optimally allocate the resources

Test Test precision precision (testing (testing pop.)pop.)

Diversity Diversity (breedin(breedin

g pop.)g pop.)

Main findingsMain findings

• Spruce, BP < 50 is beneficial, as clonal test= higher benefit from the gain-generating capacity,

• Pine, BP ~ 50, as the gain-generating capacity of the testing strategy is not powerful enough to motivate reduction of gene diversity.

Parameters and scenariosParameters and scenariosParameters

Main scenario values

Alternative scenario values

Testing strateg y Phenotype Clone; Progeny

Additive variance A2 ) 1 -

Dominance variance, % of the additive variance D2) 25 -

Narrow -sense heritability ( h2) (obtained by changing E2) 0.1 0.5

Additive standard deviation at mature age within family ( CV Am ), % 10 5 to 20 by 2

Weighting factor for diversity loss per cycle ( c), % 200 50 to 1000 by 50

Time before establishment of the selection test, years 1 (Phenotype)

5 (Clone) 17 (Progeny)

-

Rotation age ( RA ), years 60 -

Cost for cycling a BP member ( CRECOMB ), € 30 -

Cost per test genotype ( Cg ), € 0.1 (Clone) 1 (Pr ogeny)

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Cost per test plant ( Cp ), € 1 -

Annual budget for all breeding population, € (the constraint) 500 50 to 2000 by 50

Annual progress in Group Merit (GM/Y ) To be maximized

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Testing strategyTesting strategy

Annual progress would benefit from lower BP for spruce, where testing can be clonal!

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Testing strategyTesting strategy•For Phenotype: the optimal is above 50, but only slightly. However, if budget is higher, it is better to increase breeding pop size beyond 50, than to increase offspring size.

•For Progeny the low optimum may reflect high testing cost, the total cost must be reduced by low BP size. Note that progeny is superior to phenotype at very high budget!

•For a mixed Phenotype/Progeny philosophy, similar low numbers as for progeny appeared.

• For Clone, low BP size probably reflects the high gain, which makes the gene diversity loss important

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HeritabilityHeritability

High heritability boosts gain and makes loss of gene diversity less important.

Low heritability justifies higher BP size, but the dependence is not strong, and I suggest we can regard the dependence as unimportant.

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Annual BudgetAnnual Budget

Optimal BP size increases with the budget, but only marginally and unimportant. But if spruce has a higher budget than pine, it is also an argument for a larger BP.

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Optimum share of resource invested in Optimum share of resource invested in testing increases with the budgettesting increases with the budget

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Cost of gene diversityCost of gene diversity

Optimal BP is very dependent (close to linear) on cost of gene diversity. It is critical and is difficult to assign a value. Main scenario approach is that the cost is double as high as if all production were lost if no gene diversity remains. This seems sufficiently conservative.

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main scenario = 200

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Genetic variationGenetic variation

Optimal BP size is very dependent on genetic variation in value for forestry. It ought to be possible to assign better estimates as trials grow older. The main scenario approach is that the CV of value for forestry is 10% within family, an educated guess based on estimates from younger trials is 12.5% (which may be adjusted to 10 for uncertanties).

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Genetic variation in value for forestry, CV main scenario=10 %

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Genetic variationGenetic variation

We are now exploring genetic variation in value for forestry in old trials, if we find that to be smaller than CV=10%, that may be reason to increase breeding population size.

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Less balance in spruce!?Less balance in spruce!? Economically more important for Sweden (Economically more important for Sweden (BP)BP) More plants produced (More plants produced (BP)BP) Higher investment in breeding (Higher investment in breeding (BP)BP) Higher site index (Higher site index (?)?) More flexible, present populations may later be More flexible, present populations may later be

merged (merged (BP)BP) Can be more efficiently bred by clonal testing Can be more efficiently bred by clonal testing

((BP)BP) A lower BP may be defended. Instead I suggest to A lower BP may be defended. Instead I suggest to

breed more aggressively, thus less balance in the breed more aggressively, thus less balance in the selections.selections.

Spruce breeding populationSpruce breeding population We have decided that 50 is needed and We have decided that 50 is needed and

should not be keen on reducing it only a should not be keen on reducing it only a decade later. decade later.

However there is another reason to reduce However there is another reason to reduce spruce BP, that is that it is more flexible, thus spruce BP, that is that it is more flexible, thus zones can be larger. zones can be larger.

I suggest to manage spruce BP more I suggest to manage spruce BP more unbalanced than pine. unbalanced than pine.

And be more prepared for a reduction some And be more prepared for a reduction some decades ahead by reducing the number of decades ahead by reducing the number of populations.populations.

For pine it is more important to go For pine it is more important to go on with present BPon with present BP

Lower investment in breeding (Lower investment in breeding ( = BP) = BP)

Less flexible, more difficult to draw on adjacent Less flexible, more difficult to draw on adjacent zones (zones ( = BP) = BP)

Can not be bred by clonal testing (Can not be bred by clonal testing (= BP)= BP)

Thus for long term breeding insufficient reason to Thus for long term breeding insufficient reason to decrease or increase BP and it may be desirable to decrease or increase BP and it may be desirable to keep breeding rather balanced.keep breeding rather balanced.

End of the slidesEnd of the slidesShall we have a final discussion?Shall we have a final discussion?

Or someone may have tried Breeding Cycler and experienced a problem?

End slide beerEnd slide beer

Ibreeding

Ibreeding

Ibreeding

Ibreeding

Or just relax?