Combining genetic gain, gene diversity, time components, cost

components when optimizing breeding strategies

Dag LindgrenSeminar at the research school of

forest genetics and breedingUmeå 08-09-15Two parts:

1. Published 2002-2005 (many heard the essentials 2004, but not the research school doctorands)

2. In press (galley proof received) or preparation (breeders heard parts of it in May, but it is improved calculations, also for meeting tomorrow).

Key issues• Strategy;

• Genetic Gain;

• Gene Diversity;

• Time;

• Cost.

Consider all!

The program “Breeding cycler” studies what happens during one

complete breeding cycle

Long-term breedingSelectio

n

Mating

Testing

Breeding cycler explores selection of selecting the best within a full sib family!

Acknowledgement: Large thanks to Swedish breeding for the justification to construct a reasonable simple breeding cycler! Breeding population size is set to 50 and each is parent to two full sib families and from each the best individual is recruited to the next breeding population! Thus - to optimize Swedish breeding - it is usually sufficient to consider a single full sib family. That is the first part.

Acknowledgement also to Ola Rosvall, who thought outside the box, and is spiritual father of thinking outside the 50 and a single generation. That is the second part.

Inputs• Genetic variance components like:

– Additive genetic variation in goal character (goal character is value for forestry but numerically volume production at mature age other characters unchanged)

– Juvenile-mature correlation• Time components (duration for different actions)

like:– Testing (age at selection)– Crossing– Wait for flowering

• Cost components like:– Cost for additional plants– Cost for cycling the breeding population– Cost for additional parents used in crosses

• Strategy: Structuring components e.g.:– Wait for flowering - mate - establish field test - select

Combined concepts• Genetic Gain (breeding value) and Gene Diversity combined into “Group Merit” (the sum).

• Cost expressed per founder and cycle

• Time and Cost combined to “annual cost” (yearly budget)

•“Group Merit progress at annual cost” combines all issues into a single measure, which can be studied and maximized.

How it works…

Results

• Input parameters

• Get results

• Use “trial and error” to find what is best

Inpu

ts

Inputs – commonly used

• Chosen to be relevant for to discussions about breeding of Swedish (=Nordic) Norway spruce and Scots pine (we have also made studies on poplars and Eucalyps)

• Many alternative scenarios evaluated to home in on optimum• Annual budget 10 “test plant equivalents per year and founder”• Cycling cost 30 per founder• Crossing possible at age 10-15 for pine and 20 for spruce• Clone testing possible for spruce but not pine• CVAm = 14% (additive variation in value (volume) among trees at mature age)• Dominance variance ¼ of additive• Heritability almost 0.2 (within family heritability =0.1)• Note than in breeding cycler papers 2000-2005 is the population considered a

single full sib family, thus variance components are within family. That is explained and correct, but may still be misleading. In coming papers we will give it for whole population.

• Selection gain is created by selecting the best individual from each full sib or through one offspring per grandparent.

• Diversity loss with balanced 50 founder breeding, “group coancestry”, is punished as percent of forest production (probably high estimate)

• Rotation age 60• Juvenile-mature correlation according to Lambeth (1981).

Comparison of main testing strategies – best genotypes are selected based

on

• Progeny – trees with good progeny

• Clone – trees with good vegetative copies

• Phenotype – trees with good appearance

Ann

ual G

roup

Mer

it, %

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0 0.1 0.2 0.3 0.4 0.5 0.6

Narrow-sense within family heritability

Phenotype

Clone

Progeny

Clone test strategy is best

• Clone was superior for all realistic scenarios.• Swedish breeding uses clone testing with near optimal

design (acc to breeding cycler) for Norway spruce and has initiated it for lodgepole pine. Development with clone testing is initiated for Scots pine. These approaches are strongly supported by BREEDING CYCLER results.

• The optimal scenario for Norway spruce suggests later selection age in field trials than Swedish breeding heads for (20 instead of 15 years). The late sexual maturity of Norway spruce is an argument.

Phenotypic selection may be slightly superior to Progeny-testing,

for the most realistic scenarios

Time for initiation (flowering)

Early flowering improves the efficiency of progeny-testing only marginally.Early flowering may make progeny-testing marginally superior to selection on phenotype

0.05

0.10

0.15

0.20

0 3 6 9 12 15 18

Delay before establishment of

selection test (years)

Progeny

Phenotype

Annual Group Merit , %

Annual budget

Phenotype get more superior at low budget, Phenotype get more superior at low budget, progeny slightly superior at high budgetprogeny slightly superior at high budget

Progeny

Phenotype

0.0

0.1

0.2

0.3

0 5 10 15 20 25

Budget per year and parent

An

nu

al G

rou

p M

erit

, %

As phenotypic and progeny are similar, it seems logic to combine them in a two-stage strategy.

Pre-selection of phenotypes, which are progeny-tested and the best reselected.

Waiting time to sexual maturity is used for phenotypic testing!

MatingMating

Stage1: Phenotype test and pre-selection

Phenotype/Progeny strategy

Stage 2:.Sexual propagation of

pre-selected individuals

Stage 2:.Sexual propagation of

pre-selected individuals

Testing of the progenyTesting of

the progeny

Reselection based on

performance of the progeny

Reselection based on

performance of the progeny

Phenotype/Progeny strategy superior to either single stage

strategy for most relevant cases

At high budget, successful flower stimulation and low heritability, progeny test is superior.

At low budget, high heritability, low cycling cost and low penalty for diversity, phenotypic selection is preferable.

Result: 2-stage seems preferrable to Scots pine

• Early flowering at Early flowering at age 3 can make age 3 can make progeny-test progeny-test compatible with compatible with 2-stage2-stage

Main scenario

0.0

0.3

0.6

0 5 10 15 20 25

An

nu

al G

rou

p M

erit

(%

)

Age of mating for progeny test (years)

• Sexual maturity at Sexual maturity at age 10 seems optimal, age 10 seems optimal, but no marked loss if but no marked loss if sexual maturity occur sexual maturity occur first at age 15.first at age 15.

Pheno/Progeny

Progeny

Suggested good scenario for Scots pine (for one family at given annual budget)

Long-term

breedingStage 2. Progeny-test with 30 offspring

Stage 1: Test 70 phenotypes

Mating3 years

CrossPolymix (3 years)

Cycle time= 26 Gain=8%

Select the best when

progeny- test is 10 years

“Preselect”

Select 5 at age 10

Size of the breeding population

• The size of the breeding population (50) has been chosen because it is “sufficient”. We tried to optimize with breeding cycler!;

• 50 (as used in Sweden) seemed about right for spruce and pine in Sweden;

• May be a little lower for Norway spruce;

• Maybe a little higher for Scots pine;

The rest of the stuff is not published (one study in press, one in manus)

• Idea: Keep balance by monitoring grandparents instead of parents. Each grand-parent give the same contribution but parents/grandparent is an input.

• “Grandparents” can be regarded a synonym to “founders” for the situation in Sweden (50 founders/bpop).

Main result - short• Scots pine in central Sweden with 50 founders (=grandparents)• New method (balance among grandparents, 300 parents)• Earlier assumed best strategy (phenotypic selection strategy, 50 parents,

Hannrup et al 2007)• Comparison assuming the same budget and gene diversity

0

0.05

0.1

0.15

0.2

0.25

0.3

New Current

An

nu

al G

enet

ic G

ain

, %

} = 54%

Why phenotypic selection?

• Well-documentet (CJFR by Swedish breeders

• Advantage of 2-stage not large

• Special case of granparental balance with parents/grandparent = 1.

(…) (…)F1

SPM with parental balance(almost current Swedish program)

Grand parents (=founders), F0

Mating grand parentsSelect and mate 2 best sibs

(…) (…)F2

(…)(…)

2nd rank family

(…)

1st rank family

(…)

3rd rank family

(…)

nth rank family

(…)

Multiple SPMsGrandparents

=founders

Green trees show pedigree

F0

F1

F2

Cross e.g. 4 best sibs in the 2 best families (2 parents per grandparent)

Cross 4 best sibs

• Note that retrospectively SPM and multiple SPM have identical pedigrees, thus identical increase of coancestry.

• Simple SPM (phenotypic selection) is a special case of multiple SPM (“combined selection”) with 1 parent per grandparent.

Standard scenario• Heading to be relevant for Scots pine in central Sweden• Costs, field trial plant is the unit, cost components are

derived from Hannrup et al. 2007. Genetic variance components derived from Rosvall et al 2001.

• Annual budget 50/grandparent• Scots pine, cycling cost 100/grandparent• Added parent 50• 6 parents/grandparent (near optimal)• Rotation time 70 years• Field test selection at 15 (optimal slightly lower but

marginal reduction)• Breeding cycle length 20 years.• Juvenile-mature correlations for Scots pine derived from

Jansson et al (2003).

Jansson et al. 2003 is for Scots pine in southern Sweden, which is most relevant. 15 year testing time seem near optimal.

0.0

0.1

0.2

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0.4

0.5

3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21Time, years

An

nu

al g

en

eti

c g

ain

, %

Jansson et al. 2003 Gwase et al. 2000

Lambeth & Dill 2001 Lambeth 1980

Genetic gain at different parents per grandparent

Parent cost=50

0.15

0.20

0.25

0.30

0 1 2 3 4 5 6 7 8 9 10111213141516

Number of parents per grandparent

An

nu

al g

ain

, %

Optimum at 6

Phenotypic strategy

54 % better

Optimum is not strongly dependent on parent cost

0.15

0.20

0.25

0.30

0 1 2 3 4 5 6 7 8 9 10111213141516

Number of parents per grandparent

An

nu

al g

ain

, %

Cparent=100 Cparent=50

Cparent=0

Optimum P/GP rises linearly with budget

10.5

6

4.5

0

2

4

6

8

10

12

14

16

Annual budget per grandparent

Op

tim

um

nu

mb

er o

f p

aren

ts p

er

gra

nd

par

ent

Cparent=50

Cparent=100

Cparent=0

10 50 100

This study supports that the suggested strategy 5 (which will be more discussed 090816) is the best

way to breed Scots pine, and suggest the strategy is substantially

better than other alternatives.The details of the strategy as

suggested in end of December 2007 seem optimal.

This is however further investigated.

Note that the start (“phenotypic preselection) is identical to the two stage strategy, final decision need

to be done first at crossings

end