Long term tree Long term tree breeding as analyzed breeding as analyzed by the breeding cycler by the breeding cycler

tooltool

DaDa DaDa

(Dag & Darius) or(Dag & Darius) or

(Darius & Dag) (Darius & Dag)

http://www.genfys.slu.se/staff/dagl/http://www.genfys.slu.se/staff/dagl/

This seminar has a homepage with This seminar has a homepage with useful information for further useful information for further discussions about long-term breeding. discussions about long-term breeding.

In particular we try to formulate a In particular we try to formulate a document with possible implicationsdocument with possible implications

The breeding cycler EXCEL tool is on the The breeding cycler EXCEL tool is on the web. It is free to anyone to make own web. It is free to anyone to make own assumptions or developments. We assumptions or developments. We would be happy to help.would be happy to help.

Information on the net…Information on the net…

Breeding cycler and the road to it…Breeding cycler and the road to it…Breeding cycler and the road to it…Breeding cycler and the road to it…

Message: Breeding cycler Message: Breeding cycler contains accumulated contains accumulated

knowledge over several knowledge over several decadesdecades

Earlier formula handlingEarlier formula handling• Ca 1976 I made calculations for the efficiency of Ca 1976 I made calculations for the efficiency of

progeny testing. Progenies in Swedish tree progeny testing. Progenies in Swedish tree breeding appeared much too large to be efficient breeding appeared much too large to be efficient (they are now smaller)(they are now smaller)

• 1983 I was in Australia and thought clone testing 1983 I was in Australia and thought clone testing was good, and this could be supported by was good, and this could be supported by calculations. I contacted Martin Wernercalculations. I contacted Martin Werner

• That resulted in gain equations in year book and That resulted in gain equations in year book and later (1988) in spruce proceeding on a sib seed later (1988) in spruce proceeding on a sib seed orchard based on clonal tested full sibs (with more orchard based on clonal tested full sibs (with more precise gain formulas formulated in cooperation precise gain formulas formulated in cooperation with Öje Danell).with Öje Danell).

• It dealt with key elements simultaneously: gain, It dealt with key elements simultaneously: gain, diversity, cost, time and technique, but in a clumsy diversity, cost, time and technique, but in a clumsy way.way.

““GAINPRED” was developedGAINPRED” was developed• Deterministic Excel-based simulator available to the Deterministic Excel-based simulator available to the

World at my “Tree Breeding Tool” web site was World at my “Tree Breeding Tool” web site was developed.developed.

• I believed at that time that the World would gratefully I believed at that time that the World would gratefully receive the tools offered. But that was a receive the tools offered. But that was a disappointment, the only users seem to be my disappointment, the only users seem to be my collaborators. But the tools were useful in producing collaborators. But the tools were useful in producing papers by me and collaborators (even for collaborators papers by me and collaborators (even for collaborators operating independent). That has contributed to that I operating independent). That has contributed to that I may appear a bit scientific narrow, but otherwise been may appear a bit scientific narrow, but otherwise been fruitful.fruitful.

• Rosvall et al 2001 SkogForsk redogörelse 1 is inspired Rosvall et al 2001 SkogForsk redogörelse 1 is inspired from gain predfrom gain pred

• Gain pred is linear, it goes from plus tree selection Gain pred is linear, it goes from plus tree selection over some breeding activities to seed orchards.over some breeding activities to seed orchards.

• It was later developed to Breeding Cycler for a long-It was later developed to Breeding Cycler for a long-term benefitterm benefit

Key-problem: How to deal with Key-problem: How to deal with relatedness, effective number and gene relatedness, effective number and gene

diversitydiversity

Solution: Solution: Group coancestryGroup coancestry (equivalent (equivalent Status number, New Zealand, Xmas Status number, New Zealand, Xmas 1993)1993)

The probability for IBD is group coancestry.

f

Let's put all homologous genes in a pool

Take two (at random with replacement).

GD = 1 - group coancestry = the probability that the genes are non-identical, thus diverse.

1GD 1GD

Group coancestry is a measure of gene diversity lost!

Gene diversity and group Gene diversity and group coancestrycoancestry

Components of Tree Components of Tree BreedingBreeding

Plus trees

Long-term breedingSelectio

n

Mating

Gain

Seed orchard

Testing

Initiation

Long term breeding goes on Long term breeding goes on for many repeated cyclesfor many repeated cycles

Long-term breedingSelectio

n

Mating

Testing

GainPred is linearGainPred is linear

Mating?Testing?

Initiation

Plus trees

Gain

Seed orchard

Non-repeated activities instead of repeated in cycles

Breeding cycler studies what Breeding cycler studies what happens in happens in one completeone complete cycle cycle

Long-term breedingSelectio

n

Mating

Testing

During During one completeone complete cycle cycle

Long-term breeding

The breeding value increases

The gene diversity decreases

How to assign a single value to the increase in breeding value and the decrease in gene diversity?

weighted average of

Breeding Value and Gene

Diversity 

Weight = “Penalty coefficient”;

depends on the specific circumstances

Group meritGroup merit

Lindgren and Mullin 1997

Inbreeding follows group Inbreeding follows group coancestrycoancestry

Simulation of Swedish Norway spruce breeding program by POPSIM,

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

0

0.02

0.04

0.06

0.08

0 2 4 6 8 10Generations

Pro

bab

ility

of

iden

tity

by

des

cen

t

f

Rosvall, Lindgren & Mullin 1999

Message: Group coancestry can often be regarded as a potential inbreeding, which becomes realized some generations later

During During one completeone complete cycle cycle

Long-term breeding

How to consider the cycle time?

The cycle takes a number of years, depending on the duration of testing, mating and different waiting times

Selection

Mating

Testing

Progress in annualProgress in annual Group Merit Group Merit considers three key factors:considers three key factors:

Wei and Lindgren 2001

• Genetic gain;

• Gene diversity;

• Time.

During During one completeone complete cycle cycle

Long-term breeding

How to consider the cost?

Costs during a cycle is depending on number of test plants, mating techniques, testing strategy etc.

Selection

Mating

Testing

Annual Group Merit progress Annual Group Merit progress at a given at a given annual costannual cost considers four key factors: considers four key factors:

Danusevicius and Lindgren 2002

• Genetic gain;

• Gene diversity;

• Time;

• Cost.

Earlier there were analogous Earlier there were analogous equivalents…equivalents…

But now we have digital ways..But now we have digital ways..

We have thought We have thought a lot on how to a lot on how to get the cycler get the cycler

good and good and relevantrelevant

Breeding cycler is based on Breeding cycler is based on within family selectionwithin family selection

Acknowledgement: Large thanks to Acknowledgement: Large thanks to Swedish breeding for giving us the Swedish breeding for giving us the justification to construct a reasonable justification to construct a reasonable simple breeding cycler, that is balanced simple breeding cycler, that is balanced and where each breeding pop member and where each breeding pop member get exactly one offspring in next get exactly one offspring in next generation breeding population. Loss of generation breeding population. Loss of gene diversity is only a function of gene diversity is only a function of Breeding Population Size. It would have Breeding Population Size. It would have been much harder without this been much harder without this simplification!simplification!

DaDaDaDa

Examples of what Breeding Examples of what Breeding Cycler can doCycler can do

•Which is the best testing strategy Which is the best testing strategy

•What is optimum What is optimum breeding population size? breeding population size?

•What is the influence of the parameters? What is the influence of the parameters?

•When to select and what numbers to test When to select and what numbers to test ??

•Where to allocate resources to strengthen your Where to allocate resources to strengthen your breeding plan?breeding plan?

How the Cycler works (in How the Cycler works (in principle) principle)

Long-term

breedingSelection age ?

Mating

Testing size ?

Inputs•Genetic parameters

•Time components

•Cost component

Find resource allocation that maximises GM/year?

Test methodClone?Progeny?

Size of breeding population?

How the Cycler works…How the Cycler works…

Results

You do almost nothing – input the parameters and look for result

Inpu

ts

Variables - Genetic Variables - Genetic parametersparameters

• Additive variance in testAdditive variance in test

• Dominance variance in testDominance variance in test

• Environmental variance in testEnvironmental variance in test

• Coefficient of variance for additive Coefficient of variance for additive “value for forestry” at mature age“value for forestry” at mature age

• Breeding population sizeBreeding population size

Time and cost Time and cost componentscomponents

•Recombination (cost can be either per BP member or in total)•Cost per tested genotype (it costs to do a clone or a progeny)•Test plant can be economical unit

Cycle cost

Under budget constraint

•Recombination•Time for e.g. cloning or creation of progeny•Production of test plants•Testing time (actually usually calculated from other inputs (annual cost)•Note that a longer cycle allows higher cost during the cycle

Cycle time

Variables - OthersVariables - Others

• Rotation time (for J*M considerations)Rotation time (for J*M considerations)

• Annual budget (the most important Annual budget (the most important factor as any breeder knows)factor as any breeder knows)

• Test method (clonal, progeny or Test method (clonal, progeny or phenotype)phenotype)

• J*M development curveJ*M development curve

• Weighting factor for diversity versus Weighting factor for diversity versus gaingain

J-M correlation is important J-M correlation is important

Choice can Choice can be made of be made of J-M function J-M function including including customcustom, , Lambeth and Lambeth and Dill 2001 Dill 2001 (genetic) is (genetic) is our favouriteour favourite..

0.0

0.2

0.4

0.6

0.8

1.0

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)

J-M

co

rre

lati

on

Lambeth (1980)Lambeth (2001)Gwaze (2000)Custom

How the Cycler workHow the Cycler workInsert all red values (or let them remain at the initial choices). The worksheet will calculate the blue values with information of the consequences of your choices.

You may use the tool just to compare alternatives.

Technical Tip: It may be a good idea to use empty space on the worksheet to note outcomes of different alternatives.

To optimise with breeding To optimise with breeding cyclercycler

1. Choose the red inputs to be optimised2. Input relevant values for the other parameters3. Let “EXCEL SOLVER” find the values (allocation) which

maximise progress in group merit