Post on 21-Dec-2015
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.
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.