Long term tree breeding as analyzed by the breeding cycler tool

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Long term tree breeding as analyzed by the
breeding cycler tool

• DaDa
• (Dag Darius) or
• (Darius Dag)

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Information on the net
http//www.genfys.slu.se/staff/dagl/ This seminar
has a homepage with useful information for
further discussions about long-term breeding. In
particular we try to formulate a document with
possible implications The breeding cycler EXCEL
tool is on the web. It is free to anyone to make
own assumptions or developments. We would be
happy to help.
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Breeding cycler and the road to it
Breeding cycler and the road to it

• Message Breeding cycler contains accumulated
  knowledge over several decades

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Earlier formula handling

• Ca 1976 I made calculations for the efficiency of
  progeny testing. Progenies in Swedish tree
  breeding appeared much too large to be efficient
  (they are now smaller)
• 1983 I was in Australia and thought clone testing
  was good, and this could be supported by
  calculations. I contacted Martin Werner
• That resulted in gain equations in year book and
  later (1988) in spruce proceeding on a sib seed
  orchard based on clonal tested full sibs (with
  more precise gain formulas formulated in
  cooperation with Öje Danell).
• It dealt with key elements simultaneously gain,
  diversity, cost, time and technique, but in a
  clumsy way.

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GAINPRED was developed

• Deterministic Excel-based simulator available to
  the World at my Tree Breeding Tool web site was
  developed.
• I believed at that time that the World would
  gratefully receive the tools offered. But that
  was a disappointment, the only users seem to be
  my collaborators. But the tools were useful in
  producing papers by me and collaborators (even
  for collaborators operating independent). That
  has contributed to that I may appear a bit
  scientific narrow, but otherwise been fruitful.
• Rosvall et al 2001 SkogForsk redogörelse 1 is
  inspired from gain pred
• Gain pred is linear, it goes from plus tree
  selection over some breeding activities to seed
  orchards.
• It was later developed to Breeding Cycler for a
  long-term benefit

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

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

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Gene diversity and group coancestry
GD 1 - group coancestry the probability that
the genes are non-identical, thus diverse.
Group coancestry is a measure of gene diversity
lost!
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Components of Tree Breeding
Gain
Initiation
Plus trees
Seed orchard
Long-term breeding
Testing
Selection
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Long term breeding goes on for many repeated
cycles
Mating
Long-term breeding
Testing
Selection
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GainPred is linear
Non-repeated activities instead of repeated in
cycles
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Breeding cycler studies what happens in one
complete cycle
Mating
Long-term breeding
Testing
Selection
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During one complete cycle
The breeding value increases
The gene diversity decreases
Long-term breeding
How to assign a single value to the increase in
breeding value and the decrease in gene diversity?
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Group merit
weighted average of Breeding Value and Gene
Diversity   Weight Penalty coefficient
depends on the specific circumstances
Lindgren and Mullin 1997
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Inbreeding follows group coancestry
Simulation of Swedish Norway spruce breeding
program by POPSIM, BP48, DPM, equal
representation (2/parent)
0.08
Message Group coancestry can often be regarded
as a potential inbreeding, which becomes realized
some generations later
0.06
f
Probability of identity by descent
0.04
0.02
0
0
2
4
6
8
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Generations
Rosvall, Lindgren Mullin 1999
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During one complete cycle
The cycle takes a number of years, depending on
the duration of testing, mating and different
waiting times
Mating
Long-term breeding
Testing
Selection
How to consider the cycle time?
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Progress in annual Group Merit considers three
key factors

• Genetic gain
• Gene diversity
• Time.

Wei and Lindgren 2001
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During one complete cycle
Costs during a cycle is depending on number of
test plants, mating techniques, testing strategy
etc.
Mating
Long-term breeding
Testing
Selection
How to consider the cost?
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Annual Group Merit progress at a given annual
cost considers four key factors

• Genetic gain
• Gene diversity
• Time
• Cost.

Danusevicius and Lindgren 2002
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Earlier there were analogous equivalents
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But now we have digital ways..
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We have thought a lot on how to get the cycler
good and relevant
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Breeding cycler is based on within family
selection

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

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Examples of what Breeding Cycler can do

• Which is the best testing strategy
• What is optimum breeding population size?
• What is the influence of the parameters?
• When to select and what numbers to test ?
• Where to allocate resources to strengthen your
  breeding plan?

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How the Cycler works (in principle)
Size of breeding population?
Test methodClone?Progeny?
Mating

• Inputs
• Genetic parameters
• Time components
• Cost component

Long-term breeding
Selection age ?
Testing size ?
Find resource allocation that maximises GM/year?
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How the Cycler works
Results
You do almost nothing input the parameters and
look for result
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Variables - Genetic parameters

• Additive variance in test
• Dominance variance in test
• Environmental variance in test
• Coefficient of variance for additive value for
  forestry at mature age
• Breeding population size

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Time and cost components

• 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

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Variables - Others

• Rotation time (for JM considerations)
• Annual budget (the most important factor as any
  breeder knows)
• Test method (clonal, progeny or phenotype)
• JM development curve
• Weighting factor for diversity versus gain

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J-M correlation is important
Choice can be made of J-M function including
custom, Lambeth and Dill 2001 (genetic) is our
favourite.
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How the Cycler work
Insert 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.
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To optimise with breeding cycler

1. Choose the red inputs to be optimised
2. Input relevant values for the other parameters
3. Let EXCEL SOLVER find the values (allocation)
   which maximise progress in group merit