Transcript Long term trTree breeding as analysed by the breeding

Long term tree breeding
as analyzed by the
breeding cycler tool
DaDa
(Dag & Darius) or
(Darius & Dag)
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.
Breeding cycler and the road to it…
Message: Breeding cycler contains
accumulated knowledge over
several decades
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.
“GAINPRED” was developed
• Deterministic Excel-based simulator available to the World at
•
•
•
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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
Key-problem: How to deal with relatedness,
effective number and gene diversity
Solution: Group coancestry (equivalent
Status number, New Zealand, Xmas 1993)
Let's put all homologous genes in a pool
Take two (at random with replacement).
The probability for IBD is group coancestry.
f
Gene diversity and group coancestry
GD  1  
GD = 1 - group coancestry = the probability that
the genes are non-identical, thus diverse.
Group coancestry is a measure of gene
diversity lost!
Components of Tree Breeding
Gain
Initiation
Plus trees
Selection
Mating
Long-term
breeding
Seed orchard
Testing
Long term breeding goes on for
many repeated cycles
Mating
Selection
Long-term
breeding
Testing
GainPred is linear
Initiation
Gain
Plus trees
Testing?
Mating?
Seed orchard
Non-repeated activities instead of repeated in cycles
Breeding cycler studies what
happens in one complete cycle
Mating
Selection
Long-term
breeding
Testing
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?
Group merit
weighted average of
Breeding Value and Gene
Diversity
Weight = “Penalty coefficient”;
depends on the specific circumstances
Lindgren and Mullin 1997
Inbreeding follows group coancestry
Simulation of Swedish Norway spruce breeding program
by POPSIM,
BP=48, DPM, equal representation (2/parent)
Probability of identity by descent
0.08
Message: Group coancestry can often be
regarded as a potential inbreeding, which
becomes realized some generations later
0.06
f
0.04
0.02
0
0
2
4
6
8
10
Generations
Rosvall, Lindgren & Mullin 1999
During one complete cycle
The cycle takes a number of years, depending on the duration of
testing, mating and different waiting times
Mating
Selection
Long-term
breeding
Testing
How to consider the cycle time?
Progress in annual Group Merit
considers three key factors:
• Genetic gain;
• Gene diversity;
• Time.
Wei and Lindgren 2001
During one complete cycle
Costs during a cycle is depending on number of test plants, mating
techniques, testing strategy etc.
Mating
Selection
Long-term
breeding
How to consider the cost?
Testing
Annual Group Merit progress at a given
annual cost considers four key factors:
• Genetic gain;
• Gene diversity;
• Time;
• Cost.
Danusevicius and Lindgren 2002
Earlier there were analogous
equivalents…
But now we have digital ways..
We have thought a
lot on how to get
the cycler good
and relevant
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
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?
How the Cycler works (in principle)
Size of breeding
population?
Mating
Inputs
•Genetic parameters
•Time components
•Cost component
Selection
age ?
Find resource allocation that
maximises GM/year?
Test method
Clone?
Progeny?
Long-term
breeding
Testing
size ?
How the Cycler works…
Results
You do almost nothing – input the parameters and look for
result
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
Time and cost components
Cycle cost
Under budget
constraint
•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 time
•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
Variables - Others
• Rotation time (for J*M considerations)
• Annual budget (the most important factor
as any breeder knows)
• Test method (clonal, progeny or
phenotype)
• J*M development curve
• Weighting factor for diversity versus gain
J-M correlation is important
Lambeth and
Dill 2001
(genetic) is our
favourite.
0.8
J-M correlation
Choice can be
made of J-M
function
including
custom,
1.0
0.6
0.4
0.2
Lambeth (1980)
Lambeth (2001)
Gwaze (2000)
Custom
0.0
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)
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.
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