Long term tree breeding as analyzed by the breeding cycler tool DaDa (Dag & Darius) or (Darius & Dag)

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. Information on the net…

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) 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 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). 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. 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 my “Tree Breeding Tool” web site 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. 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 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. 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 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) 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. Group coancestry is a measure of gene diversity lost! Gene diversity and group coancestry

Components of Tree Breeding Plus trees Long-term breeding Selection Mating Gain Seed orchard Testing Initiation

Long term breeding goes on for many repeated cycles Long-term breeding Selection Mating Testing

GainPred is linear Mating? Testing? Initiation Plus trees Gain Seed orchard Non-repeated activities instead of repeated in cycles

Breeding cycler studies what happens in one complete cycle Long-term breeding Selection Mating Testing

During one complete 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 merit Lindgren and Mullin 1997

Inbreeding follows group coancestry Simulation of Swedish Norway spruce breeding program by POPSIM, BP=48, DPM, equal representation (2/parent) Generations Probability of identity by descent f Rosvall, Lindgren & Mullin 1999 Message: Group coancestry can often be regarded as a potential inbreeding, which becomes realized some generations later

During one complete 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 annual Group Merit considers three key factors: Wei and Lindgren 2001 Genetic gain; Gene diversity; Time.

During one complete 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 at a given annual cost considers four key factors: Danusevicius and Lindgren 2002 Genetic gain; Gene diversity; Time; Cost.

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 strategyWhich is the best testing strategy What is optimum breeding population size?What is optimum 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 breeding plan?Where to allocate resources to strengthen your breeding plan?

How the Cycler works (in principle) Long-term breeding Selection age ? Mating Testing size ? Inputs Genetic parameters Time components Cost component Find resource allocation that maximises GM/year? Test method Clone? Progeny? Size of breeding population?

How the Cycler works… Results You do almost nothing – input the parameters and look for result Inputs

Variables - Genetic parameters Additive variance in test Additive variance in test Dominance variance in test Dominance variance in test Environmental variance in test Environmental variance in test Coefficient of variance for additive “value for forestry” at mature age Coefficient of variance for additive “value for forestry” at mature age Breeding population size Breeding population size

Time and cost components 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 - Others Rotation time (for J*M considerations) Rotation time (for J*M considerations) Annual budget (the most important factor as any breeder knows) Annual budget (the most important factor as any breeder knows) Test method (clonal, progeny or phenotype) Test method (clonal, progeny or phenotype) J*M development curve J*M development curve Weighting factor for diversity versus gain Weighting factor for diversity versus gain

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

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