Tree Breeding Tools

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Tree Breeding Tools

• Arker assisted selection
• Dag Lindgren

Presentation in Finland 01-03-24
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Website

• http//www.genfys.slu.se/staff/dagl
• contains
• Documents
• Documentation
• Newsletter
• Thesis
• Research group
• Research targets
• Teaching
• Links
• Home page
• Tree Breeding Tools

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Tree Breeding Tools

• Downloadable programs
• by Dag L and collaborators
• many EXCEL worksheets(ark or arkki)
• Tutorial tools
• Seldom about characters or data

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Why Tree Breeding Tools?
Think first!!!
Notes common sense is also useful! Garbage in
garbage out!
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Why Worksheets?

• Transparent relations
• Works on most computers
• Place for lots of explanation
• Easy to change and update
• Customers can develop and adjust the tool
• Formula collection
• Own training

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Central factors in tree breeding

• Environment
• Breeding value (Genetic Gain)
• Genetic parameters
• Gene diversity
• Time
• Cost
• Technique

Conflicting goals!!
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Environment description

• Temperature climate
• Light climate

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Temperature climateTEMPPRED.EXE

• Average temperature in Sweden and Finland
• Accumulated heat sums
• From official stations representative for forest
  land 1961-1990

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Example
Night length and temp is ...

• Conf site
• Mekrijärvi 6246N 3059E 150 m asl
• March 24, 2001
• Note Outcome indicated program is about as
  reliable as Finnish weather forcast service

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Light climateDagL.exe

• Returns night length as a function of date, place
  and night criteria.

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Environment -adaptation
ADAPTATION.XLS

• Plantations site and seed source value
• Flexibility of seed source
• Seed orchards have gain and wider adaptation!
• Choose zone size!

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Environment -adaptation
Systematic GE Plantation sites and seed origins
described by a single value Flexibility (C) of
seed source
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Environment -adaptation
Wider zones more maladaptation
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EnvironmentGE for Random sitesHow many for
testing clones or progenies?sites2001.xls

• Given the range of environment
• InputsAvailable resources cost per plant and
  per siteVGEVP within site and entry
• Results number of plant/site and
  sitesEfficiency

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Central factors in tree breeding

• Environment
• Breeding value (Genetic Gain)
• Genetic parameters
• Gene diversity
• Time
• Cost
• Technique

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Selection in normaldist SELEINT.EXE SELENOR.EXE

• Selection intensity,i , proportional to gain
• Variance in truncation selected proportion

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Selection in N(0, 1)
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Central factors in tree breeding

• Environment
• Breeding value (Genetic Gain)
• Genetic parameters
• Gene diversity
• Time
• Cost
• Technique

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Gene diversity!
Arkfeature to conserve diversity
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Group coancestry

• Average coancestry including self-coancestry
  (genomsnittligt släktskap)
• Coancestry genes IBD, gene diversity genes not
  identical.
• Loss of gene diversity group coancestry
• Needs a reference (source or wild, as
  inbreeding or coancestry does)

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Status number

• Effective number
• Gene diversity loss - number with the same loss
• The same cumulated drift of gene frequencies (cf
  variance effective number, per generation)
• Inbreeding - number which at random mating
  produces as much inbreeding

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Status numberstatus.exe

• Input a text file with genotypes and their
  pedigree tracking back to founders
• Returns status number
• Made by Gea, Jefferson and Weaver, New Zealand

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Group coancestrycoancestry_matrix.xls

• Tutorial, simple pedigree, but transparent

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Gene drop analysesretention.xls

• Drops founder genes through a geneology
• Returns the probability that different numbers
  remains
• By Leopoldo Sanchez-Rodrigues

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Central factors in tree breedingjoint
consideration

• Environment
• Breeding value (Genetic Gain)
• Genetic parameters
• Gene diversity
• Time
• Cost
• Technique

Linear Deployment Group Merit Selection
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Linear deployment

• Maximises gain at given gene diversity
• It is optimal to deploy genetic materials
  linearly related to their breeding value

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Linear deploymentLinear Deploymen2000.xls

• Any line is a solution, the question is to what
  problem

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Linear deployment

• Works also with constraint (genetic thinning of
  seed orchards)

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Linear deploymentselenor3.exe

• General optimal linear deployment solutions for
  normal distribution

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Group Merit SelectionCoaDemo.xls

• For demonstration
• By ZhengLindgren
• Input five candidates
• Selects three, which maximises the average of
  breeding value and group coancestry

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Group Merit SelectionSelection tool

• By Thuy Olsson
• Windows oriented, unpack and install
• Input files with candidates and weight of gain
  versus diversity
• Output A group which maximises the average of
  breeding value and group coancestry

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Orchard Manager orchard_management.xls

• By Kang and Lindgren

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Central factors in tree breeding- joint
consideration

• Environment
• Breeding value (Genetic Gain)
• Genetic parameters
• Gene diversity
• Time
• Cost
• Technique

Gain predictor Breeding cycler
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Gain predictorGainpred.xls

• Predicts actually much more than gain
• Linear, short-term. Starts with plus trees and
  ends with a seed orchard

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Breeding cyclerBreeding_cycle.xls

• By Danusevicius and Lindgren
• Long-term cyclic breeding

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Tutorials

• Mini course on quantitative genetics
• Examples

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Message from a senior professor of Forest
Genetics

• At least one week attention on the concepts
  behind TBT is needed each five years
• For all who call them-selves forest tree breeders
• For all who get the doctors title in forest
  genetics in the future
• For most professional forest geneticists

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End of slide show - Time for sauna!