tree breeding tools “arker assisted selection” dag lindgren presentation in finland 01-03-24

Tree Breeding Tree Breeding ToolsTools

““Arker assisted selection”Arker assisted selection”

Dag LindgrenDag Lindgren

Presentation in Finland 01-03-24

WebsiteWebsitehttp://www.genfys.slu.se/staff/dagl

contains:

• Documents

• Documentation

• Newsletter

• Thesis

• Research group

• Research targets

• Teaching

• Links

• Home page

• Tree Breeding Tools

Tree Breeding ToolsTree Breeding Tools

• Downloadable programsDownloadable programs

• by Dag L and collaboratorsby Dag L and collaborators

• many EXCEL worksheetsmany EXCEL worksheets(“ark” or “arkki”)(“ark” or “arkki”)

• Tutorial toolsTutorial tools

• Seldom about characters or dataSeldom about characters or data

Why Tree Breeding Tools?Why Tree Breeding Tools?

Think first!!!Think first!!!

Ibreeding

Notes: common sense is also useful!

Garbage in = garbage out!

Why Worksheets?Why Worksheets?

• Transparent relationsTransparent relations

• Works on most computersWorks on most computers

• Place for lots of explanationPlace for lots of explanation

• Easy to change and update Easy to change and update

• Customers can develop and adjust the toolCustomers can develop and adjust the tool

• Formula collectionFormula collection

• Own trainingOwn training

Central factors in tree Central factors in tree breedingbreeding

• EnvironmentEnvironment

• Breeding value (Genetic Gain)Breeding value (Genetic Gain)

• Genetic parametersGenetic parameters

• Gene diversityGene diversity

• TimeTime

• CostCost

• TechniqueTechnique

More

gain!

More diversit

y!

Cheaper!Faste

r!

Conflicting goals!!

Environment descriptionEnvironment description

• Temperature climateTemperature climate

• Light climateLight climate

Temperature climateTemperature climateTEMPPRED.EXETEMPPRED.EXE

• Average temperature in Sweden and FinlandAverage temperature in Sweden and Finland

• Accumulated heat sumsAccumulated heat sums

• From official stations representative for From official stations representative for forest land 1961-1990forest land 1961-1990

Example:Example:

Conf site:Conf site:

Mekrijärvi 62°46’N 30°59’E 150 m asl

March 24, 2001

Note: Outcome indicated program is about as Note: Outcome indicated program is about as reliable as Finnish weather forcast servicereliable as Finnish weather forcast service

Night length and temp is ...

Light climateLight climateDagL.exeDagL.exe

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

Environment -adaptationEnvironment -adaptation ADAPTATION.XLS

• Plantations site and seed source Plantations site and seed source valuevalue

• Flexibility of seed sourceFlexibility of seed source

• Seed orchards have gain and Seed orchards have gain and wider adaptwider adaptatation!ion!

• Choose zone size!Choose zone size!

Environment -adaptationEnvironment -adaptation

Systematic G*EPlantation sites and seed origins described by a single value

Flexibility (C) of seed sourceCauchy function

0

1

Site type value

Per

form

ance

C

B

A

Environment -adaptationEnvironment -adaptationWider zones = more maladaptation

Performance as a function of zone size

0

0.2

0.4

0.6

0.8

1.0

1.2

0 0.2 0.4 0.6 0.8 1 1.2Zone size (flex units)

Pe

rfo

rma

nc

e (m

ax=

1)

at zone periphery

average over zone

For Scots pine a flex unit is around 3 lat

EnvironmentEnvironmentG*E for Random sitesG*E for Random sites

How many for testing clones or progenies?How many for testing clones or progenies?sites2001.xlssites2001.xls

• Given: the range of environmentGiven: the range of environment

• Inputs:Inputs:Available resources Available resources cost per plant and per sitecost per plant and per siteVVG*EG*E

VVP within site and entryP within site and entry

• Results: Results: number of plant/site and sitesnumber of plant/site and sitesEfficiencyEfficiency

Central factors in tree Central factors in tree breedingbreeding

• EnvironmentEnvironment

• Breeding value (Genetic Gain)Breeding value (Genetic Gain)

• Genetic parametersGenetic parameters

• Gene diversityGene diversity

• TimeTime

• CostCost

• TechniqueTechnique

Selection in normaldistSelection in normaldist SELEINT.EXE; SELENOR.EXESELEINT.EXE; SELENOR.EXE

• Selection intensity,Selection intensity,ii , proportional to , proportional to gaingain

• Variance in truncation selected Variance in truncation selected proportionproportion

AihG

Selection in N(0, 1)Selection in N(0, 1)

2)()()1,0(

2/2xexxfN

0.0

0.2

0.4

-3.0 0.0 3.0

truncation point

selection intensity

variation

Central factors in tree Central factors in tree breedingbreeding

• EnvironmentEnvironment

• Breeding value (Genetic Gain)Breeding value (Genetic Gain)

• Genetic parametersGenetic parameters

• Gene diversityGene diversity

• TimeTime

• CostCost

• TechniqueTechnique

Gene diversity!Gene diversity!

Ark=feature to conserve diversity

Group coancestryGroup coancestry

• Average coancestry including self-coancestry Average coancestry including self-coancestry (“genomsnittligt släktskap”)(“genomsnittligt släktskap”)

• Coancestry genes IBD, gene diversity = genes Coancestry genes IBD, gene diversity = genes not identical.not identical.

• Loss of Loss of gene diversitygene diversity = group coancestry = group coancestry

• Needs a reference (“source” or “wild”, as Needs a reference (“source” or “wild”, as inbreeding or coancestry does)inbreeding or coancestry does)

Status numberStatus number

• Effective numberEffective number

• Gene diversityGene diversity loss - number with the loss - number with the same losssame loss

• TThe samehe same cumulated cumulated drift of gene drift of gene frequenciesfrequencies (cf variance effective number, (cf variance effective number, per generation) per generation)

• Inbreeding - number which at random mating Inbreeding - number which at random mating produces as much inbreedingproduces as much inbreeding

Status numberStatus numberstatus.exestatus.exe

• Input a text file with genotypes and Input a text file with genotypes and their pedigree tracking back to their pedigree tracking back to foundersfounders

• Returns status numberReturns status number

• Made by Gea, Jefferson and Weaver, Made by Gea, Jefferson and Weaver, New ZealandNew Zealand

Group coancestryGroup coancestrycoancestry_matrix.xlscoancestry_matrix.xls

• Tutorial, Tutorial, simplesimple pedigree, but pedigree, but transparenttransparent

mother

sister

aunt

uncle

cousin

What is the group coancestry of this ”family”?

Gene drop analysesGene drop analysesretention.xlsretention.xls

• ““Drops” founder genes through a Drops” founder genes through a geneologygeneology

• Returns the probability that Returns the probability that different numbers remains different numbers remains

• By Leopoldo Sanchez-RodriguesBy Leopoldo Sanchez-Rodrigues

Central factors in tree Central factors in tree breedingbreeding

joint considerationjoint consideration• EnvironmentEnvironment

• Breeding value (Genetic Gain)Breeding value (Genetic Gain)• Genetic parametersGenetic parameters

• Gene diversityGene diversity• TimeTime

• CostCost

• TechniqueTechnique

Linear DeploymentLinear DeploymentGroup Merit SelectionGroup Merit Selection

Linear deploymentLinear deployment• Maximises gain at given gene Maximises gain at given gene

diversitydiversity

• It is It is optimal optimal to deploy genetic to deploy genetic materials linearly related to their materials linearly related to their breeding valuebreeding value

Fre

qu

ency

, Pro

por

tion

Performance = Breeding Value

Linear deployment

g0 (intercept) b (slope)

Linear deploymentLinear deploymentLinear Deploymen2000.xlsLinear Deploymen2000.xls

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

Frequency, ProportionPer

form

ance

= B

reed

ing

Val

ue

Linear deployment

g0 (intercept)

b (slope)

Linear deploymentLinear deployment• Works also with constraint (genetic Works also with constraint (genetic

thinning of seed orchards)thinning of seed orchards)F

req

uen

cy, P

rop

orti

on

Performance

Linear deployment

with constraint

Linear deploymentLinear deploymentselenor3.exeselenor3.exe

• General “optimal” linear deployment General “optimal” linear deployment solutions for normal distributionsolutions for normal distribution

GGroup Merit Selectionroup Merit SelectionCoaCoaDemo.xlsDemo.xls

• For demonstrationFor demonstration

• By Zheng&LindgrenBy Zheng&Lindgren

• Input: five candidatesInput: five candidates

• Selects three, which maximises the Selects three, which maximises the average of breeding value and average of breeding value and group coancestrygroup coancestry

GGroup Merit Selectionroup Merit SelectionSelection toolSelection tool

• By Thuy OlssonBy Thuy Olsson

• Windows oriented, unpack and installWindows oriented, unpack and install

• Input: files with candidates and weight of Input: files with candidates and weight of gain versus diversitygain versus diversity

• Output: A group which maximises the Output: A group which maximises the average of breeding value and group average of breeding value and group coancestrycoancestry

Orchard Manager Orchard Manager orchard_management.xlsorchard_management.xls

• By Kang and LindgrenBy Kang and Lindgren

Central factors in tree Central factors in tree breedingbreeding

- joint consideration- joint consideration• EnvironmentEnvironment

• Breeding value (Genetic Gain)Breeding value (Genetic Gain)

• Genetic parametersGenetic parameters

• Gene diversityGene diversity

• TimeTime

• CostCost

• TechniqueTechnique Gain predictorGain predictorBreeding cyclerBreeding cycler

Gain predictorGain predictorGainpred.xlsGainpred.xls

• Predicts actually much more than Predicts actually much more than gaingain

• Linear, short-term. ”Starts with plus Linear, short-term. ”Starts with plus trees and ends with a seed orchard”trees and ends with a seed orchard”

Breeding cyclerBreeding cyclerBreeding_cycle.xlsBreeding_cycle.xls

• By Danusevicius and LindgrenBy Danusevicius and Lindgren

• Long-term cyclic breedingLong-term cyclic breeding

TutorialsTutorials

• Mini course on quantitative geneticsMini course on quantitative genetics

• ExamplesExamples

MessageMessage from a senior from a senior professor of Forest professor of Forest

GeneticsGenetics

At least one week attention on the concepts At least one week attention on the concepts behind TBT is needed each five yearsbehind TBT is needed each five years

• For all who call them-selFor all who call them-selvesves forest tree forest tree breedersbreeders

• For all who get the doctors title in forest For all who get the doctors title in forest genetics in the futuregenetics in the future

• For most professional forest geneticistsFor most professional forest geneticists

End of slide show - Time

for sauna!

Ibreeding