1. Tree Breeding Tools “Arker assisted selection” Dag Lindgren Presentation in Finland 01-03-24

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

3. Downloadable programsDownloadable programs by Dag L and collaboratorsby Dag L and collaborators many EXCEL worksheets (“ark” or “arkki”)many EXCEL worksheets (“ark” or “arkki”) Tutorial toolsTutorial tools Seldom about characters or dataSeldom about characters or data

4. Why Tree Breeding Tools? Think first!!! I  breeding Notes: common sense is also useful! Garbage in = garbage out!

5. 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 updateEasy to change and update Customers can develop and adjust the toolCustomers can develop and adjust the tool Formula collectionFormula collection Own trainingOwn training

6. Central factors in tree breeding EnvironmentEnvironment Breeding value (Genetic Gain)Breeding value (Genetic Gain) Genetic parametersGenetic parameters Gene diversityGene diversity TimeTime CostCost TechniqueTechnique More gain! More diversity ! Cheape r! Faster ! Conflicting goals!!

7. Environment description Temperature climateTemperature climate Light climateLight climate

8. Temperature climate TEMPPRED.EXE Average temperature in Sweden and FinlandAverage temperature in Sweden and Finland Accumulated heat sumsAccumulated heat sums From official stations representative for forest land 1961-1990From official stations representative for forest land 1961-1990

9. Example: Conf site: Mekrijärvi62°46’N30°59’E150 m asl March 24, 2001 Note: Outcome indicated program is about as reliable as Finnish weather forcast service Night length and temp is...

10. Light climate DagL.exe Returns night length as a function of date, place and night criteria.Returns night length as a function of date, place and night criteria.

11. Environment -adaptation ADAPTATION.XLS Plantations site and seed source value Plantations site and seed source value Flexibility of seed source Flexibility of seed source Seed orchards have gain and wider adaptation! Seed orchards have gain and wider adaptation! Choose zone size!Choose zone size!

12. Environment -adaptation Systematic G*E Plantation sites and seed origins described by a single value Flexibility (C) of seed source Cauchy function 0 1 Site type value Performance C B A

13. Environment -adaptation Wider zones = more maladaptation Performance as a function of zone size 0 0.2 0.4 0.6 0.8 1.0 1.2 00.20.40.60.811.2 Zone size (flex units) Performance (max=1) at zone periphery average over zone For Scots pine a flex unit is around 3 lat

14. Environment G*E for Random sites How many for testing clones or progenies? sites2001.xls Given: the range of environmentGiven: the range of environment Inputs: Available resources cost per plant and per site V G*E V P within site and entryInputs: Available resources cost per plant and per site V G*E V P within site and entry Results: number of plant/site and sites EfficiencyResults: number of plant/site and sites Efficiency

15. Central factors in tree breeding EnvironmentEnvironment Breeding value (Genetic Gain)Breeding value (Genetic Gain) Genetic parametersGenetic parameters Gene diversityGene diversity TimeTime CostCost TechniqueTechnique

16. Selection in normaldist SELEINT.EXE; SELENOR.EXE Selection intensity,i, proportional to gainSelection intensity,i, proportional to gain Variance in truncation selected proportionVariance in truncation selected proportion

17. Selection in N(0, 1) 0.0 0.2 0.4 -3.00.03.0 truncation point selection intensity variation

18. Central factors in tree breeding EnvironmentEnvironment Breeding value (Genetic Gain)Breeding value (Genetic Gain) Genetic parametersGenetic parameters Gene diversityGene diversity TimeTime CostCost TechniqueTechnique

19. Gene diversity! Ark=feature to conserve diversity

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

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

22. Status number status.exe Input a text file with genotypes and their pedigree tracking back to foundersInput a text file with genotypes and their pedigree tracking back to founders Returns status numberReturns status number Made by Gea, Jefferson and Weaver, New ZealandMade by Gea, Jefferson and Weaver, New Zealand

23. Group coancestry coancestry_matrix.xls Tutorial, simple pedigree, but transparentTutorial, simple pedigree, but transparent mother sister aunt uncle cousin What is the group coancestry of this ”family”?

24. Gene drop analyses retention.xls “Drops” founder genes through a geneology“Drops” founder genes through a geneology Returns the probability that different numbers remainsReturns the probability that different numbers remains By Leopoldo Sanchez-RodriguesBy Leopoldo Sanchez-Rodrigues

25. Central factors in tree breeding joint consideration EnvironmentEnvironment Breeding value (Genetic Gain)Breeding value (Genetic Gain) Genetic parametersGenetic parameters Gene diversityGene diversity TimeTime CostCost TechniqueTechnique Linear Deployment Group Merit Selection

26. Linear deployment Maximises gain at given gene diversityMaximises gain at given gene diversity It is optimal to deploy genetic materials linearly related to their breeding valueIt is optimal to deploy genetic materials linearly related to their breeding value Frequency, Proportion Performance = Breeding Value Linear deployment g 0 (intercept) b (slope)

27. Linear deployment Linear Deploymen2000.xls Any line is a solution, the question is to what problemAny line is a solution, the question is to what problem Frequency, Proportion Performance= Breeding Value Linear deployment g 0 (intercept) b (slope)

28. Linear deployment Works also with constraint (genetic thinning of seed orchards)Works also with constraint (genetic thinning of seed orchards) Frequency, Proportion Performance Linear deployment with constraint

29. Linear deployment selenor3.exe General “optimal” linear deployment solutions for normal distributionGeneral “optimal” linear deployment solutions for normal distribution

30. Group Merit Selection Coa Demo.xls For demonstrationFor demonstration By Zheng&LindgrenBy Zheng&Lindgren Input: five candidatesInput: five candidates Selects three, which maximises the average of breeding value and group coancestrySelects three, which maximises the average of breeding value and group coancestry

31. Group Merit Selection Selection tool By Thuy OlssonBy Thuy Olsson Windows oriented, unpack and installWindows oriented, unpack and install Input: files with candidates and weight of gain versus diversityInput: files with candidates and weight of gain versus diversity Output: A group which maximises the average of breeding value and group coancestryOutput: A group which maximises the average of breeding value and group coancestry

32. Orchard Manager orchard_management.xls By Kang and LindgrenBy Kang and Lindgren

33. Central factors in tree breeding - joint consideration EnvironmentEnvironment Breeding value (Genetic Gain)Breeding value (Genetic Gain) Genetic parametersGenetic parameters Gene diversityGene diversity TimeTime CostCost TechniqueTechnique Gain predictor Breeding cycler

34. Gain predictor Gainpred.xls Predicts actually much more than gainPredicts actually much more than gain Linear, short-term. ”Starts with plus trees and ends with a seed orchard”Linear, short-term. ”Starts with plus trees and ends with a seed orchard”

35. Breeding cycler Breeding_cycle.xls By Danusevicius and LindgrenBy Danusevicius and Lindgren Long-term cyclic breedingLong-term cyclic breeding

36. Tutorials Mini course on quantitative geneticsMini course on quantitative genetics ExamplesExamples

37. 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 breedersFor all who call them-selves forest tree breeders For all who get the doctors title in forest genetics in the futureFor all who get the doctors title in forest genetics in the future For most professional forest geneticistsFor most professional forest geneticists

38. End of slide show - Time for sauna! I  breeding