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Tree Breeding Tools

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

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  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. Tree Breeding Tools • Downloadable programs • by Dag L and collaborators • many EXCEL worksheets(“ark” or “arkki”) • Tutorial tools • Seldom about characters or data

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

  5. 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

  6. Cheaper! More diversity! Faster! More gain! Central factors in tree breeding • Environment • Breeding value (Genetic Gain) • Genetic parameters • Gene diversity • Time • Cost • Technique Conflicting goals!!

  7. Environment description • Temperature climate • Light climate

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

  9. Night length and temp is ... Example: Conf site: Mekrijärvi 62°46’N 30°59’E 150 m asl March 24, 2001 Note: Outcome indicated program is about as reliable as Finnish weather forcast service

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

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

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

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

  14. EnvironmentG*E for Random sitesHow many for testing clones or progenies?sites2001.xls • Given: the range of environment • Inputs:Available resources cost per plant and per siteVG*EVP within site and entry • Results: number of plant/site and sitesEfficiency

  15. Central factors in tree breeding • Environment • Breeding value (Genetic Gain) • Genetic parameters • Gene diversity • Time • Cost • Technique

  16. Selection in normaldistSELEINT.EXE; SELENOR.EXE • Selection intensity,i , proportional to gain • Variance in truncation selected proportion

  17. 0.4 selectionintensity 0.2 truncation point variation 0.0 -3.0 0.0 3.0 Selection in N(0, 1)

  18. Central factors in tree breeding • Environment • Breeding value (Genetic Gain) • Genetic parameters • Gene diversity • Time • Cost • Technique

  19. Gene diversity! Ark=feature to conserve diversity

  20. 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)

  21. 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

  22. 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

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

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

  25. Central factors in tree breedingjoint consideration • Environment • Breeding value (Genetic Gain) • Genetic parameters • Gene diversity • Time • Cost • Technique Linear Deployment Group Merit Selection

  26. Linear deployment Frequency, Proportion g0 (intercept) b (slope) Performance = Breeding Value Linear deployment • Maximises gain at given gene diversity • It is optimal to deploy genetic materials linearly related to their breeding value

  27. Linear deployment b (slope) Performance= Breeding Value g0 (intercept) Frequency, Proportion Linear deploymentLinear Deploymen2000.xls • Any line is a solution, the question is to what problem

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

  29. Linear deploymentselenor3.exe • General “optimal” linear deployment solutions for normal distribution

  30. Group Merit SelectionCoaDemo.xls • For demonstration • By Zheng&Lindgren • Input: five candidates • Selects three, which maximises the average of breeding value and group coancestry

  31. 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

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

  33. Central factors in tree breeding- joint consideration • Environment • Breeding value (Genetic Gain) • Genetic parameters • Gene diversity • Time • Cost • Technique Gain predictor Breeding cycler

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

  35. Breeding cyclerBreeding_cycle.xls • By Danusevicius and Lindgren • Long-term cyclic breeding

  36. Tutorials • Mini course on quantitative genetics • Examples

  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 breeders • For all who get the doctors title in forest genetics in the future • For most professional forest geneticists

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

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