Transcript 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
Tree Breeding Tools
• Downloadable programs
• by Dag L and collaborators
• many EXCEL worksheets
(“ark” or “arkki”)
• Tutorial tools
• Seldom about characters or data
Why Tree Breeding Tools?
Think first!!!
Notes: common sense is also useful!
Garbage in = garbage out!
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
Central factors in tree breeding
• Environment
• Breeding value (Genetic Gain)
• Genetic parameters
• Gene diversity
More
gain!
More
diversity
!
Faster
!
Cheape
r!
• Time
• Cost
• Technique
Conflicting goals!!
Environment description
• Temperature climate
• Light climate
Temperature climate
TEMPPRED.EXE
• Average temperature in Sweden and
Finland
• Accumulated heat sums
• From official stations representative for
forest land 1961-1990
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
Light climate
DagL.exe
• Returns night length as a function of
date, place and night criteria.
Environment -adaptation
ADAPTATION.XLS
• Plantations site and seed source
value
• Flexibility of seed source
• Seed orchards have gain and wider
adaptation!
• Choose zone size!
Environment -adaptation
Systematic G*E
Plantation sites and seed origins described by a single value
Flexibility (C) of seed source
Performance
Cauchy function
1
C
A
B
0
Site type value
Environment -adaptation
Wider zones = more maladaptation
Performance (max=1)
Performance as a function of zone size
1.2
1.0
0.8
0.6
0.4
at zone periphery
0.2
average over zone
For Scots pine a flex
unit is around 3 lat
0
0
0.2
0.4
0.6
0.8
Zone size (flex units)
1
1.2
Environment
G*E for Random sites
How many for testing clones or progenies?
sites2001.xls
• Given: the range of environment
• Inputs:
Available resources
cost per plant and per site
VG*E
VP within site and entry
• Results:
number of plant/site and sites
Efficiency
Central factors in tree breeding
• Environment
• Breeding value (Genetic Gain)
• Genetic parameters
• Gene diversity
• Time
• Cost
• Technique
G  ih A
Selection in normaldist
SELEINT.EXE; SELENOR.EXE
• Selection intensity,i , proportional to gain
• Variance in truncation selected proportion
Selection in N(0, 1)
N (0,1)  f ( x)   ( x) 
e
 x2 / 2
2
0.4
selection intensity
0.2
truncation
point
variation
0.0
-3.0
0.0
3.0
Central factors in tree breeding
• Environment
• Breeding value (Genetic Gain)
• Genetic parameters
• Gene diversity
• Time
• Cost
• Technique
Gene diversity!
Ark=feature to
conserve diversity
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)
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
Status number
status.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
Group coancestry
coancestry_matrix.xls
• Tutorial, simple pedigree, but transparent
mother
aunt
uncle
sister
cousin
What is the group coancestry
of this ”family”?
Gene drop analyses
retention.xls
• “Drops” founder genes through a
geneology
• Returns the probability that different
numbers remains
• By Leopoldo Sanchez-Rodrigues
Central factors in tree breeding
joint consideration
• Environment
• Breeding value (Genetic Gain)
• Genetic parameters
• Gene diversity
• Time
• Cost
• Technique
Linear Deployment
Group Merit Selection
Linear deployment
• Maximises gain at given gene diversity
• It is optimal to deploy genetic materials
linearly related to their breeding value
Linear deployment
Linear Deploymen2000.xls
Performance= Breeding Value
• Any line is a solution, the question is to
what problem
Linear deployment
b (slope)
g0 (intercept)
Frequency, Proportion
Linear deployment
Frequency, Proportion
• Works also with constraint (genetic
thinning of seed orchards)
Linear deployment
with constraint
Performance
Linear deployment
selenor3.exe
• General “optimal” linear deployment
solutions for normal distribution
Group Merit Selection
CoaDemo.xls
• For demonstration
• By Zheng&Lindgren
• Input: five candidates
• Selects three, which maximises the
average of breeding value and group
coancestry
Group Merit Selection
Selection 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
Orchard Manager
orchard_management.xls
• By Kang and Lindgren
Central factors in tree breeding
- joint consideration
• Environment
• Breeding value (Genetic Gain)
• Genetic parameters
• Gene diversity
• Time
• Cost
• Technique
Gain predictor
Breeding cycler
Gain predictor
Gainpred.xls
• Predicts actually much more than gain
• Linear, short-term. ”Starts with plus trees
and ends with a seed orchard”
Breeding cycler
Breeding_cycle.xls
• By Danusevicius and Lindgren
• Long-term cyclic breeding
Tutorials
• Mini course on quantitative genetics
• Examples
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
End of slide
show - Time
for sauna!