Post on 31-Dec-2015
Male reproductive investment and success in a Larix occidentalis seed orchard population
Tomas FundaFaculty of Forestry, University of British Columbia, Canada
tfunda@interchange.ubc.ca
Outline• Introduction– Seed orchards– Fertility variation
• Materials and Methods– Western larch clonal seed orchard– Microsatellite DNA paternity analysis
• Results– Regression analyses– Genetic gain and diversity estimates
• Summary– Benefits of the simplified methods
Seed orchards Artificial populations of genetically superior trees Mass production of improved seed
http://www.hupptreefarm.com/seed_orchard.htm
Genetic gain Parental breeding values Reproductive success Pollen contamination
Number of parents Reproductive success Mating pattern Co-ancestry Inbreeding
Genetic diversity
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Reproductive investment vs. success
Investment Female• Number/volume/weight of seed cones• Number of seed per cone• Proportion of filled seed
Male• Number/volume of pollen buds/cones
Reproductive investment vs. success
???
Investment Success
unknown
Reproductive investment vs. success
???
Investment Success
unknown
Reproductive investment methods
M0: Male reproductive success is assumed to be equal to parental representation (i.e., number of ramets per plus tree)
Example: two parents in a seed orchard parent #1: 9 ramets parent #2: 1 ramets then parent #1 assumed to produce 90% of successful male gametes in seed crop whereas parent #2 only 10%
or
Reproductive investment methods
M0: Parental representation
M1: Male reproductive success is assumed to be proportional to crown volume or age of a particular parent
Reproductive investment methods
M0: Parental representation
M1: Crown volume or age adjustment
M2: Visual assessment of pollen production on at least 50% of ramets (partial pollen survey)
M3: Visual assessment of pollen production on every ramet (full pollen survey)
Seed orchard
Species: western larch, 1st generationLocation: Vernon, British Columbia, Canada
(50°14’N, 119°16’E, 480 m a.s.l.)Established: 1989Population size: 41 parents (as of 2005)
Plant material Parental population young foliage from 41 parents
Plant material Parental population young foliage from 41 parents
Offspring population37 half-sib families
• dormant vegetative buds from 2-year-old seedlings• 3-cm-long embryos
Reproductive success
10 nuclear microsatellite DNA markers multilocus probability of exclusion ≅ 1
Reproductive success
10 nuclear microsatellite DNA markers
Paternity assignment using CERVUS 3.0.3Maternal parentage knownUnassigned offspring – contamination
– insufficiently informative genotypes
Reproductive success
10 nuclear microsatellite DNA markers
Paternity assignment using CERVUS 3.0.3
Linear regression using SAS 9.1.3Dependent variable – DNA-based male reproductive success (baseline)Independent variables – fecundity scores for each simplified method(M0, M1, M2, or M3)
Reproductive success
10 nuclear microsatellite DNA markers
Paternity assignment using CERVUS 3.0.3
Linear regression using SAS 9.1.3Dependent variable – DNA based male reproductive success
(baseline)Independent variables – fecundity scores for each simplified method(M0, M1, M2, or M3)
Evaluation based on R2, RMSE, and 95% prediction intervals
Reproductive success
10 nuclear microsatellite DNA markers
Paternity assignment using CERVUS 3.0.3
Linear regression using SAS 9.1.3Dependent variable – DNA based male reproductive success
(baseline)Independent variables – fecundity scores for each simplified method(M0, M1, M2, or M3)
Evaluation based on R2, RMSE, and 95% prediction intervals
Impact on genetic gain and diversityError? Bias?
Does parental representation reflect actual male reproductive success?
Questions
Is male reproductive investment assessed through a field survey a good indication of actual male reproductive success?
Does this assessment provide unbiased estimates of crops’ genetic parameters, such as gain and diversity?
Questions
Genetic diversity status effective number (Ne)
– fertility variation– co-ancestry
Does parental representation reflect actual male reproductive success?
Is male reproductive investment assessed through a field survey a good indication of actual male reproductive success?
Does this assessment provide unbiased estimates of crops’ genetic parameters, such as gain and diversity?
Pedigree reconstruction
Total number of analyzed offspring: 2088
Assigned to one of the 41 candidate fathers: 1848 (88.5%) maximum pollen contamination 11.5%
Selfing 7.6%
Methods’ evaluationM0: Male reproductive success is a function of parental representation
R2 RMSE
M0 0.275 0.072
M1 0.499 0.060
M2 0.702 0.046
M3 0.731 0.0440.001 0.01 0.1
0.00
0.25
0.50
Male reproductive investment (M0)
Mal
e re
prod
uctiv
e su
cces
s (D
NA)
Methods’ evaluationM1: Male reproductive success is a function of parental representation adjusted for crown volume
0.001 0.01 0.10.00
0.25
0.50
Male reproductive investment (M1)
Mal
e re
prod
uctiv
e su
cces
s (D
NA)R2 RMSE
M0 0.275 0.072
M1 0.499 0.060
M2 0.702 0.046
M3 0.731 0.044
Methods’ evaluationM2: Male reproductive success is a function of male fecundity scored on 50% of trees (partial pollen survey)
R2 RMSE
M0 0.275 0.072
M1 0.499 0.060
M2 0.702 0.046
M3 0.731 0.0440.000666666666666665 0.0666666666666665
0.00
0.25
0.50
Male reproductive investment (M2)
Mal
e re
prod
uctiv
e su
cces
s (DN
A)
Methods’ evaluationM3: Male reproductive success is a function of male fecundity scored on all trees (full pollen survey)
R2 RMSE
M0 0.275 0.072
M1 0.499 0.060
M2 0.702 0.046
M3 0.731 0.044
0.00
0.25
0.50
Male reproductive investment (M3)M
ale
rep
rod
ucti
ve s
ucc
ess
(DN
A)
Methods’ evaluationM2: Male reproductive success is a function of male fecundity scored on 50% of trees (partial pollen survey)
R2 RMSE
M0 0.275 0.072
M1 0.499 0.060
M2 0.702 0.046
M3 0.731 0.0440.000666666666666665 0.0666666666666665
0.00
0.25
0.50
Male reproductive investment (M2)
Mal
e re
prod
uctiv
e su
cces
s (DN
A)
correlation = 0.97
Crops’ genetic parameters
M0 M1 M2 M3 DNA0
10
20
30
40
32.830.5
16.4 17.0 18.6
Status effective number
Stat
us e
ffecti
ve n
umbe
r
M0 M1 M2 M3 DNA
M0 M1 M2 M3 DNA10
12
14
16
18
15.915.3
15.9 15.815.3
Genetic worth
Gen
etic
wor
th
M0 M1 M2 M3 DNA
Does parental representation reflect actual male reproductive success?X No, it does not due to substantial male fertility variation.
Questions
Questions
Is male reproductive investment assessed through a field survey a good indication of actual male reproductive success?
Does parental representation reflect actual male reproductive success?
X No, it does not due to substantial male fertility variation.
Yes, it is. ü
Does this assessment provide unbiased estimates of crops’ genetic parameters, such as gain and diversity? Yes, it does, at least in western larch.
Questions
Is male reproductive investment assessed through a field survey a good indication of actual male reproductive success?
Does parental representation reflect actual male reproductive success?
X No, it does not due to substantial male fertility variation.
Yes, it is. ü
ü
“Congruence between parental reproductive investment and success determined by DNA-based pedigree reconstruction in conifer seed orchards”
Canadian Journal of Forest Research (in press)
Acknowledgement
Co-authors:Cherdsak LiewlaksaneeyanawinCharles ChenIrena FundovaChris WalshJack Woods
Supervisor:Yousry A. El-Kassaby
Thank you for your attention
Does this assessment provide unbiased estimates of crops’ genetic parameters, such as gain and diversity? Yes, it does, at least in western larch.
Questions
Is male reproductive investment assessed through a field survey a good indication of actual male reproductive success?
Does parental representation reflect actual male reproductive success?
X No, it does not due to substantial male fertility variation.
Yes, it is. ü
ü