The future is genomic:
rapid clone selection forteak productivity and value
Andrew Callister

Treehouse Forest Research LLC
University of Melbourne
Olman Murillo
Instituto Tecnológico de Costa Rica
GENFORESJose Pablo Jiménez Instituto Tecnológico de Costa Rica
Abstract ID: 58875
Session Title: T2.29 Strengthening Teak Forest Management for Sustainable
Teakwood Supply Chains and Trade1

MAIN MESSAGES
1. Genomic tools have improved tree improvement outcomes acrossspecies
2. Teak improvement programs could benefit enormously:• Correcting pedigree and identity errors• Pedigree reconstruction and population merging• Improved genetic value accuracy• Faster clone selection

3. Our case study demonstrates pedigree reconstruction andgenomic prediction for teak clone selection
4. Starting from scratch: what is required to ‘get in the game’?
5. The best way forward is collaborative2

Benefits of error detection“To make no mistakes is not in the power of man”
(Plutarch, Greek philosopher)

11%5%6% - 38%

Parentage errors

30%
33%

Douglas-fir

Loblolly pine

Identity errors

10%3

Benefits of pedigree reconstruction4

Benefits of faster clone selection
For example, Lebedev et al. 2020 review:• More than 60 genomic prediction studies with forest trees• 25 species and 4 hybrid complexes

5Demonstration study:
genomic prediction for teak clone selection
GENFORES: Company cooperative across 6 Latin American countries
Data and samples were generated from a single-site clone trial in Central Costa Rica:• Genotypes for 33 clones• 10,816 SNP markers• Genetic clone values from analysis in SELEGEN for 8 traits in 36 clones• 26 clones were common to genotyped and phenotyped sets

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Relationships discovered!
Seven small full-sib families,
Each containing 2 to 3 clones.
• Clone 6P is half-sib to the full-sib
family [5M, 2M, 1M]

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Genomic Prediction results
Predictive Ability
Trait
BayesA BayesB BayesC
Form
0.40
0.40
0.39
Volume
0.60
0.59
0.57
DBH
0.65
0.64
0.66
Specific Gravity 0.58
0.57
0.58
Heartwood%
0.38
0.40
0.39
colorA-0.46-0.51 -0.51
colorB-0.03-0.03 -0.12
colorC-0.13-0.09 -0.14

BayesLasso BRR
0.37
0.40
0.58
0.60
0.56
0.66
0.51
0.59
0.380.40
-0.49
-0.51
-0.22
-0.08
-0.16
-0.11

Top 5 of 26
Joint Selection
333220048

Joint Selection
3 of 5Predicted-Observed clone
values for DBH (r=0.66):• Correlation is strongly
dependent on three
data points.
• Skewed distribution ofpredicted values

9Predicted-Observed clone
values for Specific Gravity(r=0.59):

Joint Selection
2 of 5• Data are reasonably
well distributed.

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Marker Associations: all traits
Trait

Significant
Markers

Stem Form

4 (4)Volume11 (8)DBH

8 (7)Specific Gravity

9 (8)Heartwood %0

Color A (lightness)

11 (5)

Color B (redness)0

Color C (yellowness)

1 (1)11 significant markers but
3 were completely collinear.
8 Markers contributinginformation
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Marker Associations for volume

The ‘Manhattan Plot’ shows statistical significance of each marker’s trait association

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Marker Associations: Clone Selection
Genomic Selection

Lightness

Plots of genomic index VS clone value for two promising traits –Color A has a better distribution of genomic index amongst its 5 informative markers
than Volume does amongst its 8 informative markers (less collinearity for Color13Lightness)Is genomic selection profitable for teak?
Commercial situations are unique, however in general:• State enterprises:
Longer rotations/lower MAI
Higher value productVery large estates
Large and diverse breeding populations• Investment fund-driven enterprises:
Shorter rotations/higher MAI
Smaller estates
Wide variation in access to breeding material
LET’S HAVE A CLOSER LOOK:
Assuming:• 4000 ha estate• 20-year rotation with thinning at 12 years• 10 commercial clones already in deployment• Mean MAI 7.0 m3/ha/year• Stumpage 80 USD/m314

Genomic Selection at scale: an example
Breeding As Usual
Progeny-testing(including progeny~ 5 yearsof clones)

Clone testingof best ~100genotypes~ 5 years

SELECT NEW
COMMERCIAL CLONES

Breeding population(including commercial clones)

Genomic Selection

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NPV for GS in short-rotation teak
NET PRESENT VALUE• Compared with ‘Breeding As Usual’• Initial spend 100,000 USD on
genomics (e.g. 2500 genotypes @40USD each)• 5 years shorter selection cycle• 12% discount rate
• 10 commercial clones already indeployment• Variable 1 to 10 new clones with10% greater productivity• Mean MAI 7.0 m3/ha/year• Stumpage 80 USD/m3

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We can’tafford it

Collaborate!

Yeah, but…
Collaborate!

A consortium of companies could
reduce the development cost to~ $10K each
Genomics can be used to discover
relationships amongst different
material sets

We don’t have a
breeding population
Spread the risk
Collaborate!
What if it
Share in the know-how
doesn’t work?
Share in the skills
That technology
Collaborate!
isn’t in our country
Our scientists don’t
have these skills
Collaborate!

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Thank You!

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