Tree Improvement 2018: Challenges and Opportunities

on the Horizon

G.R. Hodge

INIA Conference on Tree Improvement, Aug 9, 2018

• Climate Change• Globalization• Pests and Pathogens• Hybrids• Genomics

E. grandis plantations, Colombia

New Challenges, New Opportunities

Projected TemperatureChange (˚C)

Summer Winter

Nea

r Fut

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2039

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stan

t Fu

ture

(2

075

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Blázquez et al. 2012. Atmospheric and Climate Sciences 2: 381-400

Summer Winter

Nea

r Fut

ure

(201

5 –

2039

)Di

stan

t Fu

ture

(2

075

–20

99)

Projected PrecipitationChange (mm/day)

Blázquez et al. 2012. Atmospheric and Climate Sciences 2: 381-400

Climate Outlook for Uruguay

• Summer temperatures warmer• Winter temperatures similar (or slightly lower)• Precipitation similar• Slightly higher year-to-year variation in temperature and precipitation.

Mar 16, 2018Will today’s commercial species be well adapted to the climate of 2030? Or 2050?• When are we going to develop

those genetic resources?

Unimproved P. greggii and P. tecunumaniicompetitive with improved seed orchard P. taeda

P. greggii – an alternate pine species for La Plata Basin?

P. taeda OrchardTop P. taeda Families38% and 48% gain

2nd Gen P. greggii Progeny Test – La Fortaleza, Argentina

3-year Results 80% of 2nd gen P. greggii families are better than

the P. taeda seed orchard bulk.

Several P. greggii families are as good as the best commercial families of P. taeda

▫ with +38% and +48% gain estimates.

P. greggii – an alternate pine species for La Plata Basin?

Climate – Pest/Pathogen Interactions

Direct Impacts Higher temperatures, milder winters

▫ Greater over-winter survival▫ Increased spore production

Longer growing seasons▫ Accelerated life-cycles, generations per year▫ Earlier appearance in spring

Indirect Impacts Host plants

▫ Distribution?▫ Plant metabolism?

Biotic factors▫ Predators?▫ Competitors?

Abiotic factors▫ Drought? ▫ Heat? ▫ Flooding?

Pests and Pathogen problems in forestry will be more common in the future. (Wingfield et al. 2001, Wingfield 2003, Burdon et al. 2006)

• Climate change• Connected world (93,000 commercial flights daily)

http://www.flixxy.com/scheduled-airline-flights-worldwide.htm

Globalization

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Pests Pathogens

Globalization

Recorded pests and pathogens on eucalypts in South Africa

Forest Pests / Pathogens

Generally can find genetic resistance in most species to most pests and pathogens For example, P. taeda (and P. elliottii) and Cronartium fusiformae

▫ Some families / clones are almost immune!

R50 = 6(resistant)

R50 = 75(susceptible)

Forest Pests / Pathogens

Acacia mangium Important hardwood plantation species in southeast Asia

▫ Significant plantation programs began in the 1980s.▫ Several million hectares in Indonesia, Malaysia, and other tropical countries.

Forest Pests / Pathogens

Disease symptoms caused by Ceratocystis acaciivora sp. nov. and C. manginecanson A.mangium trees in Indonesia. Photos by Tarigan et al. 2010, SAfrJBotany.

Acacia mangium Important hardwood plantation species in southeast Asia

▫ Significant plantation programs began in the 1980s.▫ Several million hectares in Indonesia, Malaysia, and other tropical countries.

Ceratocystis acaciavora first described in 2010.▫ Apparently no resistance found within Acacia mangium.▫ Species is effectively lost as a commercial option.

Forest Pests / Pathogens Nambiar et al. 2018. Paths to sustainable wood supply to the pulp and paper industry in Indonesia after diseases have forced a change of species from acacia to eucalypts. Aus For https://doi.org/10.1080/00049158.2018.1482798

ABSTRACTIn Sumatra and Kalimantan in Indonesia and Sabah in Malaysia,

the spread of two diseases, aggravated by damage by fauna, and by the humid tropical environment, has forced a change of planted species from Acacia mangium to Eucalyptus pellita and related interspecific hybrids, at a scale unprecedented in the history of plantation forestry. This experience highlights the risks of relying on any single species for large contiguous plantation estates in environments with endemic biotic and abiotic stresses.

Forest Pests / Pathogens

Eucalyptus grandis the most important commercial eucalyptus species worldwide Leptocybe invasa (gall wasp)

▫ Native to Australia, introduced into 34 countries (Asia, Africa, Europe, Latin America, Middle East, and North America) worldwide as of 2012.

▫ Galls induce extremely stunted new growth , malformed stems, and mortality.▫ Commercial utility severely threatened; must move to other species or hybrids.

Photo by Z. Mendel, FAO, 2012. Photo by R. Nadel, ICFR, South Africa, 2011

Forest Pests / Pathogens

Other pathogens – potential threats• Botryosphaeria• Ceratocystis• Chrysoporthe• … and many more!

Eucalyptus rust Austropuccinia psidii, a pathogen

native to MesoAmerica which attacks native Myrtaceae.

The pathogen infected exotic eucalypt plantations, and is now a worldwide concern

pest.ceris.purdue.edu

DFP (Dano Foliar del Pino) on P. radiata, Chile• First detected in 2004• > 60,000 ha killed in 2006• Caused by a new Phytophthora species, P. pinifolia

Currently not a serious problem, but the conditions that produced the outbreak are unknown.

Forest Pests / Pathogens

Case Study: Fusarium circinatum in South Africa

Fusarium circinatum• Causes pitch canker in many pine species.• Native to southeastern US or Mexico.

Pitch canker disease on P. radiata in California

Forest Pests / Pathogens - Value of Species Diversity

Pinus patula• Primary pine species in South Africa• Grown for more than 100 years• Very susceptible to pitch canker.

F. circinatum in South Africa• First noted in early 1990s.• Severe impacts in nurseries and on first-year survival of P. patula.• On more than half land base, commercial plantations not viable.

Case Study: Fusarium circinatum

Large variation among species in resistance to Fusarium• Very susceptible: P. radiata, P. patula.• Moderately resistant: P. taeda, P. elliottii• Very resistant: P. oocarpa, P. tecunumanii, P. maximinoi, P. jaliscana.

Pine Hybrid Breeding and Testing

Pine Hybrid Trials• 84 total pine hybrid trials planted

▫ > 60 trials with age 3, 5, and/or 8-year data.

Propagation of the 3rd pine hybrid series at Mondi, South Africa

6-year-old P. greggii x P. tecunumanii at AraucoArgentina

Fusarium Tolerance• P. patula is very susceptible, P. tecunumanii is very tolerant

• Pat x tec hybrid has moderate to good toleranceo Can successfully establish plantations with hybrid cuttings.

pat x tec patula

P. patula x P. tecunumanii

Shafton, KZN (Sappi)• Lat = 29° S• Elev = 1180 m• Precip = 998 mm

pat x tecL, age 5 yearspat age 5 years

P. patula x P. tecunumanii

Pine Hybrid Commercialization

P. patula x P. tecunumanii• Many South African members are pursuing pat x tec as a commercial “species”.

▫ Sappi, SAFCOL, Mondi, Merensky, York.

P. patula x P. techybrid, 9 years old, SAFCOL

Solution to F. circinatum problem in South Africa• Alternate species: P. tecunumanii, P. maximinoi. • Hybrid: P. patula x P. tecunumanii

• Intermediate to good in Fusarium resistance. • Bonus: faster growth than both parent species!• Bonus: better wood properties than P. patula!

The South African forest industry is shifting from P. patula to P. patula x P. tecunumanii.

• Scaling up – shift limited only by capacity to produce hybrid seed and cuttings.

• Rapid response possible because of 25 years of testing and development of alternate species.

Forest Pests / Pathogens - Value of Species Diversity

Pine Hybrid Breeding and Testing

P. patula x P. tecunumanii Full-Sib Breeding• Collaborative project among 8 Camcore members

▫ Hans Merensky, Komatiland Forests (KLF), Mondi, MTO Forestry, PG Bison, Sappi, York Timbers, SKC

▫ Coordinated by Camcore

• Target = 250 to 300 full-sib families▫ 43 patula

▫ 55 tec HE, 43 tec LE

• Completed 3rd year of breeding▫ Propagation for testing in 2018.

P. patula x P. tecunumaniibreeding at Sappi, South Africa

A number of successful hybrids…• Populus nigra x P. deltoides, P. trichocarpa x P. deltoides• Larix decidua x L. laricina, L. decidua x L. kaempferi• Eucalyptus grandis x E. urophylla, E. grandis x E. camaldulensis• Pinus rigida x P. taeda, P. elliottii x P. caribaea

More Hybrids in Tree Improvement in the Future

Why More Hybrids?

Insects & Diseases• Hybrids will be a way to add resistance, but keep genetic gains.

Climate Change• Hybrids will be a way to modify adaptability, but keep genetic gains.

▫ add drought tolerance, frost tolerance, better growth in warmer climates.

Why More Hybrids?

Hybrids often show heterosis for growth traits.• Complementarity?• Increased heterozygosity is beneficial?

E. grandis x E. nitens E. nitens

Mpumalanga province, South Africa

Why More Hybrids?

Hybrids often show heterosis for growth traits.• Complementarity?• Increased heterozygosity is beneficial?

P. elliottii P. elliotti x P. oocarpa

John Meikle Forest Research Station, Zimbabwe

Age 4 years, Alto Paraná, Misiones, Argentina

caribaea x tec

taeda

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Hybrid: P. caribaea x P. tecunumanii8-year data

Treatments HT (m) DBH (cm)CAR x TECL 17.2 26.4 0.3767 A

CAR x OOC 16.5 23.5 0.2910 B

P. taeda 14.2 24.8 0.2833 B

P. tecunumanii 15.8 23.6 0.2784 BC

ELL x CAR 14.7 22.5 0.2615 BCD

P. oocarpa 14.5 22.5 0.2303 CD

PAT x GRS 13.0 22.8 0.2213 D

PAT x PRI 13.2 21.4 0.2137 D

PAT x ELL 12.6 18.9 0.1452 E

ELL x TECH-26 10.0 14.5 0.0746 F

VOL (m3)

P. greggii x P. tecunumanii at 5 years of age Misiones, Argentina (Arauco Argentina)

Hybrid: P. greggii x P. tecunumanii

Different species have different advantages.

• Adaptability, Growth• Disease Tolerance• Rooting• Wood Quality

Breeders will want to put the best traits from different species together in a single package.

Why More Hybrids?

E. globulusExcellent pulp qualityCool temperate speciesDoes not root

E. camaldulensisDrought tolerantHigh density woodSlower growth.

E. pellitaGood growthGood rootingHigh densityDisease resistanceLittle frost resistance

E. grandisGood growthGood rootingDisease susceptibleLittle frost resistanceLow wood density

E. nitensVery fast growth!Good frost resistanceDoes not rootTiny flowers

Barriers to Hybridization (Species = Reproductively Isolated)• Geographic or Temporal

▫ Flowering region or time does not normally overlap• Biological or Genetic

▫ Physical, chemical, genetic▫ Pre-fertilization or Post-fertilization

Challenges with Hybrids

Mass production of hybrids • Limited seed

• Special seed orchard designs• MCP = mass control pollination

• Vegetative multiplication• Clones (easy and normal for eucalypts)• Full-sib family propagation (only option for pines)

G G G G G G G G G

G N G G N G G N G

G G G G G G G G G

G G G G G G G G G

G N G G N G G N G

G G G G G G G G G

Hybrid Quantitative Genetics

P. patula x P. tecunumanii LE• 101 families from 18 P. patula and 15 P. tecunumanii L parents

• Trait = volume 5-8 years, mean = 100%

• ± 2 σGHA-pat = ± 20.8%

• ± 2 σGHA-tecL = ± 24.7%

• ± 2 σSHA-pat x tecL = ± 17.8%

P. patula x P. tecunumanii L, age 5 years, South Africa

• Large SHA (dominance) variance pushes towards full-sib testing.

• The best full-sib families will have a good GHA-pat, good GHA-tecL, and a good SHA-pat x tecL.

Species A1 Species B1

Hybrid Progeny

Tests

Breeding Population

Breeding Population

informationinformation

Species A2 Species B2

Hybrid Progeny

Tests

informationinformation

Reciprocal Recurrent Selection

• Generally thought to be slow and expensive• Should make gain regardless of gene action

• RRS will produce 50:50 hybrids.• Are 50:50 hybrid optimal?

Are 50:50 hybrids optimal? • P. patula x P. tecunumanii hybrids in South Africa

▫ P. patula brings broad adaptability, tolerance to frost, good form▫ P. tecunumanii brings fast growth, tolerance to Fusarium, good wood properties.

• F1 hybrid would be roughly intermediate for most traits.

• Is it possible to get all of the best P. patula genes andall of the best P. tecunumanii genes into a single package?▫ Optimal blend of P. patula genes and P. tecunumanii genes will probably vary by trait.

Hybrid Breeding Strategies

Synthetic Variety (or Composite Variety)• Use F1 hybrids as a base population• Breed and Select with the F1 hybrid as though it were a pure species.• Normal recurrent selection• Valuable genes, regardless of species origin, will recombine and be selected for in

some optimum proportion.

Hybrid Breeding Strategies

Species A1

Breeding Population

Synthetic or Composite Breeding

Hybrid1

Hybrid2

for deployment(some testing?)

Species B1

informationHybrid F2Progeny

Tests

Hybrid F3Progeny

Tests

• Gain depends on gene action.• Will hybrid behave like a pure

species in terms of genetic architecture?

• Use F1 hybrids as a base population

• Breed and Select with the Hybrid as though it were a pure species.

A range of hybrid types, some more A-like, some more B-like

P. elliottii x P. caribaea, F2 and Synthetic Breeding

Comparison of F1 and F2 seedlings in Queensland, Australia• No difference in volume growth between F1 and F2 seedlots• No increase in variability in F2 seedlots• Better seed yields in the F2 than in the F1

• (seed/cone = 80 vs 20)These data support the use of Synthetic Breeding for ell x car.• (Kerr et al. 2004a, 2004b,

Dieters and Brawner 2007).

Similar results with ell x car in China (Zheng 2000) and with rigida x taeda in Korea (Byun et al. 1989).

Genomic Tools

Eucalyptus SNP chip• 240 trees from 12 species

▫ grandis, urophylla, saligna, pellita, camaldulensis, tereticornis, brassiana, globulus, benthamii, dunnii, viminalis, nitens (Symphomyrtus)

• 51,000 polymorphic SNPs▫ 28,000 to 48,000 SNPS found for related species▫ pilularis (Eucalyptus), cloeziana (Idiogenes), Corymbia

42

Juan José Acosta NCSU(Camcore)

Richard SneizkoUS Forest Service

Jill WegryznUCONN

Fikret IsikNCSU (NCSU-TIP)

Andrew Eckert VCU

Genomic Tools

Conifer SNP chips – on the horizon• USDA-NIFA grant

▫ Discover, annotate and validate SNPs from millions of potential loci.▫ Organize genomic resources in TreeGenes database for community access.

Genomic Tools

Conifer SNP chips – on the horizon• Agreements with ThermoFisher to produce operational chips (with 50K SNPs)

for six conifer species consortiums in the next six to 24 months▫ P. taeda & P. elliottii▫ Tropical Pines: P. tecunumanii, P. patula, P. greggii,

P. oocarpa, P. caribaea, P. maximinoi▫ Radiata Pine (P. radiata)▫ Scots pine (P. sylvestris)▫ Western white pine, Douglas fir▫ European pines

Fikret IsikNCSU (NCSU-TIP)

P. taeda & P. elliottii Tropical Pines

Juan José Acosta NCSU(Camcore)

Zander MyburgUniv. of Pretoria(For. Molecular Genetics)

Relatively Inexpensive• ≈ $27/sample

▫ Consortium members pay $20/sample ▫ DNA extraction ≈ $7/sample

How Can Tree Breeders Use SNP Chips?

Fingerprinting• Identify verification (rather high error rates are sometimes found!)

▫ Seed orchard clones▫ Progeny test family identification▫ Clonal ID in nurserys or tests.

• Mating dynamics in seed orchards, e.g., ▫ Pollen contamination▫ Variation in parental contribution to seed crops

• These kinds of studies can be done with other markers (e.g., SSRs or microsatellites),

• but SNP price is competitive.

How Can Tree Breeders Use SNP Chips?

Pedigree Reconstruction• Identify fathers in OP or Pollen-mix progeny tests

▫ Control male pedigree, relatedness in selections▫ Can avoid CP crossing, but still can analyze as full-sib progeny tests

• These kinds of studies can be done with other markers (e.g., SSRs or microsatellites),

• but SNP price is competitive!

Lambeth et al. 2001, El-Kassaby and Lstiburek 2009

How Can Tree Breeders Use SNP Chips?

“Breeding without Breeding”• “Mejoramiento sin cruces”• Plant unstructured “progeny tests” with orchard seed = uniform plantation

▫ Uniform plantation▫ Measure phenotype + genotype with SNPs▫ Reconstruct the pedigree▫ With pedigree + phenotype, we now have a “progeny test”.

El-Kassaby and Lstiburek 2009,Lstiburek, Hodge, and Lachout 2015

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• measure all trees• genotype all trees• Analyze as “progeny test”

How Can Tree Breeders Use SNP Chips?

“Breeding without Breeding”• Can be low-cost option for alternate species

▫ Don’t do intensive breeding and testing of all species▫ Just plant pilot plantations of possible species▫ If a species has demonstrated utility, use BwB to recover genetic information.

• Defers costs to the future, and only for a subset of alternate species options.

Lstiburek, Hodge, and Lachout 2015,Lstiburek et al. 2017

• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •• • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • •

• measure all trees• genotype all trees• Analyze as “progeny test”

How Can Tree Breeders Use SNP Chips?

Genomic Selection (GS)• Similar in concept to Marker-Aided Selection (MAS)

▫ Select based on molecular markers associated with QTL (Quantitative Trait Loci)▫ Did not work because of insufficient number of markers

• GS is “new and improved” MAS▫ Using thousand of SNPs▫ Full genome coverage▫ Can find consistent marker-phenotype associations in the population

How does GS work?• Training population, Validation population

▫ Measure phenotype (all traits of interest) and genotype (e.g., 5K to 50K SNPs)▫ Build statistical models relating markers to phenotypes on Training Pop’n▫ Test models on Validation Pop’n

• Application – future selection populations▫ Marker genotypes used to predict Genomic Breeding Values

GS for Tree Breeding – Possible Advantages

Reduce progeny testing costs• Eliminate progeny testing – reduce time for breeding cycle

▫ Increasing genetic gain per unit time• Reduce number of genotypes in progeny testing

▫ e.g., pre-select before going into clonal testing

Increase accuracy of progeny selection• Selection based on the genotype (using the markers),

not on the low-heritability phenotype▫ More accurately select the best progeny within the top families

How valuable would these advantages be for tree breeders?

GS for Tree Breeding – Reduce Breeding Cycle

GS can be done at at the seedling stage• Early selection! Good accuracy!• Measure DNA, make selections, and immediately start breeding!

How much could we reduce the breeding cycle? • Tree are long-lived organisms.• It takes time to reach reproductive maturity.

▫ 2 to 3 years for tropical eucalypts Can accelerate with paclobutrazol??

▫ 3 to 6 years for temperate conifers Can accelerate with topgrafting??

• We already do early selection near the age of reproductive maturity. ▫ Selection is often at 1/3 to ½ rotation age.▫ at age 3 to 4 for tropical eucs on 8-year rotation.▫ at age 5 to 7 for species grown on 15 to 20 year rotations.

Reduction in breeding cycle• Maybe 1 to 2 years cycle reduction for short-rotation species?• Maybe 10 to 15 years cycle reduction for long-rotation species?

P0 generation(40 parents)

F1 progeny

mating

GS modelPhenotypes,DNA markers2018

past

GS for Tree Breeding – Reducing the Breeding Cycle

Training

Validation

GS model works on Validation Population!

F2 progeny

Select Breeding Pop’nmating

GS modelfuture

F3 progenythousands

Select Breeding Pop’n,mating

future

Poor to Fair GoodWill GS model work on the future population?• LD breakdown?

DNA markers

GS for Tree Breeding – Increasing Accuracy of Selection

Growth Traits -- low heritability, normal progeny testing• Accuracy of progeny BLUPs is usually around Corr(gw,ĝw) ≈ 0.50.• GS might be able to produce Corr(g,ĝ) ≈ 0.75.

Is there another way?

Progeny testing + clonal replication• Tree breeders can clone genotypes to increase accuracy of selection.

▫ Even for pines! ▫ Hedge seedlings, make clonal replicates.▫ Not for clonal forestry, but for selection within family.

P. taeda case study (Isik et al. 2004)• 6-year volume• 25 clones/FS family, 4 test sites, 4 ramets/clone/site.• h2

f = 0.62, and h2w for clones within family = 0.70.

• Corr(g,ĝ) ≈ 0.80

Similar accuracy!• GS is expensive in $$• Clonal replication is a

substantial amount of work.

Good genotypes used for plantations

F1 progeny2018 Training

Validation

P0 generation(40 parents)

mating

GS modelPhenotypes,DNA markers

past

GS for Tree Breeding – Increasing Accuracy of Selection

GS model works on Validation Population!

New F1 progeny 2021Poor to Fair GoodDNA markers

mating

GS model will work on the Application Population!• Same families• Same markers

P0 generation(40 parents)

GS model

GS for Tree Breeding – Improved Full-sib Family Forestry

New F1 progeny 2021Poor to Fair GoodDNA markers

mating

Good genotypes used for plantations

Good genotypes identified at seedling stage• Without progeny testing, while still juvenile! • Top genotypes converted to hedges for

vegetative propagation

GS for Tree Breeding – Improved Full-sib Family Forestry

P. taeda (Zapata-Valenzuela 2011)

Methods▫ 149 clones, 13 full-sib families, 18 parents

▫ 4 to 6 sites

▫ Training population size = 75 clones

▫ Validation population = 75 clones

▫ 3406 SNPs

Results▫ 5-year height, Corr(g,ĝ) = 0.55▫ Lignin, cellulose (Corr(g,ĝ) = 0.75

Picea mariana (Lenz et al. 2017)

Methods▫ 734 progeny, 34 full-sib families, 27 parents

▫ 4 sites

▫ Ten-fold validation (Training = 90%, Validation = 10%)

▫ 4993 SNPs

Results▫ 25-year DBH, Corr(g,ĝ) = 0.84▫ Density (Corr(g,ĝ) = 0.83

Case Studies: small populations, small marker sets

New SNP chips will have 25,000 to 50,000 SNPs!

GS for Tree Breeding – Improved Full-sib Family Forestry

Should work even better with hybrids than with pure species!• Higher levels of LD• Consistent marker-phenotype associations?

P. patula x P. tecunumanii full-sib hedges, SKC, Colombia

Summary

Re-emphasize Diversity• Within-species• Species diversity• Hybrids

New Technology• Getting closer to the

genotype• Computing power to

analyze

Changing Environments• New climates• New pests• New products

Find the Balance• Understand the options

(old and new)• Find the optimum

strategy