Immediate Applications of Biotech in Tree Breeding

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Immediate Applications of Biotech in Tree
Breeding????

• 061201
• Dag Lindgren

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Background

• Harvesting time, now Swedish Forest Tree Breeding
  wants to harvest the knowledge generated by the
  investment in the research school. The structured
  courses are now over. Of course you cannot have
  made much research, but you should be aware of
  things like molecular breeding immediatly
  available done somewhere in the world and you
  should have learnt to think. You should new more
  about the detailed and what happened recently
  than the senior scientists! Now Swedish Forest
  Tree Breeding want to benefit from that. I do not
  mean that you should comment now, but in the
  coming months, preferable to me or Bengt.
• I am asked to do this and not a specialist on
  some of what I say or talk about a chosen subject
  or my speciality. But there is a process
  initiated to draw out what is available now for
  operations.
• This presentation is partly a start up of a long
  discussion, not only a statement of facts. Part
  of it I have never presented before. Some
  sentences are generalisations meant to stimulate
  thought.
• SkogForsk has initiated a discussion about
  immediate biotech applications the coming year
  as a part of a revision of the Swedish Tree
  Breeding plan. Bengt and I will think
  particularly on biotech. This presentation can
  (among other things) be seen as a preparation for
  that. The other presentations Dec 1 will give a
  good and updated introduction, and we may revise
  with the new knowledge they bring. I ask Rosario
  and Pär to send Bengt and me any material
  relevant to (almost) immediate applications. A
  part of the discussion is off course what is
  immediate, but this is not the right place and
  time for that.
• GMO half the time - will be about GMO and is
  almost identical to a presentation in Umeå
  06-03-08. However, I may rush it through if times
  get short in the end
• Is GMO immediate? Skogen Oktober 2006
• Om mindre än ett decennium kan det finnas
  genetiskt modifierade lövplantor på marknaden
  menar Ove Nilsson. Therefore it is a need of
  reviewing this subject in the context immediate
  applications. There are many present now, which
  were not present at the earlier presentation.
• http//www.genfys.slu.se/staff/dagl/Documentations
  /GMOs/GMO_presentation_06.ppt
• GMO presentation is available on the web with the
  URL given, the first presentation I feel will
  rather soon be improved so I do not want to share
  it too widely yet. But if you ask me for it on
  email you will get it as a reply (when I get your
  email also).

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Earlier history not encouraging!

• Triploidi!
• The initiating event in plant breeding was that
  the plant breeder Nilsson-Ehle detected 1935 that
  an aspen with big leaves was triploid, thus a
  direct link between genetic constitution and
  production. The picture is a ramet of that tree.
  Triploids was the first idea tried, but never
  become important.

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Mutations

• I have a BSc in physics and was employed at the
  Royal College of Forestry 1967 to run dosimetry
  for mutation research. The professor at that time
  (Åke Gustafsson) thought that mutations could
  become useful. I soon realised that this was a
  dead end for forest trees and started to think on
  something else.

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1995 SkogForsk förädlingsutredninginitiated work
with

• Early tests
• Faster cycling (early flowering)
• Early tests (mostly in phytotron) did not work.
• Flowering stimulation not evaluated yet

Still I think people are keen to go on with the
same desires so most of the questions will off
course remain evergreens..
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What do I think is useful?

• System studies, our forest tree breeding has
  become more efficient by a factor of 2 (?) the
  last 3 decades. Modern biotech and better
  understanding of genes (even the simple
  Mendelian) has not been very helpful for
  operative tree breeding till now.
• Some reasons for faster improvement
• -Less emphasise on each plus tree, but instead
  more plus trees.
• -Less unproductive waiting for controlled crosses
  in seed orchards.
• -Clonal testing instead of progeny testing for
  Norway spruce.
• -Better electronic data management and better
  calculation methods (BLUP, group merit selection)
• -More streamlined plant production and field
  trials.
• -Single tree plots.
• Modern biotech has been less important

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Marker aided selection

• Important genes may not be identifyable and
  reproducible, it may just appear so.
• Negative genes (inbreeding) may seem important,
  thus MAS effort may result in weeding of
  unimportant genes rather than selection for
  important
• Important gene in one genetic and physical
  environment may not be important in another (thus
  a lot of possible interactions not considered in
  simple experiments).
• Field performance is the added action of all
  important genes, MAS gives just a small part of
  them.
• Higher selection effort for one thing means lower
  for all others. The breeding stock is often a
  limited resource.
• A large added administrative trouble, costs for
  sampling and preparation, costs for analyses,
  costs for compiling data from different sources.
• If one start select for good DNA-pieces, it is an
  evident risk of faster accumulation of coancestry
  and subsequent inbreeding.
• Growth in mature age may be the most important,
  and probably to composite and complex to locate
  on the gene map.
• Etc

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MAS

• 20 years of QTL research gave us good insight
  about genome organization, but no meaningful QTL
  to hang the hat on.
• FAO conference 2003 on MAS. From summary 2.7
  Practical applications of MAS Although
  documentation was limited, the current impact
  seemed small   
• Efforts have been going on for at least a decade
  for forest trees in Sweden, without coming near
  to an application.
• At least one scientist reasearching it in Sweden
  (Reza Yasdani) got the sack and no-one of the
  pioneers in MAS applied to forest tree breeding
  is with us any more

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Not extreme close linkage

• Cis- and trans- different in different families
• Different associations in different materials

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Associations (populationwide linkage
disequilibrium)

• Usually not large effects
• It will probably take some time (10 years) till
  the pine and spruce genome will be densily
  covered. (???? Pärs föredrag)
• Not that mature field, so remains to see what
  will come

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I searched my 50 first hits on the webI also
looked in Vicopedia

• Association mapping I found no successful
  breeding operation
• QTL I found no successful breeding operation
• (the limit to successful may be debated)

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Place in system

• MAS research should not be seen as applied and
  motivated by the possible practical applications.
• Instead it should be viewed as basic research.
• Guess it is on way down internationally as both
  basic and applied research. (My feeling only.)

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Parentage

• It is now possible to decide which (among
  suspects) are the parents to a tree. That could
  find immediate applications in operative
  breeding.
• Reliability is high enough.
• Costs is probably affordable for some
  applications and decreases.

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• Can more directly estimate effective size
  (status number), which actually is a requirement
  in BC. (Similar to Wrights FST)

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Error elimination

• The breeding population could be checked for
  errors in pedigree.
• Erronously tagged clones occur. Yoshinary
  suggests 10 on average and 50 in special cases.
  Johan checked an Umeå seed orchard material and
  found no error in 36 ramets. A month ago I
  personally checked a Turkish seed orchard and
  found at least one error among 75 ramets.
• I believe Swedish breeders are extremely clever
  and careful, so the error-rate in breeding
  material is probably below 5. But this figure
  could be good to verify!
• Probably it is not justified to make it a
  routine, but at least it is something which
  requires some more discussion

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Routine DNA sampling?

• Perhaps a good idea to routinely store a DNA
  sample of every member of the breeding population
  forever? (Gene conservation)

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Polycross

• Progeny testing and creating of progenies for
  selection of a new breeding population may be
  more efficiently combined.
• Trees can be mated with mixtures of pollen from
  good trees for parental ranking, and in the same
  time creating a new breeding population with
  known pedigrees by identifying which of the
  fathers with markers.

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Molecular diagnostic tools

• The state of plants not always directly coupled
  to the genes that control the physiological
  process will be easier to record with molecular
  symptoms. New measurement devices for relevant
  characters can be foreseen.

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Breeding without breeding

• Molecular parentage control has the potential to
  make controlled crosses redundant. Controlled
  cross (recombination) is one of the bottlenecks
  in tree breeding and it is a much bigger obstacle
  than generally accepted. No convincing schemes
  have been presented yet, but the concept is new
  and I believe it will be possible to identify
  procedures which could be practically useful and
  efficient immediatly.
• E.g. Norway spruce are tested in clone trials in
  operative breeding and based on the results the
  best clones are later mated in archives. If
  instead the trial was measured first when cones
  were emerging open pollination from the best
  clones collected and progeny checked for if the
  father also was among top clones and if so cloned
  and tested. It may be a more efficient design
  than the present

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Flower stimulation

• Hormons (gibberrelins) are involved and an
  important background for the history of this
  department and the Umeå plant physiology group
  (Arne Dunberg), but the history is older than
  that.
• Gibberrelins are used operationally to get
  crossings of Scots pine, which speeds up
  operations somewhat. However, top working is
  regarded as operatively more promising.
• Not used operationally in seed orchards and
  efforts give variable results
• Even if it would succeed in seed orchards it is
  not given it would be allowed (work hazards)
• I do not foresee large progress the next years
  (thus breeding plan should be based on operative
  methods).

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Clones for conifer massmultiplication

• Cuttings
• SE
• Both systems operative for conifers (as well as
  others)
• Both systems results in considerable more
  expensive plants
• Cutting propagation takes time to multiply a
  clone
• To store clones for cutting propagation is
  expensive and troublesum
• SE propagation is fast, clone storage is cheap
  and simple.
• A slight risk for accumulation of somatic
  mutations
• Ease of multiplication varies among genotypes,
  more so for SE than cuttings.

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Ekonomisk kalkyl presenterad av Lennart Eriksson
050823, http//www.nordgen.org/nsfp/doc/konferense
r/2005frosta/NSFP2005_lennart_eriksson.ppt,G36
gran, omloppstid 51 år, 3000 plantor/ha, 2
kalkylränta, kkr/ha, Dag komplettering
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Economic calculation Lennart Eriksson 050823,
http//www.nordgen.org/nsfp/doc/konferenser/2005fr
osta/NSFP2005_lennart_eriksson.ppt,G36 spruce,
rotation 51 years, 3000 plants/ha, 2 interest,
kkr/ha, Dag complement
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The message

• If calculations are the right, the increase in
  present value of the stand or in land value can
  more than pay even for expensive ways to get
  genetic gain
• For some reason forestry does not seem to have as
  clever economists as SLU, it is difficult to get
  them to buy this argument!
• But at least 5 years ago forestry bought the idea
  for seed orchard seeds.
• But it requires a 50 fold increase in dedication
  of forestry to accept the clonal idea!

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Cutting
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Avvecklat, för dyrt!
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Växthusplantage ett sätt att producera
råmaterial till bulkförökning!
Avvecklat, för dyrt!
Kuvattu maaliskuussa, 1995
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Vegetative propagation programs with Norway
spruce in Sweden
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Use of clones over the World

• Eucalyptus
• -total of 15 000 000 ha
• P mariana east Canada
• 1500 ha annually
• P sitchensis Ireland and Scotland
• - 2500 ha annually
• Estimated from Sonesson et al 2003

• Eucalyptus spp.
• total of 1 217 000 ha
• Acacia spp.
• total of over 200 000 ha
• Populus spp.
• total of 1 567 000 ha
• in Europe 949 000 ha
• Salix spp.
• in Europe 20 000 ha
• Cryptomeria japonica (sugi)
• in Japan 5 000 000 ha
• Cupressus / Chamaecyparis spp.
• -total of 40 000 ha
• Pinus spp.
• -total of 30 000 ha
• According to B. Kellison, IUFRO 2004

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Clonal forestry in Nordic countries (total)
Based on Questionnaire 2002 Nordic Group for
The Management of Genetic resources of
Trees Summarised by Steve Lee
Hybrid Aspen gt500 ha since 1999
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Clonal forestry in Nordic countries vision for
year 2012 (annual)(of total annual planting
300 000? ha)
Questionnaire 2002 Nordic Group for The
Management of Genetic resources of
Trees Summarised by Steve Lee
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A million SE plants. Plum Creek Nursery in Georgia
Photo Dag Lingren Sept 06
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Plantation with SE trees Sept 06 in Georgia
Photo Dag Lingren Sept 06
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Transplantation maching, SE miniplugs are
transplanted to open land. Nursery in Georgia
Photo Dag Lingren Sept 06
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Forestry with clones

• It is technically and biologically possible to
  propagate spruce by clones for practical
  forestry.
• One or a few percent of the plant market may be
  penetrated with expensive clonal propagation for
  curiosity or foreseen development. The rest will
  not be willing to pay the price.
• My guess is that the vision of clonal forestry
  will remain, but that it does not justify much
  extra effort in breeding.

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Science with clonesPotential better science

• Replications
• Reproducibility

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Clone is a tool for a more effective breeding!   

• Used for seed production
• Gains faster realized
• Clonal test means testing the sum of genes
  deployed, progeny testing often are confounded by
  paternal genes just contributes to noise
• A seedling is genetically unique clones can be
  optimally replicated.
• Clonal test gives in practice much information
  about ability to transfer gene to progeny
• More efficient use of the variation occurring
  after sexual propagation

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Clone is a tool for a more effective breeding!   

• The efficiency of clonal testing depends on costs
• Collaborators instead of competitors
  (non-egoistic clones)
• Test on many environments and choose for wider
  adaptation
• Test in the field and cross in the archive
• Combine wood in the field and reproduction in
  archive
• Biotechnical breeding - like transgenetic trees -
  becomes more feasible

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Clonal selection
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Phenotypic selection
Breeding value
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Comparison (at the same dimensioning) of clonal
or seedling
based testing for the Swedish Norway spruce long
term
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breeding program. Clonal testing adds around
30 to gain. (Rosvall 1999)
2
0
0
500
1000
1500
2000
2500
Test size (plants)
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Multigenerational comparison of testing
strategies in Swedish conifer breeding

• Clonal testing is much superior to
  progeny-testing
• Phenotypic testing better than progeny-testing at
  low budget

Danusevicius and Lindgren 2002
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Clone is a tool for a more effective breeding!   

• Clone testing with cuttings has operatively
  replaced progeny testing for Norway spruce in
  Sweden
• It may be possible to do the same for Scots pine.
  Development is going on and continuing small
  scaled practical applications in part of breeding
  is recommended for pines (lodgepole and Scots)
• Although in the end I guess it will be found
  usable but not cost efficient for Scots pine. The
  donour plants are to large and expensive and the
  success rate will vary too much among clones.

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End
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• Wait for GeneCar conference?
• Send questineear to all suggest something!
• Molekylär, i första hand MAS. Både individer och
  organisationer, i första hand förädlare i andra
  hand forskare, Eucalyptus kan förekomma men gans,
  gör en lista över utlänningar, forskare kan vara
  alla viktiga svenska
• Dag kan ta GMO biten med det samma eftersom den
  är enklast
• Det gör väl inte så mycket vad som står i ett
  utredningsdokument som först går till Bengt och
  Bo och tvättas där och sedan till deras chef Ola
  och tvättas där och sedan editeras och kommer ut
  som en rapport. Nog törs man ta ut svängarna lite
  grand i grunddokumentet och behöver inte koppla
  in politiken där. Sedan har jag ju gjort
  fullständigt klart att jag blir besvärlig, så jag
  behöver inte dra mig för att bli det.
• Vegetativ förökning kan vi skriva själva, kanske
  avsett för kapitlet före. Men eftersom Bengt
  deltar i båda kan han i slutändan se till att
  editeringen blir sådan att det inte står samma
  ska på två ställen

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Genetic gain for massmultiplication

• Selection in nursery of good plants in good
  provenances
• Selected genotype phenotype
• Selected mother progeny test
• Best of selected clones
• The gain increases over time