session4 dag terje endresen - nordgen · 2010-05-25 · • primitive crops and traditional...
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corn, maize
wild tomato
tomato
teosinte
Traditional landracesCrop Wild Relatives Modern cultivars
Genetic bottlenecks during crop domestication and during modern plant breeding.
The circles represent allelic variation. The funnels represents allelic variation of genes
found in the crop wild relatives, but gradually lost during domestication, traditional
cultivation and modern plant breeding.
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• Scientists and plant breeders want a
few hundred germplasm accessions
to evaluate for a particular trait.
• How does the scientist select a small
subset likely to have the useful trait?
• Example: More than 560 000 wheat
accessions in genebanks worldwide.
6Slide adopted from a slide by Ken Street, ICARDA (FIGS team)
• The scientist or the breeder
need a smaller subset to cope
with the field screening
experiments.
• A common approach is to
create a so-called core
collection.
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• Given that the trait
property you are looking
for is relatively rare:
• Perhaps as rare as a
unique allele for one
single landrace cultivar...
• Getting what you want is
largely a question of
LUCK!
8Slide adopted from a slide by Ken Street, ICARDA (FIGS team)
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Objective of this study:
– Explore climate data as a
prediction model for “computer
pre-screening” of crop traits
BEFORE full scale field trials.
– Identification of landraces with a
higher probability of holding an
interesting trait property.
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Wild relatives are shaped
by the environment
Primitive cultivated crops
are shaped by local
climate and humans
Traditional cultivated crops
(landraces) are shaped by
climate and humans
Modern cultivated crops are
mostly shaped by humans
(plant breeders)
Perhaps future crops are
shaped in the molecular
laboratory…? 11
• Primitive crops and traditional landraces are an important source for novel traits
for improvement of modern crops.
• Landraces are often not well described
for the economically valuable traits.
• Identification of novel crop traits will often be the result of a larger field trial
screening project (thousands of individual plants).
• Large scale field trials are very costly, area and human working hours.
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Assumption: the climate at the
original source location, where
the landrace was developed
during long-term traditional
cultivation, is correlated to the
trait score.
Aim: to build a computer
model explaining the crop trait
score (dependent variables) from
the climate data (independent
variables).
1) Landrace samples (genebank seed accessions)
2) Trait observations (experimental design) - High cost data
3) Climate data (for the landrace location of origin) - Low cost data
• The accession identifier (accession number) provides the bridge to the crop trait observations.
• The longitude, latitude coordinates for the original collecting site of the accessions (landraces) provide the
bridge to the environmental data.
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Lima, Peru
Benin
Alnarp, Sweden
Svalbard
http://barley.ipk-gatersleben.de
16Powdery Mildew,
Blumeria graminis
Leaf spots
Ascochyta sp.
Yellow rust
Puccinia strilformis
Black stem rust
Puccinia graminis
Faba bean, Finland Field trials, Gatersleben, Germany
Forage crops, Dotnuva, Lithuania Radish (S. Jeppson)
Potato Priekuli Latvia
Linnés äpple
The climate data is extracted from
the WorldClim dataset.
http://www.worldclim.org/
Data from weather stations
worldwide are combined to a
continuous surface layer.
Climate data for each landrace is
extracted from this surface layer.Precipitation: 20 590 stations
Temperature: 7 280 stations
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FIGS selection is a
new method to
predict crop traits of
primitive cultivated
material from
climate variables by
using multivariate
statistical methods.
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Origin of Concept (1980s):Wheat and barley landraces from marine soils in the Mediterranean region provided genetic variation for boron toxicity.
What is FFocusedocused IIdentificationdentification of GGermplasmermplasm SStrategytrategy
Slide made byMichael Mackay 1995
http://www.figstraitmine.org/
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South Australia
Mediterranean region
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FIGS
The FIGS technology takes much of the guess
work out of choosing which accessions are most
likely to contain the specific characteristics being
sought by plant breeders to improve plant
productivity across numerous challenging
environments. http://www.figstraitmine.org/
FIGS salinity setFIGS salinity set20
Temperature
Salinity score
Elevation
Rainfall
Agro-climatic zone
Disease distribution
F I G SOCUSED DENTIFICATION OF ERMPLASM TRATEGY
Data layers sieve accessions
based on latitude & longitude
Slide made byMichael Mackay 1995
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No sources of Sunn pest resistance previously found in hexaploid wheat.2 000 accessions screened at ICARDA without result (during last 7 years).A FIGS set of 534 accessions was developed and screened (2007, 2008). 10 resistant accessions were found!
• The FIGS selection started from 16 000 landraces from VIR, ICARDA and AWCC
• Exclude origin CHN, PAK, IND were Sunn pest only recently reported (6 328 acc).
• Only accession per collecting site (2 830 acc).• Excluding dry environments below 280 mm/year• Excluding sites of low winter temperature below 10
degrees Celsius (1 502 acc)
http://dx.doi.org/10.1007/s10722-009-9427-1
Slide adopted from Ken Street, ICARDA (FIGS team)
27Priekuli (L) Bjorke (N) Landskrona (S)
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Heading Ripening Length H-Index Vol wgt TGW Priekuli (L) Bjorke (N) Landskrona (S)
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Eddy De Pauw
Climate data
Harold Bockelman
Net blotch data
Ken Street
FIGS project leader
Michael Mackay
FIGS coordinator
Dag Endresen
Data analysis
• Barley (Hordeum vulgare ssp. vulgare) collected from different countries worldwide screened for susceptibility of net blotch infection (1676 greenhouse + 2975 field observations).
• Net blotch is a common disease of barley caused by the fungus Pyrenophora teres.
• Screened at four USDA research stations: North Dakota (Langdon, Fargo), Minnesota (Stephen), Georgia (Athens).
• 1-3 are basically resistant � group 1• 4-6 are intermediate � group 2• 7-9 are susceptible � group 3
• Discriminant analysis (DA):• Correctly classified groups: 45.9% in the training set
and 44.4% in the test set.• Work in progress! (SIMCA, D-PLS)
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