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Importance and Utilization of the
Genetic Resources of Cultivated
Species
Candice Gardner, USDA-ARS, Ames, IA
Universidad Nacional Agraria La Molina
50th Anniversary of the Escuela de Post Grado
“Research for a Sustainable Development”
September 16-17, 2008
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Food security
depends upon germplasm
collections.
http://www.fao.org
In agriculture, the most
important resources are
soil, water, air, and
germplasm collections. Science 1986
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Plant genetic resources (PGR) have been utilized over the millennia to improve the human condition. Development of crops that provided stable supplies of food, feed, fiber and fuel offered alternatives to nomadic existence, and enabled societies to develop and flourish around the world.
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The development of improved crops and cropping systems, and
the increased availability of materials essential for sustenance,
growth and development
made possible the rapid evolution of human intellectual capacity,
discovery and invention. As a result, the nature of human society
and human behavior changed.
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Conservation and utilization of PGR have made possible the continuous varietal improvement necessary to provide solutions for agricultural production challenges, the development of new crops and new uses, and improvements in health and nutrition.
Growing global energy needs coupled with the increasing demands for food and other plant-based resources have highlighted the critical importance of PGR now more than ever. Demand for well-documented PGR increases annually.
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The Four F’s
• Food
• Feed
• Fiber
• Fuel
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The World’s #1 Crop
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The Other World’s #1 Crop
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Grapes in Washington State, USA
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Soya in Brazil
Courtesy of Luciano Nass,
EMBRAPA
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The Early Plant Explorers
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Nikolai I. Vavilov is recognized
as the foremost plant
geographer of contemporary
times. To explore the major
agricultural centers in this
country and abroad, Vavilov
organized and took part in over
100 collecting missions,
including those to Iran (1916),
the United States, Central and
South America (1921, 1930,
1932), the Mediterranean and
Ethiopia (1926-1927). He and
his colleagues were the first to
thoroughly collect potato
germplasm in the Andes.
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1910, the Office of Foreign
Seed and Plant Introduction
of the United States sent
Frank N. Meyer, one of
world’s most outstanding
collectors, to the Sinkiang
Province of China. He was
also to go to Europe, Russia,
and Tibet. During 1910 to
1911, Meyer explored Irkutsk,
Kashgar, Yarkand, and
from there to Ak-Suand and
on to Kul’dzhe, always in
search of hardy crop plants
and their wild relatives that
could tolerate abiotic
stresses.
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Potato Germplasm Collection
Development
The dedication and effort of pioneer taxonomist Carlos Ochoa formed the
foundation of the CIP-held collection of potato genetic resources. This
Peruvian scholar, whose crusade to find wild species in the Andes began
more than 40 years ago, has discovered 80 different species—about one-third of all the wild potatoes known
to exist. http://www.cipotato.org/potato/
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Drs. Salas & Spooner
Collecting Wild Germplasm
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“THE DISAPPEARANCE OF OLD VARIETIES,
the
landraces of crop plants, and their wild progenitors
could eventually be recognized as the great sleeper
issue in the last decades of the 20th century.
It is difficult for us to visualize a scenario more
profound in its implications, yet less appreciated
by funding institutions, governments, and the
general public, than that entailed in the mass
elimination of a large number of plant species that
has taken place and continues to take place in the
centers of their diversity.”
(Qualset and Shands, 2005).
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Recent Threats to Global Food
Production
• Insect and Disease Pests
– Wheat Stem Rust Reemerges
• Fertility Costs and Availability
• Energy Costs
• Water
• Stable Supply of Adapted Cultivars
• Land Use / Land Loss
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Plant Germplasm Collection
Development Today
• Collection expeditions
• Germplasm originators
• Exchange between institutions
– Within National Institutions
– Between Nations, governed by
the ITPGRFA
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• Targeted acquisition
• Documentation
• Effective maintenance and regeneration programs
• Thorough evaluation and characterization
• Effective use of associated information
• Distribution of PGR to research communities
Successful Conservation & Utilization
of PGR Depends On:
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Last but not least…
• Pre-breeding activities to facilitate utilization.
• Thorough understanding of the phenotypic and genetic variability of a crop and its wild relatives, their adaptation, life forms, breeding systems, traits and biological properties supports PGR conservation activities, and is essential to realize their potential for contribution.
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Current Status: Plant Genetic
Resources
• An estimated 6 million
samples in genebanks
world-wide; of these,
1.5 million are probably
unique.
• About 10% of the
samples are held by the
IARCs.
• Most samples are in
genebanks controlled by
national governments.
• Large national
genebanks in the U.S.,
Canada, Australia,
Japan,
S. Korea, India, China,
Brazil, Russia,
Germany, South Africa.
• Public gardens, NGOs,
universities, and
companies also hold
thousands of samples.
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The Global Crop Diversity Trust is an independent international organization which exists to help ensure the conservation and availability of crop diversity for food security worldwide. It was established through a partnership between the United Nations Food and Agriculture Organization (FAO) and the Consultative Group on International Agricultural Research (CGIAR).
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Annex 1 Crops of the ITPGRFA
The crops listed include: breadfruit, asparagus, oat, beet, brassicas (the cabbage family including broccoli and cauliflower), pigeon pea, chickpea, citrus, coconut, aroids (including taro and cocoyam), carrot, yams, finger millet, strawberry, sunflower, barley, sweet potato, grass pea, lentil, apple, cassava, banana/plantain, rice, pearl millet, beans, pea, rye, potato, eggplant, sorghum, triticale, wheat, faba bean, cowpea, maize and more than 80 forage species from 30 different genera.
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The U.S. National Plant
Germplasm System (NPGS)
• “Base collection”;
preservation research.
• GRIN database:
www.ars-grin.gov
• Acquisition via plant
exploration and
exchange .
• Germplasm quarantine
activities now part of
APHIS; ARS conducts
related research.
• 26 active US sites
manage clonally and
seed-propagated
collections.
• Conduct associated
research.
• Crop Germplasm
Committees;
university, NGO,
industry cooperators,
and ARS.
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National Plant Germplasm System
Types of germplasm
Wild crop relatives
Landrace collections
Genetic stocks
Domestic breeding lines
Heirloom accessions
Cultivars
Plant mycosymbionts
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US Regional Plant Introduction
Station Functions
• Conserve Plant Genetic Diversity.
• Encourage Use of Germplasm.
• Conduct Research to Improve Genetic
Resource Management Programs.
• Generate Information to Better Target
Germplasm Use by the User Community.
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Activities of the NPGS Integrate Data
Acquisition to Enhance their Efficiency
and Collection Value
Acquisition
Documentation
Maintenance & Regeneration
Characterization
Evaluation
Distribution
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Germplasm collection now
utilizes GIS technology
Participants in a 2001Kazakhstan expedition:
Richard Hannan
Stephanie L. Greene
Alexandr Afonin
Nickolai Dzubenko
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Institutes involved
• USDA, ARS National Plant Germplasm System
• Kazakhstan Institute of Agricultural Science-
Aral Sea Experiment Station
• N.I. Vavilov Institute of Plant Industry, Russia
• University of St. Petersburg, Russia
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Results
• Trip covered 1180 km (~ 730 miles)
• Collections were made at 89 sites
• 432 accessions were collected:
– 138 Medicago
– 86 Legumes (Astragalus, Vicia, Lathyrus, Trifolium)
– 48 Grasses
– 58 Wild onions (2-3 species)
– 102 Other horticulture (wild forms of hops, medicinal species, lettuce,ornamentals, cultivated garlic, apples)
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Hypericum Collection in the
Ozarks
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Wild Helianthus Collection in
California
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US NPGS System Holdings
• 26 Active Sites + the NCGRP (Ft. Collins)
+ the NGRL
• 33 Designated Collections
• 508,622 Accessions as of September 13,
2008
• 20-25% of Accessions Distributed Yearly
• 2,126 Genera; range of 1-583 per site
• 13,111 Species; range of 1-3,058 per site
• 235 Families Represented
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Activities of the NPGS Integrate Data
Acquisition to Enhance their Efficiency
and Collection Value
Acquisition
Documentation
Maintenance & Regeneration
Characterization
Evaluation
Distribution
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Crop Evolution Lab Records
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Acquisition of Images
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Genebank Information Databases
A major function of a genebank is to manage the information associated with collections and provide them in a usable format, both for collection management and to facilitate utilization.
Examples of germplasm information databases would include GRIN, SINGER, and EURISCO, among others.
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• Information associated with the collections increases their value to researchers and to genebank managers, enables better targeting to meet research objectives.
• Automation of data collection and transfer activities improve genebank resource use efficiency.
• IT and IM Tech transfer between sites and between researchers is increasingly critical for successful germplasm conservation and utilization.
• Interoperability with genomic databases is a high priority
• Stakeholder input is key to the future utility of PGR information delivery systems.
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Use of Existing Information to Assist
in Collection Development Strategies
too much information can be
overwhelming…
not enough
Readily accessible, useful
information is enabling
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GRIN-Global
GRIN-Global is a project whose mission is to create a new scalable, version of the GRIN system suitable for use by any interested genebank in the world. It is being developed in a joint effort with the Global Crop Diversity Trust, Bioversity International, and the Agricultural Research Service of the USDA. Replacement of the current GRIN system for NPGS use with the GRIN-Global system is scheduled for the last quarter of 2010.
http://cool.ars-grin.gov/wiki/index.php/Main_Page
http://cool.ars-grin.gov/gringlobal/forums/
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Project Goals
• To provide the world’s crop genebanks with a powerful, flexible, easy-to-use global plant genetic resource (PGR) information management system that will constitute the keystone for a sustainable, rational, efficient, and effective global network of genebanks to permanently safeguard PGR vital to global food security, and to encourage the use of PGR by researchers, breeders, and farmer-producers.
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• The database and interface(s) will be
designed to accommodate both commercial
and open-source programming tools, to be
database-flexible, and to require no
licensing fees for genebank use. This will
enable institutions with limited IT
resources, as well as better-supported
genebanks, to adopt GRIN-Global. The
database will be deployable on local stand-
alone computers at sites with limited
computational capabilities, as well as at
networked sites.
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Genetic resources flow chart
Accession in genebank
Accession Utilization
GRIN
Passport
Data, GIS
Morphological data
Phenotypic data Disease
Nutrition
Yield components
Genotypic data
C. Coyne, Pullman, WA
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Activities of the NPGS Integrate Data
Acquisition to Enhance their Efficiency
and Collection Value
Acquisition
Documentation
Maintenance & Regeneration
Characterization
Evaluation
Distribution
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The objective of Maintenance and
Regeneration is to provide high
quality seed and plant materials
which are true to the original genetic
profile.
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Viability & Preservation Research
• The main research efforts in this area within the USDA are conducted at the NCGRP in Ft. Collins, CO, but also at several other sites.
• Lipid chemistry is known to impact effective storage practices.
• Cryopreservation techniques are being successfully developed for woody species; apple, willow, and ash are recent examples.
• Tissue culture is essential to both micro-propagation of species such as strawberry or potato; it also provides for resolution of some phytosanitary issues.
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•Controlled pollination is necessary for
cross-pollinated crops, and is
accomplished by hand- or insect-
mediated methods.
•Clonal and micropropagation
methods require controlled conditions
for the production of pathogen-free
propagules
•ALL CONTAMINATION IS BAD,
REGARDLESS OF THE SOURCE
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Phaseolus regeneration in Pullman, WA
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Tents
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Seed Storage at the National Small
Grains Collection, Aberdeen, ID
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Seed Jars
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Activities of the NPGS Integrate Data
Acquisition to Enhance their Efficiency
and Collection Value
Acquisition
Maintenance & Regeneration
Characterization
Evaluation
Documentation
Distribution
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Use of DNA Capture Cards for
Molecular Characterization of
Collections
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Sequencing, annotation, and database
management of the genome of
Theobroma cacao
• A composite linkage map from the combination of three crosses made from commercial clones of cacao, T. cacao L. Tropical Tree Genomics and Genetics. DOI 10.1007/s/2042-008-9011-4. Brown J. Steven Brown, Robert T. Sautter, Cecile Olano, James W. Borrone, David N. Kuhn, and Raymond J. Schnell. 2008.
• Development of a Marker Assisted Selection Program for Cacao. Phytopathology Vol 97, No 12, 1665-1669. Schnell, R. J., D. N. Kuhn, J. S. Brown, C. T. Olano, and J. C. Motamayor. 2007.
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.
IITA CRIN Nigeria
CCI Papua New Guinea
Univ. of Hawaii HARC
CATIE Costa Rica
INIAP Ecuador
CRIG Ghana
SHRS Miami TARS
Puerto Rico
CEPLAC Bahia and Belem
Almirante
PSU
Reading Univ. UK
CIRAD France
UNAS Peru
SCA and other formal and informal collaborative projects for cacao breeding and genomics
Malaysian Cocoa Board
Almirante Mars Exp. Farm
CNRA Cote d’Ivoire IRAD Cameroon
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Research Stations Genotypes
South and Central America
CATIE, Costa Rica 4,000 INIAP, Ecuador 12,500 MARS Farm Almirante, Brazil 4,500 IBE, Peru 500 West Africa CNRA, Cote d’Ivoire 1,500 CRIG, Ghana 5,000 CRIN, Nigeria 500 IRAD, Cameroon 300 Asia CCI, PNG 2,000 USA Miami (quarantine and nursery) 250 Mayaguez (germplasm collection) 350 Hawaii (selection on Oahu and Hawaii) 1,600 Total genotypes for project 33,000
Current field evaluations
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cir252 0.0
cir19 5.1
cir240 9.2
cir3 16.0 Tce089 20.9 cir129 23.4 shrs21 shrs6 23.8
ca797995 32.3 cir268 cir152 37.4
shrs13 38.5
cir60 48.5 cir139 cir165 50.1
shrs2 51.3 cir162 57.7
cir48 70.5
cir230 85.4 cir228 86.1 WRKY-03 88.0 cir68 cir261 93.5
cir73 cir269 100.5
2
cir184 0.0
cir161 cir118 11.6
cf974239 15.7
cir143 cir159 28.9
cir102 39.4 WRKY-14 45.0 cir29 46.5 cf972885 51.0
cir249 53.3 shrs3 54.7 cir244 60.4 shrs23 61.1 cir246 62.7 cir273 65.8 cir286 68.4 shrs34 69.0
Tce574 80.1
cir275 87.7 cir264 89.9 cir22 93.5 RGH11 cir194 97.0
1 cir242 0.0 cir234 1.5 cir241 3.8 cir233 5.1 Tce195 9.4 cir117 11.2 cir33 14.5 cir237 14.8 cir95 20.6 shrs33 23.3 cir32 26.2 cir43 32.0 cir12 34.2
cir213 cir206 48.6
Tce380 59.4
cir115 75.3
4 cir120 cir150 0.0
cir153 2.1 cir198 3.8 TIR2 5.4 cir146 9.6 cir21 10.7 cir192 10.9 cir62 11.6 cir40 12.3 cir247 13.9 cir204 17.0 Tce380A 19.5 cir180 21.6 cir175 31.4 cir280 39.6 cir289 40.6 cir78 42.0 cir263 45.4 cir219 48.0 cir254 63.6 cir135 63.9 cir128 64.1 cir140 66.4 shrs7 70.1 shrs5 cir226 70.4
cir131 70.8 cir202 71.4 cir144 72.1 ca798018 73.0 cir81 79.5 ca795469 91.6
3 WRKY-10 0.0 cir111 0.3 cir232 1.3 cir119 2.1 shrs37 5.2 shrs12 7.4 shrs11 7.6 cir148 13.5 shrs22 18.2 cir10 21.5 Tce030 26.1 cir196 cir123 26.8
cir42 27.7 cir169 31.5 cir149 cir256 39.8
cir170 40.7 shrs19 47.7 cir245 48.8 cir69 WRKY-11 49.1
TIR4 52.3 TIR3 52.6 shrs4 63.7 cir87 67.6 cir80 73.0
cir109 cir101 84.9
cir274 85.3
5
cir103 0.0 cir134 3.0 cir189 5.4
Tce487 13.5 cir26 16.8
cir200 23.0
cir211 shrs20 33.3
cir225 35.2
cir282 45.1
cir1 51.1
8 ca972846 0.0
cir186 1.7 cir277 cir116
3.2
cir179 4.4 cir177 5.7 cir147 8.0 cir55 10.2 cir56 12.4 cir46 cir181
16.6
RGH4 22.8 RGH5 26.1 cir13 33.1 RGH1 37.4 cir190 43.7 cir141 44.1
7
cir79 0.0 cir85 3.4
cir64 cir98 24.0
cir283 24.8
cir212 32.8 RGH2 cir58 36.4
cir8 45.0 cir178 47.5
cir160 55.2 cir157 58.0 cir35 60.5 cf972909 67.0 cir24 68.5 cir251 73.3 cir30 74.1 cir166 79.5 cir250 83.2 cir126 86.0 cir108 88.1 cir266 88.6 cir72 cir287 94.6
cir243 95.4
9
cir6 0.0 cir136 1.5
5.4
cir53 10.5
cir71 32.2 cir276 34.3
34.7 cir25 37.4
cir209 54.3 cir9 57.9 cir291 59.9
6
cir37 0.0
cir223 4.7
RGH7 11.2 RGH8 13.4
cir61 23.3
cir104 40.6 cir155 41.3
cir229 57.8
10
Pod Number
Trunk Circumference
Pod Number & Wet Bean Weight
Witches’ Broom
Resistance
Pod Weight
Frosty Pod Resistance & Wet Bean Weight
Bean Length
Jorquette Height
Frosty Pod
Resistance
Bean Length, Seed Weight,Ovule Number, & Trunk Circumference
Black Pod
Bean Weight, Bean Thickness,
Pod Weight & Pod Length
~40 identified QTLs in cacao
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Family n WB BP WB+BP
T85/799x SCA6
79 19 6 2
N8/122 x SCA6
90 28 19 6
SCA6 x NA34
109 34 11 6
T63/967 x SCA6
119 11 1 0
T63/971 x SCA6
15 4 2 1
412 96 39 15
Number of plants with the favorable alleles for disease resistance at the two QTL for WB and three QTL for FP in families currently under evaluation at CRIG in Ghana.
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Where are we going next?
Choice field location on Kona side of Hawaii
The development of SNP markers in genes involved with
disease resistance, productivity, and quality.
To do this we need to sequence the genome and produce a
physical map to complement the genetic linkage map.
The MAS breeding program would be greatly enhanced thereby
accelerating the delivery of improved, productive, disease
resistant cultivars to cocoa farmers.
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Sequencing the T. cacao genome
Species Genome size
Yeast 12 Mb
Arabidopsis 119 Mb
Theobroma cacao 415 Mb
Rice 430 Mb
Dog 2,400 Mb
Human 3,300 Mb
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CUGI
USDA-Miami SNP development
Whole genome sequencing workflow
BAC Library Construction
Solexa sequencing & Alpheus pipelining services
NCGR
New Mexico
Year 1&2
Using DNA from Matina 1-6
Physical map construction
Using DNA from eight parents used in mapping populations
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Whole genome sequencing workflow
Sequence the genome Using 454
Annotation and IP
USDA Stoneville Miss.
Year 1&2
Year 2,3,4&5
IBM
WSU
Mars Inc.
ARS-Miami
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Activities of the NPGS Integrate Data
Acquisition to Enhance their Efficiency
and Collection Value
Acquisition
Documentation
Maintenance & Regeneration
Characterization
Evaluation
Distribution
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Adaptation Criteria
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Ames in the Wintertime
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Ames, IA in the Summertime
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50%
Highland
Tropical
Maize –
Unadapted
to the
MidWest
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GEM Project
Has
Successfully
Introgressed
Exotic
Germplasm –
190 Lines
Released with
Adaption to
the Midwest or
Southeast
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Activities of the NPGS Integrate Data
Acquisition to Enhance their Efficiency
and Collection Value
Acquisition
Documentation
Maintenance & Regeneration
Characterization
Evaluation
Distribution
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CRIS Project Search for US - NCR
A search of the Cooperative Research Information
System (CSREES and ARS Projects) resulted in
identification of 528 projects using plant genetic
resources on September 4, 2008.
1,459,816 samples were distributed by the NPGS
from 2000-2006, or an average of 25% of
collection holdings annually. Between 30 and 40%
were distributed to international recipients.
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Next three slides courtesy of
Luciano Nass, EMBRAPA-Labex
USA
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BRAZIL – SUGARCANE in 2008
(1,000 tons)
TOTAL
SUGAR AND ETHANOL INDUSTRY
OTHERS
TOTAL
SUGAR
ETHANOL
710,280
558,720
240,890
43%
317,830
57%
151,560
Source: CONAB, 2008
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BREEDING AND GENETIC ENGINEERING • Sugarcane varieties = interspecific hybrids
– Introduced to Brazil 14th century
– Complex genetically (2n = 70-120) with large DNA content.
Saccharum officinarum
(2n = 80)
http://www.ars-grin.gov/ http://davesgarden.com/
Saccharum spontaneum
(2n = 40-128)
Photo: H. Carrer
Saccharum robustum
(2n = 60-205)
http://www.ars-grin.gov/
Saccharum barberi
(2n = 111-120)
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BREEDING AND GENETIC ENGINEERING
• Historically Brazil has had an intensive sugarcane breeding program
– 550 varieties developed to date
– 51 varieties released since 1995
– 20 varieties account for 70% of total planted area
• Understand commercial cultivar origin
• Identification of diversity and genetic variability
• Introgression and QTLs identification (Quantitative Trait Loci)
• Diagnostics for disease resistance / tolerance
• Structural and functional genomics
• Sugarcane Genome Project
(http://sucest.cbmeg.unicamp.br/en)
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Number of published papers on sugarcane
Number of published papers on ethanol
extracted from biomass
Source: Fapesp (2008)
120
120
140
100
100
80
80
60
40
20
60
40
20
160
0
0
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Early Guayule Production for
Natural Rubber
Courtesy of Terry Coffelt, USDA-ARS, Maricopa, AZ
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Guayule – A Commercial Crop for Production of
High quality, Natural Rubber Latex for
Hypoallergenic Products
Photo courtesy of Mike Foster,
Texas A&M University
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The Zea nicaraguensis
Saga
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Education for a Sustainable Future