Transcript Current Status and Future Prospects for Public

Working in Partnership to Attain Priority
Crop Genetic Resource, Genomics, and Genetic
Improvement Research Goals
PETER BRETTING
U S DA - A G R I C U LT U R A L R E S E A R C H S E R V I C E
O F F I C E O F N AT I O N A L P R O G R A M S
PETER .BRET [email protected] .GOV
H T T P : / / W W W. A R S . U S D A . G O V/ R E S E A R C H / P R O
GRAMS/PROGRAMS.HTM?NP_CODE=301
Outline for Presentation
 American Seed Research Summit
 USDA/ARS National Program in Plant Genetic Resources,
Genomics, and Genetic Improvement


Plant Genetic Resources and Information Management
Plant Genomics, Genetic Analyses and Genome Databases


Maize and soybeans: genotyping and nested association mapping
Genetic Improvement of Crops

Maize: GEM Project
 Conclusion
American Seed Research Summit
Research, Education, and Policy Goals and Strategies
 Strengthen public and private partnerships to accomplish




national seed research priorities
Coordinate and engage industry stakeholders to support stable
funding for seed and breeding education, research, and
development
Attract and develop a pool of diverse, high-quality plant
researchers
Ensure that the regulatory system governing the development
and implementation of new technology is efficient, effective,
and science-based.
Develop an education and advocacy program to communicate
the value of seed and crop research to the public.
USDA/ARS National Program in Plant Genetic Resources,
Genomics, and Genetic Improvement (Crop Genes R’ Us!)
 Largest NP, with 125+
projects, and about $128
million gross annual
budget.
 Conducted by about 300
scientists at more than 50
ARS locations.
 Extensive public and
private sector
partnerships.
 Goal: deliver crop genetic,
genomic and bioinformatic
tools, information, genetic
resources, and improved crop
varieties to enhance U. S.
agricultural productivity and
security.
NP 301 Action Plan Research Components
 Plant and Microbial Genetic Resource
Management
 Crop Informatics, Genomics, and Genetic
Analyses
 Genetic Improvement of Crops
The USDA/ARS National Plant Germplasm System
(NPGS)
 One of the largest national
genebank systems.
 More than 510,000 samples
of more than 13,400 plant
species.
 Large collections of the
major staple crops
important to U. S. and
world agriculture.
 Large holdings of crops
without major collections at
international agricultural
research centers, e.g.,
cotton, soybean, various
horticultural and “specialty”
crops.
 Germplasm Resources
Information Network
(GRIN): an international
standard.
USDA National Plant Germplasm System (NPGS)
Plant Genetic Resource Management in Genebanks
 Acquisition
 Characterization
 Maintenance
 Evaluation
 Regeneration
 Enhancement
 Documentation and
Data Management
 Distribution
Avoidance of Cross Pollination and Seed Mixing
 Extensive quality assessment when the seed enters
the NPGS
 Procedures and protocols for regeneration



Physical isolation
Cages
Hand pollination
 Care in storage and distribution to prevent mixing
Maize in the NPGS
 Isolation from sources of out
crossing
 Regenerate ~400 accessions/year
 Sometimes plantings yield as few
as 5,000 seeds for some accessions
GRIN-Global
 GRIN = Germplasm Resources Information Network.
http://www.ars-grin.gov/ The genebank information
management system for the NPGS, and for Canada’s genebank
system (GRIN-Canada).
 The Global Crop Diversity Trust asked ARS and Bioversity
International (an International Agricultural Research Center) to
enhance and expand GRIN to address global germplasm
information management needs.
 The Trust awarded ARS a 3-year, $1.4 million grant to develop
GRIN-Global; ARS is devoting $900K in-kind support to the
project. ARS effort is located in Beltsville, MD and Ames, IA.
GRIN-Global
 Based on GRIN, but can be implemented in both a
system-wide and “stand-alone” local management
mode
 Supports multiple users via a “user-friendly” interface
 Maintains linkages with other databases and
interoperates with existing systems
 Advanced querying, custom and third-party
applications
Three Tier Architecture
Presentation
Tier
(Windows
Desktop Client)
Presentation
Tier
(Web Browser)
Business Tier
(Web Service)
Data Tier
(MySQL,
Oracle, SQL
Server)
GRIN-Global
 On-line ordering/request capability
 Database-flexible, free of recurrent licensing costs, with
interface and database schema source code open and
available without restriction to further development
 Designed to serve as the global standard plant genebank
information management system
Future Prospects
Trends in demand for NPGS germplasm and information
vs. NPGS budget
NPGS Web Page Access
Germplasm
Distributions
2,500,000
200000
2,000,000
180000
160000
1,500,000
1,000,000
NPGS Budget
45,000,000
40,000,000
35,000,000
140000
30,000,000
120000
25,000,000
100000
20,000,000
80000
15,000,000
60000
2008
2007
2006
2005
0
2004
0
2003
5,000,000
2002
20000
2001
2008
2007
2006
2005
2004
2003
2002
2001
2000
1999
0
10,000,000
2000
40000
1999
500,000
Result?: mismatch between expanding demand for PGR and static NPGS
capacity to manage it.
NP 301 Action Plan Research Components
 Plant and Microbial Genetic Resource
Management
 Crop Informatics, Genomics, and Genetic
Analyses
 Genetic Improvement of Crops
Genomic Information and Research Tools
 Genetic markers: polymorphic and heritable—simple
sequence repeats (SSRs) and single nucleotide
polymorphisms (SNPs)
 Expressed sequence tags (ESTs)
 Genetic maps
 Quantitative trait loci (QTLs)
 Physical maps
 Complete and partial genome sequences
Application of Genomic Information to Genetic Analyses:
The Nested Association Mapping (NAM) Genetic Map
[E. Buckler, J. Holland, M. McMullen (USDA/ARS), and many university and
private-sector collaborators]
NAM is the most powerful tool for dissection of the genetic bases of
quantitative traits for any species – period.
Linkage Mapping
Recent recombination
High power
Low resolution
Analysis of 2 alleles
Moderate marker density
Genome scan
Association Mapping
Historic recombination
Low power
High resolution
Analysis of many alleles
High marker density
Candidate gene testing
Nested Association Mapping
Recent and ancient recombination
High Power
High resolution
Analysis of many alleles
Moderate genetic marker density
High projected marker density
SSD
NAM






×






Tzi8
Tx303
P39
Oh7B
Oh43
NC358
NC350
MS71
Mo18W
M37W
M162W
Ky21
Ki3
Ki11
Il14H
Hp301
CML69
CML52
CML333
CML322
CML277
CML247
CML228
CML103
B97
Nested Association Analysis
25 DL
B73
F1s



1
2



200
Yu et al. (2008) Genetics 178: 539
NAM Genotyping and Genetic Map
•Genotyping with more than 1500 single nucleotide
polymorphism (SNP) genetic markers
•Map consists of 1106 loci (38 composite loci) and ~1400
cM genetic distance, therefore an average marker density of
1.3 cM/marker.
•It is a composite or consensus map and distances and
potentially order can not be assumed to translate directly
to individual family maps.
Maize Phenomics:
Massively Parallel Phenotyping of The Nested Association
Mapping Population
THE MAIZE DIVERSITY PROJECT
Experimental Evaluation of NAM
NAM lines evaluated in 2006 – 2007 at each of the following sites:
Aurora, NY
Champaign, IL
Columbia, MO
Clayton, NC
Homestead, FL
11 Total Environments
Ponce, PR
+
Tassel branch angle
Tassel main spike length
Tassel branch no.
Partitioning Genetic Variance
B73
X
NC358
B73
X
P39
B73
X
CML103
RIL1
B73
X
IL14H
B73
X
Tx303
B73
X
B97
X
M162W
B73
X
Tzi8
Line-to-line
variationB73
within a family
– dueB73
to
B73
B73
B73
differences
between alleles
from
X
X
X
X B73 and X
Ki11
NC350
Oh7Bof that Ki3
alleles
from
DiverseKy21
Line founder
B73
B73
family.B73
B737
B73
X
Mo18W
B73
X
CML52
B73
X
M37W
X
Oh43
B73
X
CML322
RIL2
…
X
MS71
B73
X
CML228
xHp301
B73
X
CML277
B73
X
CML247
…RIL
Among-Family Genetic Variance: σ2F
RIL199 RIL200
RIL1 RIL2
Family-to-family variation – due to
Within-Family
Genetic
Variances
differences among
different
founders.
σ2
σ2G(F)1
B73
X
CML69
B73
x
CML333
G(F)2
199
RIL200
The Maize Genetics and
Genomics Database (Maize GDB)
(C. Lawrence et al.)
USDA/ARS, AMES, IA www.maizegdb.org/
 Phenotypes
 Integrating structural and genetic
maps with maize genomic sequence
 Genome annotation
 Research community support
Soybean Nested Association Mapping (NAM) Project
(P. Cregan, D. Hyten, ARS-Beltsville)
Collaborators:
USDA/ARS
Iowa St. Univ.
Univ. of Nebraska
Univ. of Illinois
Univ. of Tennessee
Univ. of Maryland
Agricultural
Research
Service
Funding Support
Soybean NAM
 Design focused on yield
 Populations will be restricted to Maturity Group III
 Hub parent is IA3023
 Lines crossed with IA3023 included both elite and exotic
germplasm

121 total lines selected by research community
–
Crosses made the summer of 2008
 Parents were genotyped with the Universal Soy Linkage
Panel 1.0
What’s next with the Soybean NAM?
 During population development, the number of families
will be reduced to 40 based on field observations during
the inbreeding process.

Each population will consist of 250 F5 RILs
–
Total size: 10,000 lines
 Phenotyping will be done with a ‘connected’ incomplete
block experimental design (Tested in 30 environments)

Best Linear Unbiased Predictions (BLUPs) of grain yield, i.e., breeding
values for every RIL
The Universal Soy Linkage Panel 1.0 (USLP 1.0)
With United Soybean Board and collaborator funding 180 sets of
the USLP 1.0 (17,280 genotypes) were acquired for gene/QTL
Discovery
ARS Collaborators
Ames, IA
Beltsville, MD
Columbia, MO
Raleigh, NC
Stoneville, MS
Urbana, IL
Wooster, OH
State University
Collaborators
N. Carolina St.
Univ.
N. Dakota St. Univ.
Ohio State Univ.
So. Illinois Univ.
S. Dakota St. Univ.
Univ. of Arkansas
Univ. of Georgia
Univ. of Illinois
Univ. of Minnesota
Univ. of Missouri
Univ. of Nebraska
Virginia Tech
Universal Soy Linkage Panel (USLP 1.0)
1,536 SNPs selected from 3,110 SNPs mapped on the
Soybean Consensus Map

SNPs have diverse allele frequencies



Average polymorphism in bi-parental crosses
 Elite cultivars= 458
 PI landraces = 544
 Elite crossed with PI landrace = 590
Spread throughout the genome
Assayed using the Illumina GoldenGate assay


192 DNA samples run in three days
Large orders reduce cost from $11,000 per 96 DNA samples to $5,500
per 96 DNA samples
The Universal Soy Linkage Panel 1.0 (USLP 1.0)
for Gene/QTL Discovery
- Traits Under Study in Collaborative Projects Enhanced Seed
Composition
Resistance to
Biotic Stress
Resistance to
Abiotic Stress
Reduced linolenic acid
oil
Elevated oleic acid oil
Lower saturates
Higher protein
Soybean Cyst Nematode
Soybean Rust
Phytophthora Root Rot
Foliar Feeding Insects
Soybean Aphid
Drought
Iron Deficiency
Chlorosis
Seed Yield – Assessment and enhancement of genetic diversity
Source of Genetic Improvement for Soybean
 USDA germplasm collection is the source for new genetic
variation for soybean improvement for every important trait
USDA Soybean Collection (21,000 accessions)
1,116 wild
soybeans
17 Introduced
landraces
(86% of the
Germplasm base)
18,090 accessions
collected mostly
from Asia
(Landraces)
513 Public
cultivars
released
after
Hyten et al. 2006, PNAS 103:
16666-16671
1946
Soy HapMap
• The United Soybean Board recently agreed to fund a $2.9M
•
project to characterize the entire USDA Soybean Germplasm
Collection of 21,000+ wild and cultivated soybeans with
50,000 SNP DNA markers.
The Illumina’s Beadstation will allow genotyping of this
collection with 50,000 SNPs within three years
• New gene discovery through association analysis
• Enables breeders to select germplasm with greatest potential for
•
agronomic improvement
Decipher the signatures of selection (allele frequency changes)
associated with soybean yield improvement over 75 years of soybean
breeding to help understand yield
Soybean Genomics and
Improvement Lab
USDA, ARS, BARC-West
Beltsville, Maryland
60,800 SNP Infinium Chip
 Research by R. Shoemaker (ARS-Ames), C. Vance (ARS-St. Paul) and
collaborators at N. Dakota State Univ. and Iowa State Univ.
 Iron is a limiting growth factor on 30% of cropland
 Iron is also a major nutritional deficiency in much of the world
 Using global gene expression profiling to identify genes involved in iron
metabolism
 Currently evaluating how to control the genetic expression to enhance iron
balance in commercial plant varieties.
 Developing molecular markers to speed the public release of commercial
varieties with improved iron efficiency.
Mapping & Cloning Genes Responsible for Soybean
Protein
 Research by R. Shoemaker (ARS-Ames), C. Vance
(ARS-St. Paul), collaborators at the Univ. of Illinois
and Univ. of Nebraska
 The locus of a major trait that controls
seed protein content was mapped
Chromosome 20
 High-throughput transcript
sequencing and mapping identified
candidate genes
 Currently identifying the specific
and evaluating modifications
to change the protein content
to
15% Soluble
Carbohydrates
Soybean Seed
Composition
18% Oil
several
(sucrose, stachyose,
raffinose, others)
genes
14% Moisture,
ash, other
38% Protein
15% Insoluble
Carbohydrates
SNP Haplotypes and Linkage Disequilibrium
(R. Shoemaker, ARS-Ames)
Haplotype and Allele States for varieties
NP 301 Action Plan Research Components
 Plant and Microbial Genetic Resource
Management
 Crop Informatics, Genomics, and Genetic
Analyses
 Genetic Improvement of Crops
Germplasm Enhancement of Maize
Germplasm Enhancement of Maize (GEM) Project
A collaborative effort of public and private sector
researchers to broaden and enhance the maize germplasm
base. More than 60 collaborators.
Two permanent breeding sites:
Ames, IA for development of 25% tropical and temperate exotic
Raleigh, NC for development of 50% tropical
GEM is administered by the USDA-ARS Plant Introduction
Research Unit (PIRU) located in Ames, IA; and the Plant
Science Research Unit (PSRU) in Raleigh, NC
Technical Steering Group (TSG) provides guidelines for
research, germplasm, and methods.
Germplasm Enhancement of Maize
GEM Project Cooperators
Category
Number
Private US companies
29
Public US universities
13
USDA-ARS research units
8
Non-government organization
1
Private international companies
11
Public international institutes
4
Total
66
Germplasm Enhancement of Maize
GEM Objectives
Manage and coordinate a multi-site cooperative
program for germplasm evaluation, development,
and information sharing
Evaluate diverse maize germplasm for adaptation,
yield, stress resistance, and key value-added traits
(VATs)
Develop and release enhanced germplasm with
key traits
Develop innovative means of managing and
transferring information to the maize community
Germplasm Enhancement of Maize
GEM Germplasm Releases
Year
# Lines Released
2001
2002
2003
2003
2003
2003
2003
2004
2004
2004
2004
2005
2005
2005
2006
2006
2007
2007
2007
2008
2009
2009
Total
1*
2*
29**
1*
1
42
9*
14
2
1
9
9
1
19
13
3
10
10
1*
13
7
5
202
Institution
Germplasm Attributes
USDA-ARS Ames
Univ. of Delaware
NC State Univ.
Ohio State Univ.
Univ. of Delaware
USDA-ARS Ames
NC State Univ.
USDA-ARS Ames
Texas A&M Univ.
Univ. of Wisconsin
NC State Univ.
USDA-ARS Ames
Univ. of Delaware
NC State Univ.
USDA-ARS Ames
NC State Univ.
USDA-ARS Ames
NC State Univ.
Truman State Univ.
USDA-ARS Ames
USDA-ARS Ames
USDA-ARS Raleigh
Resistance to 1st brood ECB (non-DIMBOA)
Yield, resistance to anthracnose and GLS
Yield, earlier flowering, GLS, Fusarium Resistance
Yield, Fusarium resistance
VAT
Temperate adaptation, GLS, VAT
Yield, VAT, GLS
Temperate adaptation, yield, VAT
Stress tolerance, yield, CEW, grain mold resistance
Superior nutritional quality/yield
Yield, earlier flowering, VAT
Temperate adaptation, yield, VAT
High protein
Yield, earlier flowering, VAT
Yield, VAT
Yield, earlier flowering
Protein, oil, high starch for ethanol
50% exotics; disease resistance
Amylose maize VII line (GEMS-0067)
Temperate adaptation, yield, VAT, waxy lines
Protein, oil
50% exotic; protein, oil
* Crop Science registered and ** 20 of these 29 lines were Crop Science registered.
Germplasm Enhancement of Maize
Number of Releases by Traits
Germplasm Traits
Number
Protein above 13%
33
Amino Acid index (Met. Lys. Trp.)
17
Oil above 4.5%
13
Starch compositional properties
24
High Amylose (70%)
1
Waxy
2
Fumonisin (reduced level)
5
Aflatoxin (reduced level)
6
Leaf disease resistance (GLS, NLB, & SLB)
104
Other (yield, Y/M, etc.)
12
Germplasm Enhancement of Maize
New GEM Initiatives
Allelic diversity
New un-sampled races being tapped
Goal to assess ~300 races for adaptation in US
New elite exotic sources being acquired
More than 40 germplasm sources acquired from
Thailand, Peru, Nigeria, Argentina, Chile, and France
Provide resistance to exotic diseases
Shade house to reduce photoperiod response
Make tropical introgressions in Ames, IA
23 tropical sources (11 races) successful (so far)
Double haploid research
Explore feasibility with exotic germplasm
Germplasm Enhancement of Maize
Fusarium Ear Rot
Susceptible Line
Resistant Line
GEMS-0002 Public Release
Bill Dolezal, Pioneer Hi-Bred Int’l, Woodland, CA (2005)
Integrated national programmatic approach, with extensive
academic and private sector collaborations/partnerships
Exploit untapped genetic diversity in genebanks, and breeding
populations
Plant genomics, gene discovery
Genetic markers & Bioinformatics
Genome Databases
Genetic
Enhancement
and Breeding
American Seed Research Summit
Research, Education, and Policy Goals and Strategies
 Strengthen public and private partnerships to accomplish




national seed research priorities
Coordinate and engage industry stakeholders to support stable
funding for seed and breeding education, research, and
development
Attract and develop a pool of diverse, high-quality plant
researchers
Ensure that the regulatory system governing the development
and implementation of new technology is efficient, effective,
and science-based.
Develop an education and advocacy program to communicate
the value of seed and crop research to the public.
Thanks!
 Thanks to the NCCPB and ASTA for the invitation
to speak
 Thanks to USDA/ARS scientists for sharing
information and data
 Thanks to our partners in the seed industry and
academia for their invaluable collaboration