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Working in Partnership to Attain Priority Crop Genetic Resource, Genomics, and Genetic Improvement Research Goals Peter Bretting USDA-Agricultural Research Service Office of National Programs Peter.bretting@ars.usda.gov http://www.ars.usda.gov/research/programs/programs.htm?NP_CODE=301

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slide1

Working in Partnership to Attain PriorityCrop Genetic Resource, Genomics, and Genetic Improvement Research Goals

Peter Bretting

USDA-Agricultural Research Service

Office of National Programs

Peter.bretting@ars.usda.gov

http://www.ars.usda.gov/research/programs/programs.htm?NP_CODE=301

outline for presentation
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
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.
slide5
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
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.

The USDA/ARS National Plant Germplasm System (NPGS)
plant genetic resource management in genebanks
Plant Genetic Resource Management in Genebanks
  • Acquisition
  • Maintenance
  • Regeneration
  • Documentation and Data Management
  • Distribution
  • Characterization
  • Evaluation
  • Enhancement
avoidance of cross pollination and seed mixing
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
slide11

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-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 global13
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

(Web Browser)

Presentation Tier

(Windows Desktop Client)

Business Tier

(Web Service)

Data Tier

(MySQL, Oracle, SQL Server)

Three Tier Architecture
grin global15
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
np 301 action plan research components19
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
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
slide21

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.

slide22
Linkage Mapping

Nested Association Mapping

Recent and ancient recombination

High Power

High resolution

Analysis of many alleles

Moderate genetic marker density

High projected marker density

Association Mapping

Recent recombination

High power

Low resolution

Analysis of 2 alleles

Moderate marker density

Genome scan

Historic recombination

Low power

High resolution

Analysis of many alleles

High marker density

Candidate gene testing

nested association analysis

SSD

1

2

NAM

200

Nested Association Analysis

25 DL

B97

CML103

CML228

CML247

CML277

CML322

CML333

CML52

CML69

Hp301

Il14H

Ki11

Ki3

Ky21

M162W

M37W

Mo18W

MS71

NC350

NC358

Oh43

Oh7B

P39

Tx303

Tzi8

×B73

F1s

Yu et al. (2008) Genetics 178: 539

nam genotyping and genetic map
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
Maize Phenomics: Massively Parallel Phenotyping of The Nested Association Mapping Population

THE MAIZE DIVERSITY PROJECT

experimental evaluation of nam
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

Ponce, PR

11 Total Environments

slide27

+

Tassel main spike length

Tassel branch angle

Tassel branch no.

partitioning genetic variance

B73

X

NC358

B73

X

P39

B73

X

M37W

B73

X

IL14H

B73

X

Tx303

B73

X

B97

B73

X

Mo18W

B73

X

Ki11

B73

X

NC350

B73

X

Ky21

B73

X

Oh7B

B73

X

Ki3

B73

X

CML103

B73

X

Oh43

B73

X

MS71

B737

xHp301

B73

X

M162W

B73

X

Tzi8

B73

X

CML52

B73

X

CML228

B73

X

CML277

B73

X

CML247

B73

X

CML69

RIL1

RIL2

RIL199

RIL200

RIL1

RIL2

RIL199

RIL200

σ2G(F)2

σ2G(F)1

Partitioning Genetic Variance

Line-to-line variation within a family – due to differences between alleles from B73 and alleles from Diverse Line founder of that family.

B73

X

CML322

B73

x

CML333

Among-Family Genetic Variance: σ2F

Family-to-family variation – due to differences among different founders.

Within-Family Genetic Variances

slide29
The Maize Genetics andGenomics 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

Soybean Nested Association Mapping (NAM) Project (P. Cregan, D. Hyten, ARS-Beltsville)

Agricultural

Research

Service

Collaborators:

USDA/ARS

Iowa St. Univ.

Univ. of Nebraska

Univ. of Illinois

Univ. of Tennessee

Univ. of Maryland

Funding Support

soybean nam
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
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
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
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
The Universal Soy Linkage Panel 1.0 (USLP 1.0)for Gene/QTL Discovery

- Traits Under Study in Collaborative Projects -

Enhanced Seed Composition

Reduced linolenic acid oil

Elevated oleic acid oil

Lower saturates

Higher protein

Resistance to Biotic Stress

Soybean Cyst Nematode

Soybean Rust

Phytophthora Root Rot

Foliar Feeding Insects

Soybean Aphid

Resistance to Abiotic Stress

Drought

Iron Deficiency Chlorosis

Seed Yield –

Assessment and enhancement of genetic diversity

source of genetic improvement for soybean
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)

18,090 accessions collected mostly from Asia (Landraces)

1,116 wild soybeans

17 Introduced landraces

(86% of the Germplasm base)

513 Public cultivars released after 1946

Hyten et al. 2006, PNAS 103: 16666-16671

soy hapmap
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

controlling iron deficiency chlorosis in soybeans
Controlling Iron Deficiency Chlorosis in Soybeans
  • 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
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 to Chromosome 20
  • High-throughput transcript sequencing and mapping identified several candidate genes
  • Currently identifying the specific genes and evaluating modifications to change the protein content
haplotype and allele states for varieties
Haplotype and Allele States for varieties

SNP Haplotypes and Linkage Disequilibrium

(R. Shoemaker, ARS-Ames)

np 301 action plan research components42
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 gem project
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
GEM Project Cooperators

Germplasm Enhancement of Maize

gem objectives
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
GEM Germplasm Releases

Germplasm Enhancement of Maize

* Crop Science registered and ** 20 of these 29 lines were Crop Science registered.

number of releases by traits
Number of Releases by Traits

Germplasm Enhancement of Maize

new gem initiatives
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
Fusarium Ear Rot

Germplasm Enhancement of Maize

Susceptible Line

Resistant Line

GEMS-0002 Public Release

Bill Dolezal, Pioneer Hi-Bred Int’l, Woodland, CA (2005)

genetic enhancement and breeding

Integrated national programmatic approach, with extensive academic and private sector collaborations/partnerships

Genetic Enhancementand Breeding

Genome Databases

Exploit untapped genetic diversity in genebanks, and breeding populations

Plant genomics, gene discovery

Genetic markers & Bioinformatics

american seed research summit research education and policy goals and strategies51
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!
  • 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