SolCAP
Solanaceae Coordinated Agricultural Project
Dedicated to the Improvement of Potato and Tomato
Executive Commitee :
David Douches Walter De Jong Robin Buell David Francis
Alexandra Stone Lukas Mueller AllenVan Deynze
Supported by the National Research Initiative Plant Genome Program of USDA’s Cooperative State
Research , Education and Extension Service
Commercial Solanaceae Production
US: $5.38 billion product value (1.6 million acres)
Solanaceae Breeding Bottlenecks & Challenges
• Narrow genetic base
• Inefficient early generation selection
• Many pests
• Multi-trait evaluation
– Quality
– Resistance
– Agronomy
• Market differentiation
• Lack of markers in elite germplasm
• Small populations
In Solanaceae There is a Major Gap
Between Genomic Information and Breeding
• Tomato and potato breeding are based upon phenotypes, not
genotypes, despite the fact that they are being sequenced
• Sol Genomics Network (SGN) database is not being utilized by
breeders
• Similar genomes, few examples of orthologous gene discovery
• Marker assisted breeding (MAB) is not practiced due to:
– limited genetic diversity
– lack of genetic markers linked to traits of interest
SolCAP Project Participants
Lead Institution: Michigan State University
New York
Cornell University
Oregon
Maryland
Oregon State University
Cedar Lake Research and Consulting
USDA/ARS Beltsville
Idaho
USDA/ARS University of Idaho
California
Minnesota
West Virginia
UC Davis
Campbells R&D
University of Minnesota
West Virginia State University
Wisconsin
North Carolina
USDA/ARS University of Wisconsin
North Carolina State University
Michigan
Florida
Michigan State University
University of Florida
Ohio
Ohio State University
Principal Scientists
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David Douches (Michigan State, potato breeder)
David Francis (Ohio State, tomato breeder)
Walter De Jong (Cornell University, potato breeder)
Allen Van Deynze (UC Davis, genotyping/sequencing)
Robin Buell (Michigan State, sequencing/bioinformatics)
Lukas Mueller (Boyce Thompson Inst., bioinformatics)
Alexandra Stone (Oregon State, eXtension)
SolCAP Research Objectives
• CSREES (Two E’s focus of afternoon session)
• Primary research objective:
– To provide infrastructure to link allelic variation in genes to valuable
traits within the two most important vegetable crops in the
Solanaceae: potato and tomato
• General objectives:
– Increase the likelihood that breeding of crops in the Solanaceae
will benefit from genotype-based selection processes
– Leverage genomic resources for the improvement of multiple crops
that share taxonomic affinity and DNA homology first CAP that has
a multiple species focus
• Unique challenge because, despite having close genomic
structure, the breeding systems are different
– Expand beyond a single commodity to encompass multiple related
species will create a broader vision for translational genomics in
agricultural research.
Stakeholder-defined Core
Components
– Traits
• Carbohydrate and sugar metabolism (processing traits)
– Germplasm
• Elite germplasm, Breeder driven; Appropriate outgroups
– Tools
• Fund existing facilities to SNP genotype germplasm panels
– Flexible funding
• genotyping additional populations for validation or additional traits
• marker conversion
– Data mining and management
• SGN, SolCAP websites
– Extension
• eXtension; partner with other CAPs
– Education
• Curriculum development; breeder workshops, graduate course
How will tomato and potato breeding
benefit from SolCAP?
• Develop molecular genetic tools and infrastructure so
that applied breeders can begin to use marker-assisted
selection in elite germplasm.
• Develop 1536 SNP (or more as platforms expand)
markers that are polymorphic in elite potato and tomato
germplasm.
• SNP Genotype 480 potato clones and 480 tomato lines-provided by North American breeders -- with these
markers.
How will Tomato and potato breeding
benefit from SolCAP?
• Provide, as a service, genotyping of populations/
breeding clones in 2010, 2011 and 2012, submitted by
the breeding community.
• Develop a breeder portal for access to SGN
(sgn.cornell.edu) to improve use by applied breeders.
• Workshops for breeders, staff, and graduate students in
bioinformatics, marker theory and practice.
• Develop a distance-education course in marker-assisted
breeding.
• Generate and disseminate web-accessible outreach
materials for the public, through an eXtension community
of practice.
Objectives
• Summarize all research objectives here…
Germplasm Panels
• Collect standardized phenotypic data across multiple
environments for tomato and potato.
– standardized database of phenotypes for key traits
across germplasm panels for each commodity,
accessible through the SolCAP and Solanaceae
Genome Network (SGN) websites.
Germplasm Panels
• Cooperative tests- at least 2 locations for each crop
under the supervision of experienced field breeders.
• Through the “cooperators guide”, we will also promote a
“genomics mentality” that emphasizes increased
genotypic replication and the collection of standardized
and objective phenotypic data that can be linked to
ontologies.
High throughput analysis of
carotenoids, sugars, and
acids using IR Spectra
(Luis Rodruiguez-Saona, D. Francis, OSU)
Absorbance, A
0.08
0.06
Red Tomato
Yellow Tomato
Green Tomato
translycopene
0.04
Lycopene
0.02
0.00
3600
3200
2800
2400
2000
1600
Wavenumber, cm-1
1200
800
Pred conc (mg/100g) by ATR-IR
Lycopene Quantification
12
R=0.958
SEV = 0.80mg/100g
8
4
0
0
5
10
Lycopene conc (mg/100g sample) by HPLC
Germplasm Panel, e.g. Potato
• A subset of the germplasm panel will be:
– Lines chosen based upon CHO variation
– Important varieties and advanced lines of value to the breeder
– Solanum species and accessions introgressed into 4x
germplasm
– 4x mapping population from a russet x russet cross: primary
CHO/ vitamin C mapping population for QTL analysis
– 2x mapping population will be used for mapping SNPs
Germplasm Panel, e.g. Potato
• Field tested 2 years X 3 major environments for potato
production (PNW northern irrigated desert/fall harvest,
NC - northern humid/ fall harvest and SE southern
humid/spring or summer harvest) to collect samples for
CHO, vitamin C analysis and other traits.
– Evaluation of specific gravity, chip color, skin type, shape, vine
maturity, tuber number, vitamin C, internal defects, bruising,
anthocyanins and biotic resistances.
– K. Haynes (USDA/ARS, MD) will provide experimental design,
data management (combining genotypic and phenotypic data)
and statistical analysis of the phenotypic data for potato.
Genotyping Platform
• Develop extensive sequence data of expressed genes,
and identify Single Nucleotide Polymorphism (SNP)
markers associated with candidate genes for sugar,
carbohydrate, and vitamin biosynthetic pathways.
– Catalog allelic variation in structural and regulatory
genes and subsequently explore correlation with
corresponding traits.
cDNA Libraries for Sequencing
Using illumina Genome Analyzer (Solexa)
Tomato
•T5(CA fresh-market)
•FL7600(Florida fresh-market)
•NC84173(North Carolina fresh-market)
•OH9242(Ohio processing)
•PI114490(wild cherry tomato)
•PI128216(wild current tomato)
•H1706 (Midwest Processing; focus of
Genome sequence)
•TA496 (CA Processing; focus of EST
sequence)
Potato
•Snowden
•Atlantic
•Premier Russet
Leaf
Flower
Callus
Tuber
Leaf
Flower
Callus
Fruit
Sequencing and Marker Discovery
• Transcript assemblies
– Represent consensus sequences of all ESTs
• all alleles that are similar enough to be co-assembled under
the parameters used.
– Represent the predominant allele in the underlying EST
population
• Identify SNPs via alignment to consensus transcript
assemblies and reference genome sequence.
– computationally identify all possible SNPs within a genotype
Add data from Robin’s eSNP discovery and
cross linking to validated SNPs …
# in potato
# in tomato
Validation flags
High Throughput Genotyping
illumina Genomic Analyzer
SNP Genotyping
• Establish centralized facilities for genotyping a core set
of SNPs in standard germplasm panels in tomato and
potato.
– a uniform database (>1.47 M data points) of integrated mapped
markers and genotypes for 480 accessions of each crop.
– The genetic data will resolve population structure and facilitate
association mapping in the core collections and designing further
QTL mapping populations
– (For e.g. see Matt Robbins, OSU, presentation)
Genotyping the core collections will
impact strategies for translation.
• Potential translational approaches:
– 1) introgression from other populations (domesticated or wild)
– 2) selection for coupling phase recombinants to establish linkage
blocks of favorable alleles (e.g. disease resistance loci)
– 3) population development designed to maximize variation w/in market
classes
– 4) association approaches
– 5) whole genome approaches
• Other translational strategies will emerge under other
CAPs or through innovation in public research.
• Currently traits and populations among the breeding
communities for tomato and potato exist to implement
each of the five approaches, but there are insufficient
numbers of markers to do so.
Small Grants Program
• Address regional, individual program and emerging
needs within the Solanaceae community through a small
grants program.
• Six key areas we intend to allocate resources to are:
– Genotyping mapping populations in the core facilities requested
by the greater breeding community
– Marker conversion – developing SNP markers linked to QTL into
easily assayed (e.g. CAPs or dCAPs) markers that end-users can
readily apply in their own research programs
– QTL validation and MAS
– Population development to address emerging needs
– Extension or education special projects
– New directions not envisioned at the time of proposal submission.
Databases and Resources
• Create integrated, breeder-focused resources for
genotypic and phenotypic analysis by leveraging existing
databases and resources at SGN and MSU.
– Breeders, geneticists, and bioinformaticians will work to create
integrated genomic and phenotypic databases that serve the
entire potato and tomato breeding and genetics community
Developing “Breeder Friendly” Tools
consider dropping from PAG
• Current SGN interfaces are aimed at the molecular biologist,
with searches designed to facilitate molecular discovery
– Need a portal that is trait and germplasm centered
• Ability to search by traits relevant to (and defined by) breeders
• When a marker is identified, a protocol for use in breeding will
be provided.
• Search option that only yields polymorphic marker, phenotype,
or QTL results from elite germplasm
• Ability to search for known parents or offspring of any given
genotype
• Ability to generate a list of markers that are polymorphic
between any two parents
• Detailed tutorial/definitions of terms and traits utilized within the
database
Outcomes for Breeding from SolCAP
• A genome-wide set of markers
and bioinformatic tools
accessible by breeders
– Breeders will access germplasm for
crossing based upon SNP
polymorphism and linked QTL of
interest
– design crosses complementary for
QTL and traits, and then use MAB
in EGS.
Outcomes for Breeding from SolCAP
• Better understanding of the allelic
variation influencing CHOs
– Design crosses to create improved
sugar and starch levels and starch
quality.
– Crosses designed to manipulate and
select variation within existing elite
populations or introgress novel
alleles from wild germplasm.
– More predictable and directed
breeding effort for processing and
fresh market traits.
Outcomes for Breeding from SolCAP
• The discovery of orthologous genes through improved
bioinformatic databases
Outcomes for Breeding from SolCAP
• Changes in breeding systems. Vegetable breeding has
limitations not inherent in grain (cost of plot maintenance;
narrow harvest window)
- Influence breeders to increase
genotypic replication
- Make better use of breeding values
through incorporation of information
on population structure and kinship
- Use objective means to increase
variation in breeding populations.
SolCAP Management Structure
Stakeholder Advisory Board
Dr. Bob Hoopes, Frito-Lay
Erik Legg, Syngenta
Dr. Tom Osborn, Seminis
Chuck Rivara, CTRI
Dr. Caius Rommens, Simplot
Executive Committee
Dr. Robin Buell
Dr. Walter De Jong
Dr. David Francis
Dr. Alex Stone
Dr. Allen Van Deynze
Dr. Lukas Mueller
Genotyping
Francis
Van Deynze
Germplasm Panels
Douches
Francis
Education
De Jong
Van Deynze
Scientific Advisory Board
Dr. Glenn Bryan
Dr. Jim Giovannoni
Dr. David Neale
Dr. Dani Zamir
Project Director
Dr. David Douches
Project Assistant
Data Management
Buell
Mueller
Extension
Stone
Liedl
Francis
Small Grants Program
For Genotyping Trait
Specific Populations
Executive Committee
http://solcap.msu.edu