1. 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 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

2. Commercial Solanaceae Production US: $5.38 billion product value (1.6 million acres)

3. Solanaceae Breeding Bottlenecks & Challenges Narrow genetic baseNarrow genetic base Inefficient early generation selectionInefficient early generation selection Many pestsMany pests Multi-trait evaluationMulti-trait evaluation –Quality –Resistance –Agronomy Market differentiationMarket differentiation Lack of markers in elite germplasmLack of markers in elite germplasm Small populationsSmall populations

4. 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 sequencedTomato 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 breedersSol Genomics Network (SGN) database is not being utilized by breeders Similar genomes, few examples of orthologous gene discoverySimilar genomes, few examples of orthologous gene discovery Marker assisted breeding (MAB) is not practiced due to:Marker assisted breeding (MAB) is not practiced due to: – limited genetic diversity – lack of genetic markers linked to traits of interest

6. Principal Scientists 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)

7. SolCAP Research Objectives SolCAP Research Objectives CSREES (Two E’s focus of afternoon session)CSREES (Two E’s focus of afternoon session) Primary research objective: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: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.

8. 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

9. 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.

10. 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.

11. Summarize all research objectives here… Objectives

12. Collect standardized phenotypic data across multiple environments for tomato and potato.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

13. 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.

14. High throughput analysis of carotenoids, sugars, and acids using IR Spectra (Luis Rodruiguez-Saona, D. Francis, OSU) 3600 3200 2800 2400 2000 1600 1200 800 0.08 0.06 0.04 0.02 0.00 Wavenumber, cm-1 Absorbance, A Lycopene Red Tomato Yellow Tomato Green Tomato trans- lycopene

15. Lycopene Quantification

16. 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

17. 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.

18. 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.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. Genotyping Platform

19. Potato Snowden Atlantic Premier Russet Leaf Flower Callus Tuber 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) Leaf Flower Callus Fruit cDNA Libraries for Sequencing Using illumina Genome Analyzer (Solexa) Tomato

20. Sequencing and Marker Discovery Transcript assembliesTranscript 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.Identify SNPs via alignment to consensus transcript assemblies and reference genome sequence. –computationally identify all possible SNPs within a genotype

21. Add data from Robin’s eSNP discovery and cross linking to validated SNPs … # in potato # in tomato Validation flags

22. High Throughput Genotyping illumina Genomic Analyzer

23. Establish centralized facilities for genotyping a core set of SNPs in standard germplasm panels in tomato and potato.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) SNP Genotyping

24. Genotyping the core collections will impact strategies for translation. Potential translational approaches: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.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.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.

25. Address regional, individual program and emerging needs within the Solanaceae community through a 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: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. Small Grants Program

26. Create integrated, breeder-focused resources for genotypic and phenotypic analysis by leveraging existing databases and resources at SGN and MSU.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 Databases and Resources

27. 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

28. Outcomes for Breeding from SolCAP A genome-wide set of markers and bioinformatic tools accessible by breedersA 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.

29. Better understanding of the allelic variation influencing CHOsBetter 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

30. The discovery of orthologous genes through improved bioinformatic databasesThe discovery of orthologous genes through improved bioinformatic databases Outcomes for Breeding from SolCAP

31. Changes in breeding systems. Vegetable breeding has limitations not inherent in grain (cost of plot maintenance; narrow harvest window)Changes in breeding systems. Vegetable breeding has limitations not inherent in grain (cost of plot maintenance; narrow harvest window) Outcomes for Breeding from SolCAP - 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.

32. Stakeholder Advisory Board Dr. Bob Hoopes, Frito-Lay Erik Legg, Syngenta Dr. Tom Osborn, Seminis Chuck Rivara, CTRI Dr. Caius Rommens, Simplot Scientific Advisory Board Dr. Glenn Bryan Dr. Jim Giovannoni Dr. David Neale Dr. Dani Zamir Executive Committee Dr. Robin Buell Dr. Walter De Jong Dr. David Francis Dr. Alex Stone Dr. Allen Van Deynze Dr. Lukas Mueller Project Director Dr. David Douches Project Assistant Genotyping Francis Van Deynze Data Management Buell Mueller Small Grants Program For Genotyping Trait Specific Populations Executive Committee Germplasm Panels Douches Francis Education De Jong Van Deynze Extension Stone Liedl Francis SolCAP Management Structure

33. http://solcap.msu.edu