Source: MICHIGAN STATE UNIV submitted to NRP
TRANSLATING SOLANACEAE SEQUENCE DIVERSITY AND TRAIT VARIATION INTO APPLIED OUTCOMES THROUGH INTEGRATIVE RESEARCH, EDUCATION AND EXTENSION
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0219180
Grant No.
2009-85606-05673
Cumulative Award Amt.
$3,775,000.00
Proposal No.
2010-03613
Multistate No.
(N/A)
Project Start Date
Sep 1, 2009
Project End Date
Aug 31, 2014
Grant Year
2012
Program Code
[91710]- Applied Plant Genomics Coordinated Agricultural Project (CAP)
Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824
Performing Department
Plant, Soil and Microbial Science
Non Technical Summary
One challenge today in agriculture research involves closing the gap between the advances in plant genomics and use of this knowledge by plant breeders to develop improved varieties. We call this effort translational genomics. Our team of researchers (SolCAP) aims to reduce this gap by focusing on development of genetic maps that are relevant to breeding improved varieties in two major Solanaceae vegetable crops: potato and tomato. We will use leading high throughput sequencing and bioinformatics to identify DNA variation in genes of high value traits such as carbohydrate, sugar and vitamin content (important consumer and processor traits). We will support centralized facilities for characterizing the DNA sequence variation in relevant potato and tomato lines and breeding populations. In addition, we will support a centralized database that the breeders will use to curate and share information. Concurrently, we will also provide workshops for the breeders to learn how to integrate these new techniques and the database in their breeding efforts. We established a network of cooperating breeding programs to collect standardized data on relevant varieties, parental lines, and wild species that are broadly useful in breeding and to the scientific community. These resources will ultimately be used by breeders to develop improved varieties. Through partnerships with the Solanaceae Genomics Network and Michigan State University, we will enhance access and availability of breeder friendly analysis tools. A small grants program will leverage the DNA sequence variation characterization tools for additional genetic mapping of agronomic, disease/insect resistance and quality traits that will ultimately impact the environment positively and nutritionally enhance the consumer products (potatoes, tomatoes and processed products). Outreach efforts will consist of integrated education and extension, through developing curricula for graduate students, offering a breeder practicum, and developing a community of learning for extension specialists via the eXtension web portal to extend our impact to the national level. Continuous assessment by a designated evaluator will be used to improve effectiveness of our education and extension efforts.
Animal Health Component
34%
Research Effort Categories
Basic
33%
Applied
34%
Developmental
33%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011310104010%
2011310108040%
2011460104010%
2011460108040%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1310 - Potato; 1460 - Tomato;

Field Of Science
1040 - Molecular biology; 1080 - Genetics;
Goals / Objectives
1. Create a highly visible and innovative education program to train plant breeders, graduate students, and industry cooperators in genome-based breeding. The goal is to educate current and future plant breeders, with special emphasis on solanaceous breeders, in the theory and practice of translational genomics. This will be achieved by developing and delivering curricula that seek to increase the knowledge of translational genomics and delivering these curricula through an innovative team-taught distance education course, workshops and short courses for industry breeders. 2. Amplify outreach efforts by developing an eXtension Community of Practice (CoP) including plant breeders, seed industry professionals, extension specialists, and practitioners. SolCAP will create a web community (Plant Breeding and Genomics)that will foster cross disciplinary and cross commodity networking and collaboration within the CoP. The Plant Breeding and Genimics CoP will collaboratively generate outreach materials that will be published on the public eXtension.org site. SolCAP will provide leadership to bring all CAPs into the eGenome Community of Practice. 3. Collect standardized phenotypic data across multiple environments for tomato and potato. This will result in a standardized database of phenotypes for key traits across 480 accessions of each commodity, accessible through the SolCAP and Solanaceae Genome Network (SGN) websites. 4. 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. We will catalog allelic variation in structural and regulatory genes and subsequently explore correlation with corresponding traits. 5. Establish centralized facilities for genotyping a core set of SNPs in standard germplasm panels in tomato and potato. The outcome will be a uniform database 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. 6. Address regional, individual program and emerging needs within the Solanaceae community through a small grants program. As a service to the community, we will provide opportunities to genotype populations, validate marker linkages to major loci influencing vitamin and sugar content, validate quantitative trait loci (QTL), convert SNPs into breeder friendly markers for marker assisted selection. Up to 15 populations will be genotyped leading to increased breeder engagement with genomics, as well as the mapping of agronomic, disease/insect resistance and quality traits. The small-grants program will allow us to meet future national needs. 7. 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 Solanaceae breeding and genetics community.
Project Methods
Obj. 1. The goal is to educate current and future plant breeders in the theory and practice of translational genomics. This will be achieved by developing and delivering curricula that seek to increase the knowledge of translational genomics and delivering these curricula through an innovative team taught distance education course (jointly developed and taught at all participating institutions), workshops and short courses for industry breeders. Obj. 2. We will create a web community (Plant Breeding and Genomics) that will foster cross disciplinary and cross commodity networking and collaboration within the Community of Practice (CoP). The Plant Breeding and Genomics CoP will collaboratively generate outreach materials that will be published on the public eXtension.org site. We will provide leadership to bring all coordinated agricultural projects into the Plant Breeding and Genomics CoP. Obj.3. Germplasm panels form the core of SolCAP, linking all objectives. Each panel is assembled with Solanaceae community input. These panels will be posted and described at the SolCAP website. Obj.4. We will identify polymorphisms in genes known to be involved in sugar, CHO, and vitamin biosynthesis pathways by sequencing normalized cDNA populations from multiple tomato and potato lines not currently represented by large-scale EST or genome sequencing efforts. Normalized cDNA libraries and 2 Gb sequence for each of 3 potato and 6 tomato genotypes; SNPs and gene discovery for CHO, sugar and vitamin metabolism will be realized. Obj.5. Fixed array technology, high throughput SNP genotyping platform will provide a cost effective approach to genotype the core collections. Liquid bead assays will provide flexibility and cost effectiveness for individual populations where only a small proportion of the fixed array SNPs are polymorphic. We will utilize the SNP data generated under Obj.4 and publicly available SNPs. We will genotype the core collections of 480 accessions for each crop using the 1,536 probe Illumina design to maximize reagent use. We will deliver approximately 8 M total data points. Obj.6. The small grants program represents the principle mechanism for QTL validation and MAS approaches. It provides a flexible mechanism to reallocate resources and implement community based strategies. Funds will be used to facilitate marker conversion in order to empower individual programs to pursue specific traits or loci within their own programs. Obj. 7. We will leverage two existing bioinformatics resources to provide maximal interpretation and dissemination of the project data. The division of effort between these two bioinformatics resources will allow the expertise of each group to be maximized and provide the community with integrated interfaces for data-mining. Hyperlinks between the two resources will ensure broad dissemination of the project deliverables: Breeder-friendly interactive interfaces to query and display data from trait to gene including germplasm, phenotypic, genotypic, genomic data with links to protocols and references; marker analysis, assay and conversion resources; breeders will adopt genomic tools and markers in their breeding programs.

Progress 09/01/09 to 08/31/14

Outputs
Target Audience: The potato and tomato breeding and genetics communities of the US and abroad. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? The following personnel have been trained on the project this project: Alicia Massa, Ph.D. MSU Buell lab; Cory Hirsch, Ph.D. MSU Buell lab; Matt Zuelke, MSU undergraduate; Alison McKenna, technician, MSU potato breeding and genetics program; K. Haynes and L Wanner, USDA/ARS; Sarah Braun, Ph.D. candidate at University of Wisconsin, Madison. The following are working on the project: Kim Felcher, Ph.D. MSU Potato Breeding and Genetics Program, works on marker database, germplasm panel and SNP data analysis in Douches lab. Daniel Zarka, Post Doc MSU Potato Breeding and Genetics Program, works on SNP genotyping with the Infinium system. Kelly Zarka, technical staff at MSU Potato Breeding and Genetics Program, was trained in SNP genotyping and genotype by sequencing. Joe Coombs, technical staff at MSU Potato Breeding and Genetics Program, is participating in SNP data analysis. Candice Hirsch, Post Doc, MSU Plant Biology, worked on bioinformatics analysis of tomato and potato sequences. Amanda Labuza, Rensselaer Polytechnic Institute, Undergraduate intern in Francis lab (December 2010-January 2011). Co-funded by the OARDC Research Internship Program. Gabriel Abud, College of Wooster, Wooster, Ohio, Undergraduate intern in Francis lab (June-Aug 2010). Co-funded by the OARDC Research Internship Program. Caleb Orchard, Grove City College, Pennsylvania. Undergraduate intern in Francis lab (June-Aug 2010). Co-funded by the Summer Undergraduate Research Experience (SURE) internship program. Caleb went on to complete his MS in Horticulture and Crop Science at OSU in December 2014. Heather Merk served as a post-doctoral researcher and program manager for the eXtesnion (2011-2013) and now leads the Plant Breeding Academy for Syngenta. Jacob Schleappi, Cleveland Institute of Art, Undergraduate intern in Francis lab, June-August 2009 and 2010. Laura Bonefeld, Michigan State University, Undergraduate bioinformatics intern in Buell lab. Andy Murley: Michigan State University, Undergraduate student trained in DNA extraction and PCR in Douches lab. Kevin Stoffel: UC Davis, Senior research associate, was trained in normalized cDNA development in Van Deynze lab. Lee Heekyoung: UC Davis. Lee is a visiting scientist from Korea that was trained in molecular marker validation and analysis in Van Deynze lab. Sebastian Reyes Cin-Wo, UC Davis. Sebastian is an undergraduate student from Costa Rica who was trained in tomato field testing, bioinformatics analysis of sequence data and primer design in Van Deynze lab. Jamie Shattuck, postdoc UC Davis mange and organize tomato genomics workshop. Shawn Yarnes: UC Davis. Shawn is a postdoc in the Van Deynze lab. She is managing the research trials for tomato in 2010. Selene Clay: UC Davis. Selene is a high school student in the Van Deynze lab who has been trained in genotyping and analysis of tetraploid segregation in potato using the data generated by SolCAP. Doug Maxwell, University of Wisconsin, Madison-Mapping of virus resistance in tomato. Jay Scott, University of Florida, Mapping of virus resistance in tomato. Sam Hutton, University of Florida, Mapping of virus resistance in tomato. Martha Mustchler, Cornell University, mapping disease resistance in tomato. Dilip Panthee, North Carolina State University, mapping disease resistance in tomato. Neelima Sinha and Julin Maloof; UC Davis-Deciphering leaf traits in tomato. Leonie Moyle, Indiana State University, Mapping fruit traits in tomato. How have the results been disseminated to communities of interest? The results from SolCAP have been disseminated through journal publications, the SGN website, the SolCAP website, the Plant Breeding and Genomics community of practice (CoP), SolCAP newsletters (10), workshops (7), eXtension.org webinars and various oral presentations at scientific conferences. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The significance of SolCAP to Food and Agriculture: The Solanaceae Coordinated Agricultural Project (SolCAP) aimed to put research emerging from plant genome sequencing projects into the hands of applied breeding programs having direct impact to US Agriculture. SolCAP added significantly to the genomic resources available for potato and tomato through sequencing the gene space of 6 tomato and 4 potato lines. These resources represented the first comprehensive set of sequence data for fresh market tomato and cultivated potato. Because the sequence resources were also based on currently relevant varieties rather than model accessions, the data led to the commercialization of high-throughput SNP genotyping tools that have become the industry standard. Combining these resources with trait data significantly advanced our understanding of germplasm in potato and tomato. Outreach materials developed to help translate these research tools into practice and accessible through eXtension.org, are viewed on average 9,000 times per month, while our workshops and webinars were attended by 750 individuals, and the recordings accessed more than 89,000 times. Breeding projects that leverage the SolCAP resources are addressing nutritional quality, resistance to abiotic stress, and resistance to important diseases, establishing a clear linkage to the goals of AFRI. SolCAP developed SNP markers will considerably facilitate the development of new potato and tomato varieties. Broad Impacts: The potato genome sequence generated by the Potato Genome Sequencing Consortium was shared with SolCAP. This access allowed us to align the transcriptome sequences developed by SolCAP so that SNPs could be more robustly identified. In a reciprocal exchange, we provided the Potato Genome Sequencing Consortium our potato transcriptome data to facilitate development of SNP markers for anchoring of whole genome shotgun sequencing scaffolds to the genetic map. We have validated the concordance of the SNPs with the draft genome and corrected the alignment of a few super-scaffolds. We have made our Illumina EST sequences available to the Tomato Genome Initiative to facilitate gene annotation. We have collaborated with Germany and France to incorporate some of their SNPs based on complementary germplasm into the community Tomato Infinium chip. We are co-publishing an integrated genetic and physical map of tomato based on the SolCAP Infinium chip. We have completed the project objectives of SNP discovery, SNP platform development and deployment, and genotypic characterization of elite North American cultivated potato and tomato accessions as outlined in the initial grant proposal. Manuscripts describing SNP discovery as well as SNP platform development and validation are published. A genotypic survey of 426 tomato accessions using the SolCAP 7720 SNP Infinium Array was completed and published. A genotypic characterization of a 250-potato clone diversity panel using the SolCAP 8303 Infinium SNP array has been completed and published. The SolCAP project developed two exceptionally powerful tools - potato and tomato SNP chips - that are now in widespread use around the world. These chips have dramatically reduced the time needed for investigators to make associations between markers and traits (weeks instead of years), which will have a profound impact on the development of new cultivars going forward. Because the chips are so easy to use, they have also greatly expanded the range of scientists who can now conduct genetic analyses in potato and tomato - no prior experience in molecular biology is needed. There has been very strong interest from the international community to use the SolCAP potato and tomato SNP arrays. Hundreds of the SolCAP developed potato/tomato arrays have been used, sold, or are in the queue at either user facilities or SolCAP project facilities available to the potato and tomato research community (MSU, UC-Davis, OSU). The SNP arrays have become a common marker set for which to evaluate and compare germplasm world-wide. The SNP arrays for potato and tomato as well as the germplasm panel will be a valuable community resource. The impact of the arrays was emphasized at the International Solanaceae genomics meeting in Switzerland, August 28, 2012 with no less than 12 talks highlighting use of the arrays. The International Seed Federation is recommending the use of the tomato array for variety certification. It has 77 member countries including the US. Use of the Infinium SNP genotyping system is allowing the calling of SNP allele dosage in tetraploid genotypes in over 5000 SNPs from the array. Previous DNA marker platforms could not easily provide dosage calling. Scoring for dosage has increased our power to genetically analyze populations of cultivated tetraploid potato. We have almost complete participation of the US public potato and tomato breeding communities for the germplasm panels. We expect the broader community of breeders to contribute valuable mapping populations for SNP genotyping. Through hands-on and face-to-face interactions we have helped breeding and genetics programs handle the SNP array data. In addition, the SolCAP project has created a highly educational website, housed at eXtension.org, to help train the next generation of breeders in marker-assisted breeding approaches and strategies. SolCAP extension accomplishments include: the establishment and certification of the Plant Breeding and Genomics Community of Practice (PGBCoP) on eXtension.org, the establishment of a shared DRUPAL workspace, the development of workshops addressing the application of genomic resources to plant breeding, and the development of PBG social network, primarily through membership to the PBG newsletter. The PBGCoP has published educational materials on a variety of topics important to the plant breeding community: experimental design, statistical inference, molecular biology, phenotyping, genotyping, mapping, QTL, and population development. Impact: Among the 232 workshop participants who returned surveys (from the 2010, 2011, and 2012 SolCAP workshops at Potato Association of America, Tomato Disease Workshop, Tomato Breeders Roundtable, and the American Society of Horticultural Sciences), approximately 75 percent were professional breeders, technical staff members or related professionals; about 15 percent were students; and about 10 percent were postdocs. Impact: According to Google Analytics, the PBG eXtension website (www.eXtension.org/plant_breeding_genomics) receives over 30,000 unique visits and 108,000 pages views per year. In the past quarter, the site has averaged 20,763 page views per month. Views of PBG eXtension content in the last quarter account for 2.6% of eXtension activity for the 60 publicly launched communities. Each visit to the PBG eXtension website results in an average of 3.22 page views with an average of 3:45 minutes spent on the eXtension site. Impact: Over 69,000 high quality SNPs that meet the Illumina Infinium platform design criteria were identified for potato. Currently, ~8300 scoreable markers are represented on the potato Infinium array. Potato data has been shared with international collaborators (Scottish Crops Research Institute, SCRI) and the Potato Genome Sequencing Consortium to help anchor the potato genome sequence. Over 28,000 SNPs were identified in tomato, with 8,784 SNPs selected for development of an Illumina Infinium array. Of these, 7,720 SNPs passed production quality check and were subsequently scored on the tomato germplasm panel (n=489) representing cultivated varieties (processing, fresh market, vintage and landrace) and wild species. Impact: According to Google Analytics the SolCAP website has had a total of 2,744 unique visitors from 4,423 visits in the last year with a total of 13,691 page views. Of these visits, 58.08% were new. Stakeholder feedback suggests the data downloads are helpful.

Publications

  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Merk, H. L.; Yarnes, S. C.; Van Deynze, A.; Tong, N.; Menda, N.; Mueller, L. A.; Mutschler, M. A.; Loewen, S. A.; Myers, J. R.; Francis, D. M. Reservoirs of Phenotypic and Genetic Variation Among Regionally Adapted Processing Tomato Germplasm. Journal of the American Society for Horticultural Science 137 (6) 427-43.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Sim, S. C.; Van Deynze, A.; Stoffel, K.; Douches, D. S.; Zarka, D.; Ganal, M. W.; Chetelat, R. T.; Hutton, S. F.; Scott, J. W.; Gardner, R. G.; Panthee, D. R.; Mutschler, M.; Myers, J.; Francis, D. M.. 2012. High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding. PLoS ONE 7(9): e45520.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Sim, S.C.; Surstewitz, G.; Plieske, J.; Ganal, M.W.; Van Deynze, A.; Stoffel, K.; Hamilton, J.; Buell, C.R.; Zarka, D.; Douches, D.S.; Francis, D.M. 2012. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS ONE 7(7): e40563.
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Hutton SF, Scott JW, Yang W, Sim SC, Francis DM, Jones JB. 2010. Identification of QTL associated with resistance to bacterial spot race T4 in tomato. Theor Appl Genet. Nov;121(7):1275-87.
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Wang Y, Chen J, Francis DM, Shen H, Wu T, Yang W. 2010. Discovery of intron polymorphisms in cultivated tomato using both tomato and Arabidopsis genomic information. Theor Appl Genet. 121(7):1199-1207.
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Tecle IY, Menda N, Buels RM, van der Knaap E, Mueller LA. solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database. BMC Bioinformatics. 2010 Oct 21;11:525. PubMed PMID: 20964836; PubMed Central PMCID: PMC2984588.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Hamilton, J. P.; Sim, S. C.; Stoffel, K.; Van Deynze, A.; Buell, C. R.; Francis, D. M. 2012. Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis. The Plant Genome. Vol. 5, 17-29. 2012.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Sharma, S. K., Bolser, D., de Boer, J., Sonderkaer, M., Amoros, W., Carboni, M. F., ...Douches, D., ... & Bryan, G. J. (2013). Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.G3: Genes| Genomes| Genetics, 3(11), 2031-2047.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Hirsch, C.N., Hirsch, C.D., Felcher, K., Coombs, J., Zarka, D., Van Deynze, A., De Jong, W., Veilleux, R., Jansky, S., Bethke, P., Douches, D., Buell, C.R. 2013. Retrospective view of North American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries.Genes Genomes and Genetics. doi:10.1534/g3.113.005595.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: D. Douches, C. N. Hirsch, N. C. Manrique-Carpintero, A. N. Massa, J. Coombs, M. Hardigan, D. Bisognin, W. De Jong, and C.R. Buell. 2014. The Contribution of the Solanaceae Coordinated Agricultural Project to Potato Breeding. Potato Research (DOI 10.1007/s11540-014-9267-z)
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Hardigan, M.A., J. Bamberg, C.R. Buell, and D.S. Douches. 2015. Taxonomy and Genetic Differentiation among Wild and Cultivated Germplasm of Solanum sect. Petota. The Plant Genome, March 2015 vol. 8, no. 1.
  • Type: Journal Articles Status: Accepted Year Published: 2014 Citation: Hirsch, C.D., Evans, J., Buell, C. R., and Hirsch, C.N. 2014. Reduced representation approaches to interrogate genome diversity in large, repetitive plant genomes. Briefings in Functional Genomics 13:257-267, doi:10.1093/bfgp/elt051.
  • Type: Journal Articles Status: Accepted Year Published: 2014 Citation: Hirsch, C.D., Childs, K.L., Hamilton, J.P., Vaillancourt, B., Hirsch, C.N., Habermann, M., and Buell, C.R. 2014. The Solanaceae Genomics Resource: a comparative and integrated resource for deep data-mining of Solanaceae sequences. The Plant Genome 7 (1): -doi:10.3835/plantgenome2013.12.0042


Progress 09/01/11 to 08/31/12

Outputs
OUTPUTS: On August 1, 2012 a colloquium on Breeding in the Genomics Era: state of the art and new opportunities was organized by Dave Douches and Dave Francis and was held in Miami at the annual American Society of Horticulture Sciences meeting. The purpose of the colloquium was to help bridge the gap between progress with agronomic crops and vegetable/horticultural crops. In 2012 the last of four workshops was held at Denver, CO August 12. The workshop featured speakers from the community that presented SolCAP-generated SNP data. An online community called Plant Breeding and Genomics (PB&G) Community of Practice (CoP) was created to foster cross-disciplinary and cross commodity networking and collaboration and to amplify outreach efforts targeting an eXtension Community of Interest (CoI) of plant breeders, seed industry professionals, and practitioners. PBGworks.org is the collaborative workspace that is being used for the CoP. Content is authored and reviewed there and then transmitted to eXtension.org for publication. SolCAP collaborated with the Conifer Translational Genomics Network CAP to coordinate peer-review and publication of a multi-part series of learning modules that is focused on the fundamentals of quantitative genetics in the context of molecular tree improvement. These learning modules aim to provide a comprehensive introduction to the fundamental background science and technology required to understand and incorporate genetic markers in applied tree breeding and resource management. Field studies to collect standardized phenotypic data of tomato and potato lines from the germplasm panels were conducted in NC, NY, ID, MN, WA, WI, FL, OH and CA were completed. Genotypes for over 2500 potato and 480 tomato breeding lines with the Potato and Tomato Infinium platforms, respectively, have been assayed by SolCAP. In potato, over 5000 of the SNPs differentiate allele dosage in tetraploid potato. Germplasm panels for tomato and potato genotypes were assayed by SolCAP from the community mapping populations in 2011 and 2012. PARTICIPANTS: Numerous professionals and students have worked on this project besides the current co-PDs of Douches, Francis, Buell, Van Deynze, Mueller, De Jong and Stone. The following personnel have been trained on the project this past year: Alicia Massa, Ph.D. MSU Buell lab; Cory Hirsch, Ph.D. MSU Buell lab; Matt Zuelke, MSU undergraduate; Alison McKenna, technician, MSU potato breeding and genetics program; K. Haynes and L Wanner, USDA/ARS; Sarah Braun, Ph.D. candidate at University of Wisconsin, Madison. The following are working on the project: Kim Felcher, Ph.D. MSU Potato Breeding and Genetics Program, works on marker database, germplasm panel and SNP data analysis in Douches lab. Daniel Zarka, Post Doc MSU Potato Breeding and Genetics Program, works on SNP genotyping with the Infinium system. Kelly Zarka, technical staff at MSU Potato Breeding and Genetics Program, was trained in SNP genotyping and genotype by sequencing. Joe Coombs, technical staff at MSU Potato Breeding and Genetics Program, is participating in SNP data analysis. Candice Hirsch, Post Doc, MSU Plant Biology, worked on bioinformatics analysis of tomato and potato sequences. TARGET AUDIENCES: The potato and tomato breeding and genetics communities of the US and abroad. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
We have almost complete participation of the US public potato and tomato breeding communities for the germplasm panels. We expect the broader community of breeders to contribute valuable mapping populations for SNP genotyping. Through hands-on and face-to-face interactions we have helped breeding and genetics programs handle the SNP array data. The potato genome sequence generated by the Potato Genome Sequencing Consortium was shared with SolCAP. This access allowed us to align the transcriptome sequences developed by SolCAP so that SNPs could be more robustly identified. In a reciprocal exchange, we provided the Potato Genome Sequencing Consortium our potato transcriptome data to facilitate development of SNP markers for anchoring of whole genome shotgun sequencing scaffolds to the genetic map. We are also validating the concordance of the SNPs with the draft genome and corrected the alignment of a few scaffolds. We have used the tomato genome sequence made available through the Tomato Genome Initiative to facilitate SNP identification. We have made our Illumina EST sequences available to the Tomato Genome Initiative to facilitate gene annotation. We have collaborated with Martin Ganal, Trait Genetics, Gaterslesben, Germany and Mathilde Causse, INRA, Avignon, France to incorporate some of their SNPs based on complementary germplasm into the community Tomato Infinium chip. We will be co-publishing an integrated genetic and physical map of tomato based on the SolCAP Infinium chip. Tomato SNP arrays for over 4000 lines have been purchased. Strong interest from the international community to use the SolCAP potato SNP array: The International Potato Center, China, Canada, Scotland and Poland have included germplasm on the SNP potato genotyping panel. Researchers at The International Potato Center, Netherlands and Scotland have purchased the potato SNP array for population genotyping. The European community has been a strong adopter of the potato and tomato SNP arrays. The SNP arrays have become a common marker set for which to evaluate and compare germplasm. Use of the Infinium SNP genotyping system is allowing the calling of SNP allele dosage in tetraploid genotypes in over 5000 SNPs from the array. This has been difficult in previous DNA marker systems. Scoring for dosage has increased our power to genetically analyze populations of cultivated tetraploid potato. The SNP arrays for potato and tomato as well as the germplasm panel will be a valuable community resource for at least the next 10 years. Potato SNP arrays for over 10000 lines have been purchased. We have been interacting with Illumina to continue to the manufacture of the potato and tomato SNP arrays.

Publications

  • Robbins, M.D., Sim, S-C., Yang, W., Van Deynze, A., van der Knaap, E., Joobeur, T., and Francis, D.M. 2011. Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato. Journal of Experimental Botany 62(6):1831-1845 . [Epub ahead of print].
  • Rodriguez GR, Munoz, S. Anderson, C.,Sim, SC., Michel, A. Causse, M., McSpadden Gardener, B., Francis DM, van der Knaap E. 2011. Distribution of SUN, OVATE, LC and FAS in the Tomato Germplasm and the Relationship to Fruit Shape Diversity. Plant Physiology. 156: 275-285.
  • Felcher KJ, Coombs JJ, Massa AN, Hansey CN, Hamilton JP, et al. (2012) Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence. PLoS ONE 7(4): e36347. doi:10.1371/journal.pone.0036347.
  • Hamilton, J.P., Hansey, C.N., Whitty, B.R., Stoffel, K., Massa, A.N., Van Deynze, A. De Jong, W.S., Douches, D.S., and Buell, C. R. 2011. Single Nucleotide Polymorphism discovery in elite North American potato germplasm. BMC Genomics. 12:302.
  • Pei, C., Wang, H., Zhang, J., Francis, D. M., Yang, W. 2011. Fine mapping and analysis of a candidate gene in tomato accession PI128216 conferring hypersensitive resistance to bacterial spot race T3. Theor. Appl. Genet. [Epub ahead of print]
  • Wang, H., Hutton, S.F., Robbins, M.D. Sim, S. C., Scott, J. W., Yang, W., Jones, J. B., Francis., D. M. 2011. Molecular mapping of hypersensitive resistance from tomato Hawaii 7981 to Xanthomonas perforans race T3. Phytopathology. 101(10):1217-1223.
  • Baldo, A. M., Francis, D. M., Caramante, M., Robertson, L.D., Labate, J. A. 2011. AlleleCoder: a PERL script for coding co-dominant polymorphism data for PCA. Plant Genetic Resources pp 1-3. Published online. http://journals.cambridge.org/action/displayAbstractfromPage=online& aid=8333992.
  • Sim SC, Robbins MD, Van Deynze A, Michel AP, Francis DM. 2011. Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.). Heredity. 106: 927-935.


Progress 09/01/10 to 08/31/11

Outputs
OUTPUTS: Created an innovative education program to train graduate students in genome-based breeding. Surveys were designed and administered to the tomato and potato breeding communities to establish baseline levels of knowledge, attitude, skills, and level of use of genetic markers in breeding. Two 4-hour workshops were offered for the tomato and potato breeding communities to initiate training in translational genomics, including hands-on computer workshops Furthermore, both workshops were broadcast as webinars that were recorded and are accessible at http://solcap.msu.edu/meetingsworkshops.shtml. Powerpoints and supporting documents (scripts for statistical analysis) are available at this site and at http://pbgworks.org/tomato-workshop. An online community called Plant Breeding and Genomics (PB&G) Community of Practice (CoP) was created to foster cross-disciplinary and cross commodity networking and collaboration and to amplify outreach efforts targeting an eXtension Community of Interest (CoI) of plant breeders, seed industry professionals, and practitioners. PBGworks.org is the collaborative workspace that is being used for the CoP. Content is authored and reviewed there and then 'fed' to eXtension.org for publication. The PBG CoP publicly launched 124 pages of content in January 2011 (www.eXtension.org/plant_breeding_genomics). A project newsletter features timely updates and how to sections. Upon release of the draft potato and tomato genome sequencing we provided information to the community on how to retrieve and use the data. SolCAP co-PDs have made 33 presentations to audiences from the potato and tomato community at local, regional, national and international meetings in the US (Oregon, Michigan, Ohio, New York, Illinois, California), Netherlands, Spain, China, Scotland, Argentina, Peru and Chile to create awareness of the SolCAP project and its objectives while fostering research and education collaborations. Field studies to collect standardized phenotypic data of tomato and potato lines from the germplasm panels were conducted in NC, NY, ID, MN, WA, WI, FL, OH and CA. Extensive sequence data of expressed genes was generated from de novo Illumina sequencing of normalized cDNA libraries from 3 potato and 6 tomato lines representing elite US germplasm to develop the Illumina Infinium potato and tomato SNP arrays. Genotypes for 1152 potato and 484 tomato breeding lines with the Potato and Tomato Infinium platforms, respectively, have been assayed by SolCAP. In potato, some of the SNP assays differentiate allele dosage in tetraploid potato. Germplasm panels for tomato and potato genotypes were assayed by SolCAP from the community mapping populations in 2011. To address emerging needs within the Solanaceae community, a call for mapping populations to be SNP genotyped with the Infinium arrays was sent to the potato and tomato communities in September 2010 and March 2011, respectively. Proposals were submitted to the PD, and peer evaluated through the EC. The EC ranked the proposals. We established a project web site (www.solcap.msu) which is a centralized resource for SolCAP participants and the Solanaceae breeding community. PARTICIPANTS: Douches, D.; Francis, D.; De Jong, W.; Buell, C. R.; Van Deynze, A.; Stone, A.; Liedl, B.; Novy, R.; Yencho, C.; Thill, C.; Jansky, S. TARGET AUDIENCES: Potato and tomato breeding and genetics research communities. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Methods in bioinformatics for plant science was taught and student competence with the material increased 1.6 points on a 0-5 scale. Three plant breeding graduate students and seven postdocs/visiting scientists gained hands-on experience in basic bioinformatic scripting and statistical analyses in R, to help them prepare for manipulating and analyzing large-scale marker datasets. Results are being used to evaluate future changes in breeder knowledge, attitude, skills, and use of markers, and to inform development and refinement of the content for future stakeholder extension workshops and online educational courses. Over 120 breeders, staff and allied professionals from 8 countries and 4 continents received training at the workshops held at the Tomato Disease Workshop and Potato Association of America meetings. Both workshops were broadcast and recorded as webinars and recorded and are now available as educational resources on eXtension.org and Youtube. PB&GCoP was accepted by eXtension as a new Community of Practice. The CoP has a space on the People website of eXtension http://www.extension.org/people/communities/363. The PBGWorkspace currently has 209 people registered as members who represent 30 universities and federal agencies, 11 educational institutions outside of the USA, and 5 industry groups. All eXtension content is managed and available to all CoP members 24-7, regardless of their location. Newsletters are sent out to over 400 people via e-mail and are available on our website for others to download. Phenotype data were uploaded to SolCAP website for public access and is also incorporated into the SGN database and website. Phenotypic data will be maintained on the SolCAP and SGN databases for public access by the research community. Currently, ~8300 score-able markers are represented on the potato Infinium array. Potato data has been shared with international collaborators and the Potato Genome Sequencing Consortium to help anchor the potato genome sequence. Of the 8,784 SNPs designed, 7,627 SNPs are score-able on the tomato Infinium array. Tomato data has been shared with collaborators, 3,700 SNPs have been placed on the S. lycopersicum x S. pennellii reference map, and all markers have been placed on the physical map. Chromosome by chromosome patterns of linkage disequilibrium has been analyzed. Preliminary population structure in potato has been defined with 82 SNPs. A more extensive analysis with the 8303 potato SNPs are being worked on at this time. Over 4000 samples for each community have been committed and have/will be assayed using these common arrays. The two diploid mapping populations for potato are being used to map the SNPs to the pseudochromosomes. Between the two populations, approximately 45,000 SNPs from the potato array can be accessed for this analysis. The tetraploid mapping populations will be used to link SNPs with segregating trait data. The project website was established at MSU which is a central site for description, downloads, tools, newsletters and resources. A breeders toolbox for SGN is being modified to serve the tomato and potato breeding community.

Publications

  • Hamilton, J. P., Hansey, C. N., Whitty, B. R., Stoffel, K., Massa, A. N., Van Deynze, A., De Jong, W.S., Douches, D.S. Buell, C. R. (2011). Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genomics, 12, 302. doi: 10.1186/1471-2164-12-302


Progress 09/01/09 to 08/31/10

Outputs
OUTPUTS: To create an innovative education program to train graduate students in genome-based breeding. Surveys were designed and administered to the tomato and potato breeding communities to establish baseline levels of knowledge, attitude, skills, and level of use of genetic markers in breeding. Two workshops were offered for the tomato and potato breeding communities to initiate training in translational genomics. Although, not funded by SolCAP, a 3rd two day workshop was held at UC Davis with 10 Solanaceae participants out of 55 participants from the plant breeding community and the seed industry. SolCAP co-PDs have made over 35 presentations to audiences from the potato and tomato community to create awareness of the SolCAP project and its objectives. A web community called Plant Breeding and Genomics (PB&G) Community of Practice (CoP) was created to foster cross-disciplinary and cross commodity networking and collaboration to amplify outreach efforts targeting an eXtension Community of Interest (CoI) of plant breeders, seed industry professionals, and practitioners. PB&Gworks was initiated as the collaborative workspace that is being used for the CoP. Content development for PBG CoP has been initiated. Information on tomato or potato breeding was developed. We established a project web site (www.solcap.msu) which is a centralized resource for SolCAP participants and the Solanaceae breeding community. Project newsletter features timely updates and how to sections. Upon release of the draft potato and tomato genome sequencing we provided information to the community on how to retrieve and use the data. Existing databases (publically available Sanger-derived ESTs) were mined for both potato and tomato SNPs. Extensive sequence data of expressed genes was generated from de novo Illumina sequencing of normalized cDNA libraries from 3 potato and 6 tomato lines representing elite US germplasm. Standardized phenotypic data was collected across multiple environments for tomato and potato. To address emerging needs within the Solanaceae community a call for mapping populations was sent to the potato community. An integrated, breeder-focused resource for genotypic and phenotypic analysis was initiated by leveraging existing databases and resources at SGN and MSU. Field studies of tomato and potato lines from the germplasm panels were conducted in NC, NY, ID, FL, OH and CA. PARTICIPANTS: David Douches, David Francis, Robin Buell, Walter De Jong, Allen Van Deynze, Alex Stone, Lukas Mueller, Richard Novy, Craig Yencho, Barbara Liedl, Kathleen Haynes, Shelly Jansky, Christian Thill and John Scott received training at the workshops held at the 2009 Tomato Breeder's Roundtable and Potato Association of America meetings. SolCAP held a webinar and an eXtension.org workshop to bring other plant translational genomics Coordinated Agricultural Projects into the CoP. TARGET AUDIENCES: At the January 2009 Plant and Animal Genome (PAG) meeting, we held our first advisory committee meeting and received verbal feedback and a written report from the Solanaceae Coordinated Agricultural Project (SolCAP) advisory group that was used by the executive committee to further refine deliverables. External evaluation of extension and education activities by Dr. Michael Coe has proceeded according to plan. Institutional Review Board authorization for data collection from human subjects was obtained in early 2009. An extensive survey for Solanaceae breeders was developed and administered to a comprehensive list of potato and tomato breeders during Spring 2009. Data from this survey will provide a baseline against which to judge changes in breeder self-reported attitudes, knowledge, skills, and practices related to the use of genetic markers in their work. These data are also being used to aid in the design of education and extension materials and activities. Additional surveys were developed for use at the first two extension workshops, at the Potato Association of America annual meeting and the Tomato Breeders Round Table (TBRT). At each of these events, two evaluation instruments were used -- one asking direct questions about the quality, relevance, and utility of the workshop itself, and another (administered before and after the workshop) asking participants to self-assess particular knowledge and skills related to the application of genetic marker information in their work. Participants in these 4-hour workshops were generally very positive in their feedback about the workshops, and they provided helpful recommendations for additional extension sessions. Responses from 42 participants at TBRT and 28 participants at Potato Association of America annual meeting(PAA) indicated that the length and level of the workshops was appropriate; the presenters were well-informed, organized, and prepared; presenters were effective in style and delivery; participant self-confidence for applying markers in their work was significantly higher after the workshops; and participant self-confidence for communicating to others about the use of markers in plant breeding was significantly higher after the workshops. Findings from these questionnaires are being used in the design of future workshops, and in further development of instruments that will be used with education audiences. A detailed report on these evaluation methods and findings will be available by the end of 2010. Additional evaluation activities during the past year have included development of instruments for evaluating education activities; development and piloting of a usability testing protocol for the Breeder's Tool Box section of the SGN website; and planning for evaluation of online collaborative work involving various CAP plant breeding projects and eXtension.org. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
A graduate course in bioinformatics for plant breeding students was developed and delivered at Ohio State. A graduate course "breeding with molecular markers" was jointly delivered between Cornell and Ohio State University. Community surveys reached 163 tomato and potato breeders, their staff, and allied professionals. Over 120 breeders, staff and allied professionals received training at the workshops held at the 2009 Tomato Breeder's Roundtable and Potato Association of America meetings. SolCAP held a webinar and an eXtension.org workshop to bring other plant translational genomics Coordinated Agricultural Projects into the CoP. There are 5 CAP groups in the workspace, as well as a variety of lab groups and PBG eXtension content development and administrative groups. This plan of work was collaboratively authored in the workspace, and all SolCAP eXtension content is authored in the workspace. A YouTube video on crossing tomato for breeding purposes was created. A video on digital phenotyping has been published. Information on plant breeding, marker-assisted selection and related technologies is posted on PBGworks. The site includes project news and personnel, databases, tools, resources, project objectives and downloads. We have published five newsletters. All SNPs identified within and between Sanger-derived potato and tomato ESTs are available for download. A webpage for querying the Heniz1706 vs TA486/MicroTom SNPs has been constructed and is available at the SolCAP website. Preliminary validation of tomato eSNPs has been completed using the Illumina GoldenGate assay. We have identified high quality SNPs for development of the potato genotyping platform. We have completed the design for the potato platform and the tomato design is in progress. We have identified high quality SNPs for development of the potato genotyping platform. We have completed the design for the potato platform and the tomato design is in progress. A database of phenotypes for key traits across accessions of each commodity was initiated, accessible through SolCAP (http://solcap.msu.edu/) and Solanaceae Genome Network (SGN, http://solgenomics.net/). A cooperator's guide was developed for the collection of the phenotypic data. The research community is developing mapping populations for SNP genotyping to validate marker linkages to major loci influencing vitamin and sugar content and validate QTL. SolCAP has identified two mapping populations for SNP genotyping that met the criteria for analysis. The project website was established at MSU which is a central site for description, downloads, tools, newsletters and resources. A breeder's toolbox for SGN is being modified to serve the tomato and potato breeding community. The germplasm and intellectual property agreements for the crop panels were finalized, cooperator guides created and one field season of phenotypic evaluation completed. Flexible funds are being used to collect centralized sugar, chip color and vitamin C data (core traits for the project) in a 4x potato mapping population and also to increase the population size of the mapping population to approximately 200 progeny for 2010.

Publications

  • Rubio-Diaz, D.E., De Nardo, T., Santos, A., de Jesus, S., Francis, D., Rodriguez-Saonaa, L.E. 2010. Profiling of nutritionally important carotenoids from genetically-diverse tomatoes by infrared spectroscopy. Food Chemistry 120 (1), Pages 282-289.
  • Rodriguez GR, Moyseenko JB, Robbins MD, Huarachi Morejon N, Francis DM, van der Knaap E (2010). Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects. JoVE. 37. http://www.jove.com/index/details.stpid=1856, doi: 10.3791/1856.