Department of Plant, Soil and Microbial Sciences MSU Potato Breeding and Genetics Program

The Solanaceae Coordinated Agricultural Project (SolCAP)

The Solanaceae Coordinated Agricultural Project (SolCAP) was supported by the Agriculture and Food Research Initiative Applied Plant Genomics CAP Program of USDA's National Institute of Food and Agriculture. The project was awarded $5.4 million dollars between 10/1/2008 through 8/31/2012. MSU’s Dr. David Douches was the Principle Investigator and Kelly Zarka was the Project Assistant as well as Research Technician. The project succeeded in linking together people from public institutions, private institutions and industries dedicated to the improvement of the Solanaceae crops: potato and tomato. Through innovative research, education and training the SolCAP project focused on translating genomic advances to US tomato and potato breeding programs. The impact of this research continues to lead to significantly improved varieties that benefit the processors, the consumer and the environment.

The SolCAP project was a recipient of the 2011 U.S. Department of Agriculture (USDA) Secretary of Agriculture’s Honor Award. The Honor Awards are the most prestigious awards presented by the Secretary of Agriculture and recognize exceptional leadership, contributions, or public service.

SolCAP Team attending the 2009 Plant and Animal Genomics Conference in San Diego, CA.

SolCAP Summary and Objectives

SolCAP focused on the two most important vegetable crops in the Solanaceae: potato and tomato. Our vision moved translational genomics beyond commodity boundaries toward an emphasis on taxonomic groups and DNA sequence homology that leveraged knowledge and resources across species. Sequencing efforts in Solanaceae have lead to extensive expressed EST resources and genome sequence assemblies of both of these genomes. Understanding variation at the DNA sequence level is useful in crop improvement only to the extent that it helps us understand and/or predict phenotypic variation for agriculturally important traits. The primary research objective of this proposal provided the infrastructure to link allelic variation in genes to valuable traits in cultivated germplasm of potato and tomato. Focusing on elite breeding material increased the probability that these solanaceous crops will benefit from genotype-based selection. The extension and education components integrated training in genomics and plant breeding with curriculum aimed at students coming into the field and existing breeders seeking to make better use of sequence data in the context of crop improvement. To foster interaction across plant translational genomics CAPs we have invited other projects into our eXtension community of practice, created a Plant Breeding and Genomics workspace and developed content for publication to eXtension.org. Developing curriculum for new and practicing breeders facilitated the use of genomic resources and databases to solve problems in the Solanaceae.

SPECIFIC OBJECTIVES AND DELIVERABLES:

Obj. 1 Create an education program to train graduate students in genome-based breeding. This resulted in a standardized database of phenotypes for key traits across 480 accessions of each commodity, accessible through our website and Solanaceae Genome Network (SGN) website.

Obj. 2 Amplify outreach efforts by developing an eXtension Plant Breeding and Genomics Community of Practice (PBGCoP) to develop continuing education material aimed at practicing plant breeders, their staff, and seed industry professionals. SolCAP is created a web community (PBGCoP) and provided leadership to foster cross-disciplinary and cross–commodity networking and collaboration that generated outreach materials for publication on eXtension.org. Yearly workshops were conducted tailored to plant breeders and industry professionals in the theory and practice of translational genomics.

Obj. 3 Collect standardized phenotypic data across multiple environments for tomato and potato. A standardized database of phenotypes for key traits across core collections of each crop will be linked to the genotypic data, accessible through the Solanaceae Genome Network website (SGN; URL 7).

Obj. 4 Develop extensive sequence data of expressed genes, and identify Single Nucleotide Polymorphism (SNP) markers distributed across the genome and associated with specific candidate genes for sugar, carbohydrate, and vitamin biosynthetic pathways. Over 2 Gb of sequence is being generated from normalized cDNA libraries for each of three potato and six tomato genotypes for SNP discovery.

Obj. 5 Establish centralized facilities for genotyping a core set of SNP markers in standard germplasm panels in tomato and potato. We will develop a database of integrated and mapped markers and genotypes for at least 480 accessions for each crop. We anticipate >85% success for 7,600 potato SNPs and 1,536 tomato SNPs.

Obj. 6 Address regional, individual program and emerging needs within the Solanaceae community through a small grants program. To increase breeder engagement with genomics, we will provide opportunities to genotype up to 16 populations and validate marker linkages to major QTL.

Obj. 7 Create integrated, breeder-focused resources for genotypic and phenotypic analysis by leveraging existing databases and resources at SGN. We will create integrated genomic and phenotypic databases, the breeder’s toolbox, that serves the entire Solanaceae breeding and genetics community through SGN.

Our SolCAP team 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 were 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. There has been very strong interest from the international community to use the SolCAP potato and tomato SNP arrays. Thousands of the SolCAP developed potato/tomato arrays have been used and continue to be used. 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 are a valuable community resource. The impact of the arrays was emphasized at the International Solanaceae genomics meeting in Switzerland, August 28, 2012 with more than 12 talks highlighting use of the arrays.

SolCAP Participants

Executive Committee:

SolCAP Project MSU:

Extension/Education Board:

Stakeholder Advisory Board:

Scientific Advisory Board:

Extension/Education Evaluation:

Collaborators:

Solanaceae Coordinated Agricultural Project
Project Headquarters
Michigan State University
2100 Molecular Plant Science Building
East Lansing, Michigan 48824

SolCAP Workshops and Webinars

2012 SolCAP workshop at the Potato Association of America Meeting: SolCAP Potato Genomics Workshop

This workshop was held in conjunction with the 96th Annual Meeting of the Potato Association of America. The workshop took place in Denver, CO August 12, 2012.

2011 SolCAP workshop at the Potato Association of America Meeting: Using SolCAP phenotype and Infinium SNP data in Potato Breeding

This workshop was held in conjunction with the 95th Annual Meeting of the Potato Association of America. The workshop took place at the Hilton Wilmington Riverside, 301 North Water Street, Wilmington, North Carolina on Sunday, August 14, 2011

2011 SolCAP workshop at the Tomato Disease Workshop

This workshop was be held in conjunction with the Tomato Disease Workshop. The workshop took place at Cornell University, Ithaca, New York on Tuesday, October 11, 2011 from 1:00pm to 5:00pm.

2010 SolCAP workshop and webinar at the Tomato Disease Workshop

This workshop was held on November 16, 2010 at the University of Florida, Wimauma, Florida, designed specifically for breeders in conjunction with the Tomato Disease Workshop.

2010 SolCAP workshop and webinar at the Potato Association of America Meeting

This workshop was held on August 15, 2010 at Oregon State University, Corvallis, Oregon, designed specifically for breeders in conjunction with the Potato Association of America 94th Annual Meeting

2009 Potato Association of America SolCAP Workshop

This workshop was held on August 9, 2009 in Fredericton, New Brunswick, Canada, designed specifically for breeders in conjunction with the Potato Association of America 93rd Annual Meeting.

2009 Tomato Breeders Roundtable SolCAP Workshop

This workshop was held on June 28, 2009 in Sacramento, CA, designed specifically for breeders in conjunction with the 43rd Tomato Breeders Round Table.