What is SolCAP?
SolCAP focuses on the two most important vegetable crops in the Solanaceae: potato and tomato. Our vision is to move translational genomics beyond commodity boundaries toward an emphasis on taxonomic groups and DNA sequence homology so that we can leverage knowledge and resources across species. Sequencing efforts in Solanaceae have lead to extensive expressed EST resources and genome sequence is emerging for both potato and tomato with preliminary assemblies of both of these genomes anticipated in the near future. Ultimately, 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 is to provide the infrastructure to link allelic variation in genes to valuable traits in cultivated germplasm of potato and tomato. Focusing on elite breeding material will increase the probability that these solanaceous crops will benefit from genotype-based selection. The extension and education components will integrate 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 to leverage Web 2.0 interactive functions, and we are developing content for publication to eXtension.org. Developing curriculum for new and practicing breeders will facilitate the use of genomic resources and databases to solve problems in the Solanaceae.
The SolCAP project proposal is available for download here.
SPECIFIC OBJECTIVES AND DELIVERABLES:
Obj. 1 Create an education program to train graduate students in genome-based breeding. 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.
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 creating a web community (PBGCoP) and is providing leadership to foster cross-disciplinary and cross–commodity networking and collaboration to generate outreach materials for publication on eXtension.org. Yearly workshops will also be 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.