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Research Project: Conservation and Utilization of Priority Vegetable Crop Genetic Resources and Associated Information

Location: Plant Genetic Resources Unit (PGRU)

Title: Genotyping by sequencing of tomato. BioProject Number PRJN705205, BioSamples SAMN18077515 - SAMN18077706, Data volume: 40 Gigabases.

Author
item Labate, Joanne

Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Other
Publication Acceptance Date: 3/2/2021
Publication Date: 3/5/2021
Citation: Labate, J.A. 2021. Genotyping by sequencing of tomato. BioProject Number PRJN705205, BioSamples SAMN18077515 - SAMN18077706, Data volume: 40 Gigabases.. National Center for Biotechnology Information (NCBI). https://www.ncbi.nlm.nih.gov/bioproject/?term=705205.

Interpretive Summary: Vegetable producers require an abundance of genetic diversity to remain competitive and meet increasing consumer demands for the beneficial vitamins, minerals, dietary fiber, and other nutrients provided by these crops. In order to describe genetic diversity patterns in tomato, a panel of 190 genetic stocks was assembled for partial genome sequencing. Types included categories such as home garden, fresh market, vintage, geodiversity, landraces from primary and secondary centers of diversity, fruit shape diversity, ornamental, processing, expired Plant Variety Protection (PVP) lines, lines from private companies and public breeding programs, lines bred for disease resistance, eight ‘San Marzano’ accessions (a widely popular commercial variety), and one wild tomato sample. Results showed that these broadly diverse tomato types were closely related to each other, in general. However, a subset of the panel showed evidence of carrying many wild tomato genes. These divergent samples are promising sources of novel genes for continued crop improvement.

Technical Abstract: This BioProject consists of 40 Gbases of raw genotyping-by-sequencing (GBS) data collected in 96-plex format on an Illumina HiSeq 2000 sequencing system. Single nucleotide polymorphisms (SNPs) in tomato were identified from single plants sampled from Solanum lycopersicum (n=189) or Solanum pimpinellifolium (n=1) accessions in the USDA National Plant Germplasm System (NPGS). A total of 3,713 high quality, mapped SNPs were identified. These markers are now available for other applications such as mapping morphological differences, marker assisted breeding, germplasm characterization, taxonomy, and DNA fingerprinting.