DNA variation in a diversity panel of tomato genetic resources

Authors: Labate, Joanne

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/6/2021
Publication Date: 6/18/2021
Citation: Labate, J.A. 2021. DNA variation in a diversity panel of tomato genetic resources. Journal of the American Society for Horticultural Science. https://doi.org/10.21273/JASHS05066-21.
DOI: https://doi.org/10.21273/JASHS05066-21

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. Tomato is highly economically valuable, and constituted a $1.6 billion industry in 2019 in the USA and a $48 billion industry in 2018 worldwide. The US Department of Agriculture (USDA), Agricultural Research Service (ARS) Plant Genetic Resources Unit (PGRU) conserves 6,610 tomato accessions in the form of publicly available seed stocks. These are distributed throughout the world to requesters for purposes of breeding, research, and higher education. This is the second largest tomato collection in the world, after the The World Vegetable Center in Taiwan. We performed partial genome sequencing on 190 tomato stocks from PGRU's collection. These originated from 31 countries and included various usage types such as fresh market, ornamental, processing, breeders’ lines, landraces, and home gardening types. The results of this study provided gene discovery tools and other genetic information that can be used to increase the efficiency of choosing genetic stocks for tomato research and breeding.

Technical Abstract: A diversity panel of 190 National Plant Germplasm System (NPGS) tomato (Solanum lycopersicum L.) accessions was genotyped using genotyping by sequencing (GBS). These originated from 31 countries and included fresh market, ornamental, processing, breeders’ lines, landraces, and home gardening types, as well as six different accessions of the economically valuable variety ‘San Marzano’. The majority of discovered single nucleotide polymorphisms (SNPs) were rare and therefore excluded from downstream analyses. A total of 3,713 high quality, mapped SNPs that were present in at least two accessions were used to estimate genetic distances and population structure. Results showed that these broadly diverse NPGS tomato accessions were closely related to each other. However, a subset of divergent genotypes was identified that included landraces from primary centers of diversity (South America), secondary centers of diversity (Italy, Taiwan, and France), and genotypes that originated from wild species through 20th century breeding for disease resistance (e.g., ‘VFNT Cherry’). Extreme variant accessions produce cultivated fruit traits in a background that contains many wild or primitive genes. These accessions are promising sources of novel genes for continued crop improvement.