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ARS Home » Northeast Area » Geneva, New York » Plant Genetic Resources Unit (PGRU) » Research » Publications at this Location » Publication #336716

Research Project: Management of Genetic Resources and Associated Information for Selected Vegetable Crops

Location: Plant Genetic Resources Unit (PGRU)

Title: High-throughput genotyping of vegetable crops for germplasm conservation

item Labate, Joanne

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/21/2016
Publication Date: 1/3/2017
Citation: Labate, J.A. 2017. High-throughput genotyping of vegetable crops for germplasm conservation. Plant and Animal Genome Conference. 1.

Interpretive Summary:

Technical Abstract: Genotyping-by-sequencing (GBS) of reduced representation libraries (RRLs) can produce large amounts of single nucleotide polymorphism (SNP) data at relatively low cost per sample. Bioinformatics methods are available that do not require a reference genome sequence. National Plant Germplasm System (NPGS), Plant Genetic Resources Unit (PGRU) vegetable crop accessions that have been genotyped using GBS include tomato and wild tomato species, onion, Brassica rapa, winter squash, tomatillo and radish. As an example, results will be presented for a core set of 190 NPGS tomato accessions that were assayed by GBS. These originated from 31 countries and included six different versions of the economically valuable cultivar San Marzano, expired plant variety protection (PVP) varieties, fresh-market and processing types, landraces, home garden varieties and breeding lines. A total of 34,531 mapped, high quality SNPs were discovered in 190 DNA samples. The vast majority (30,818) of polymorphisms were rare, with the minor allele occurring less than three times in 190 samples. The 3,713 sites with at least three occurrences of the minor allele (3/380 = 0.01 minimum allele frequency) were used to estimate relationships among accessions. Extremely divergent genotypes were identified that included landraces from South America, Italy, Taiwan, and France. Some samples were found to harbor alleles that likely originated from wild tomato species through modern breeding for disease resistance. Several extremely divergent genotypes produce favorable fruit traits in a genetic background that contains many wild or primitive genes. These accessions are promising sources of novel genes for continued crop improvement.