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ARS Home » Northeast Area » Geneva, New York » Plant Genetic Resources Unit (PGRU) » Research » Publications at this Location » Publication #381308
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 Raphanus sativus. BioProject Number PRJNA691871, BioSamples SAMN17305744 - SAMN17306511, Data volume: 196 Gigabases

Author
item Labate, Joanne

Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Other
Publication Acceptance Date: 1/13/2021
Publication Date: 1/14/2021
Citation: Labate, J.A. 2021. Genotyping by sequencing of Raphanus sativus. BioProject Number PRJNA691871, BioSamples SAMN17305744 - SAMN17306511, Data volume: 196 Gigabases. National Center for Biotechnology Information (NCBI). Available: https://www.ncbi.nlm.nih.gov/biosample/17305968.

Interpretive Summary: Radish is an ancient crop that is economically valuable throughout the world. Root shape, color, market class and growing season are defining features of radish types. DNA markers are valuable for understanding the relationships among the various types, and how they can be further improved. The results of this study provided DNA markers and other genetic information that can be used to increase the efficiency of developing new, improved radish cultivars.

Technical Abstract: This BioProject consists of 196 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 radish were identified using 760 plants sampled from 152 Raphanus sativus accessions in the USDA National Plant Germplasm System (NPGS). A total of 8,539 high quality SNPs were identified and mapped using the Raphanus sativus L. cultivar 109 XYB36-2, GenBank assembly accession GCA_002197605.1, reference genome. These markers are now available for other applications such as mapping morphological differences, marker assisted breeding, germplasm characterization, taxonomy, and DNA fingerprinting.