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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: Population structure and diversity estimates in a geographical core set of radish (Raphanus sativus)

Author
item ARRO, JIE - Orise Fellow
item Labate, Joanne

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/15/2019
Publication Date: 7/21/2019
Citation: Arro, J., Labate, J.A. 2019. Population structure and diversity estimates in a geographical core set of radish (Raphanus sativus). Meeting Abstract. 1.

Interpretive Summary:

Technical Abstract: Radish (Raphanus sativus) is an ancient crop native to the Eastern Mediterranean and Eastern Asia. Radish is consumed as a root vegetable (hypocotyl plus true root), a leafy vegetable, sprouts, seeds or as seed pods and is also used as cover crop or forage crop. Cultivated radish may have experienced multiple domestication events. Consumer preferences are regionally based, resulting in morphological diversity combined with adaptation to local conditions. Economically, the crop is highly valuable and represents 2% of total vegetable production (7 million tons/year) in the world. In human diets, radish provides a rich source of vitamin A, vitamin C, minerals and carbohydrates. Breeding improvement has focused on size and shape. A Plant Genetic Resources Unit (PGRU) radish core set was assembled based on weighted geographical sampling from the germplasm collection. This resulted in 152 accessions representing 35 countries. From this core set, DNA from each of five plants per accession was isolated and genotyped using genotyping by sequencing (GBS). GBS libraries were constructed using the restriction enzyme PstI with standard barcode and common adapter sets, and assayed on a Genome Analyzer II. Output files were analyzed using the TASSEL5 pipeline and GenBank assembly accession GCA_002197605.1, Raphanus sativus cultivar XYB36-2 as a reference genome. After quality filtering, 52,643 SNPs were retained for downstream analysis of genetic diversity and population structure. These results have provided improved resolution of genetic relationships within and among accessions and geographical regions. Understanding such relationships will inform the continued germplasm conservation and genetic improvement of this important crop.