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ARS Home » Northeast Area » Geneva, New York » Plant Genetic Resources Unit (PGRU) » Research » Publications at this Location » Publication #380358

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

Location: Plant Genetic Resources Unit (PGRU)

Title: Genetic variation in a radish (Raphanus sativus L.) geodiversity collection

item ARRO, JIE - Orise Fellow
item Labate, Joanne

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/8/2021
Publication Date: 5/17/2021
Citation: Arro, J., Labate, J.A. 2021. Genetic variation in a radish (Raphanus sativus L.) geodiversity collection. Genetic Resources and Crop Evolution.

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. Radish is largely consumed raw as a condiment or salad ingredient in Europe and the USA, while it is a key ingredient in the cuisines of Japan, China, and Korea. This different emphasis in usage combined with environmental differences has produced genetically distinct types between the two regions. We performed partial genome sequencing on 152 radish stocks from around the world. The results of this study provided gene mapping tools and other genetic information that can be used to increase the efficiency of developing new, improved radish cultivars.

Technical Abstract: A radish panel of 152 accessions with diverse root shapes was assembled from the National Plant Germplasm System (NPGS) collection based on weighted geographical sampling. Accessions represented 35 countries and were categorized into eight geographical regions — North America, Europe, Africa, West Asia, Central Asia, South Asia, East Asia, and Southeast Asia. Multiple plants per accession were assayed using genotyping by sequencing (GBS), and 8,539 high-quality polymorphisms were discovered. Average observed heterozygosity (Ho) of the markers consistently ranged from 5% to 7% in all geographical regions. Central Asia was most diverse in terms of average expected heterozygosity (He = 0.107), while Southeast Asia was the least diverse (He = 0.050). Europe and East Asia were the most divergent from each other (pairwise FST = 0.155), while East Asia and South Asia were the least divergent (pairwise FST = 0.072). The clustering of genotypes based on principal components analysis (PCA) illustrated an east/west geographical pattern. Large numbers of private alleles and a substantial proportion (3%) of markers showing signals of selection based on allele frequency differences indicate that allelic variation is available for cultivar development. European and North American gene pools could be expanded by crossing with East Asian and Southeast Asian germplasm, and vice-versa. Both could potentially benefit from South Asian sources, while the addition of West Asian germplasm could increase East Asian and Southeast Asian diversity. This resource for molecular marker development combined with an understanding of global genetic relationships will inform the continued germplasm conservation and genetic improvement radish.