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

Abstract

AbstractA 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 8539 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 Southeast Asia were the most divergent from each other (pairwise FST = 0.199), while Europe and North America were the least divergent (pairwise FST = 0.022). 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 of radish.