Development of Genic Simple Sequence Repeat Panels for Population Classification of Chinese Cymbidium Species

Abstract

Chinese cymbidiums (Cymbidium sp.) are important ornamental plants because of their foliage, flower shape, and fragrance. Well-known Chinese cymbidiums mainly include Cymbidium goeringii, Cymbidium faberi, Cymbidium ensifolium, Cymbidium kanran, and Cymbidium sinense. The population genetics of Chinese cymbidiums can be efficiently analyzed using small-scale marker panels with high discriminatory power. In this study, we tested several genic simple sequence repeats (SSRs) and built six genic SSR panels. The panels included several robust markers, which can rapidly assign Chinese cymbidium accessions to their source species. Fifty-three accessions of Chinese cymbidiums were analyzed using 25 markers, which exhibited polymorphism among five species. These markers were ranked according to their discriminatory scores (D scores). The program selected six markers to build an “overall” panel for all Cymbidium classifications and yielded 95.16% population assignment accuracy. Considering one species as the “critical” population and the four other species as one population, we built five genic SSR panels: C. ensifolium panel (four markers, 98.05% accuracy), C. faberi panel (six markers, 95.90% accuracy), C. goeringii panel (six markers, 95.15% accuracy), C. sinense panel (six markers, 96.35% accuracy), and C. kanran panel (five markers, 96.10% accuracy). Genetic distance matrices calculated using the “overall” panels and those derived with the 25 markers were compared. Results showed a high correlation (R = 0.807) with statistical significance (P = 0.042). Moreover, “all panels” revealed higher genetic variations among populations than “all markers.” Hence, the developed panels are suitable for efficient population classification of Chinese cymbidiums.