Divergence and relationships of Cymbidium tortisepalum and its kindred germplasms by EST-SSR markers

ABSTRACT Molecular marker-based identification of Chinese orchids among species, genera, and hybrids before flowering has important breeding and genetic research value. In this study, the Cymbidium tortisepalum germplasm ‘Lianbansu’ was chosen for transcriptome sequencing, yielding 9,485 putative EST-SSRs discovered from 28,235 unigenes. Then, 192 primers were randomly selected from the designed primers, and 38 pairs of high-quality primers were screened out through experiments. These high-quality markers were used to examine the genetic diversity, population structure, and evolutionary history of 51 orchid germplasms. The number of alleles ranged from 3 to 12, with an average of 6. The observed and expected heterozygosity with an average of 0.4662 and 0.5973. The first two principal coordinates detected 39.66% of the total variation. It was found that the ΔK-value had one peak (When K = 2). Several germplasms of C. tortisepalum, Cymbidium sinense, Cymbidium hybridum, and some interspecific or intergeneric hybrids and unidentified germplasms could be effectively distinguished using these markers. In conclusion, a set of EST-SSR markers with outstanding transferability was created in this study that can be utilised for hybrid parent tracing and germplasm identification of orchids before flowering.