Analysis of microsatellites in the vulnerable orchid Gastrodia flavilabella: the development of microsatellite markers, and cross-species amplification in Gastrodia

Abstract

BackgroundGastrodia flabilabella is a mycoheterotrophic orchid that obtains carbohydrates and nutrients from its symbiotic mycorrhizal fungi. The species is an endemic and vulnerable species enlisted in the “A Preliminary Red List of Taiwanese Vascular Plants” according to the IUCN Red List Categories and Criteria Version 3.1. G. flabilabella dwells the underground of broadleaf and coniferous forest with richness litter. Based on herbarium records, this species is distributed in central Taiwan. Twenty eight microsatellite loci were developed in G. flabilabella and were tested for cross-species amplification in additional taxa of G. confusoides, G. elata, and G. javanica. We estimated the genetic variation that is valuable for conservation management and the development of the molecular identification system for G. elata, a traditional Chinese medicine herb.ResultsMicrosatellite primer sets were developed from G. flabilabella using the modified AFLP and magnetic bead enrichment method. In total, 257 microsatellite loci were obtained from a magnetic bead enrichment SSR library. Of the 28 microsatellite loci, 16 were polymorphic, in which the number of alleles ranged from 2 to 15, with the observed heterozygosity ranging from 0.02 to 1.00. In total, 15, 13, and 7 of the loci were found to be interspecifically amplifiable to G. confusoides, G. elata, and G. javanica, respectively.ConclusionsAmplifiable and transferable microsatellite loci are potentially useful for future studies in investigating intraspecific genetic variation, reconstructing phylogeographic patterns among closely related species, and establishing the standard operating system of molecular identification in Gastrodia.

Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

“…SSRs were used as DNA barcodes to clear identify 5 genotypes of Solanum melongena L. by Chinnappareddy et al [45]. In Orchidaceae, SSR markers were developed and utilized as identification tools in various studies [18,[46][47][48] due to their high reproducibility and variability [45,49,50]. In particular, SSRs in the chloroplast genome were reported to have a high level of polymorphism among species and loci [51].…”

New microsatellite markers recognize differences in tandem repeats among four related <i>Gastrodia</i> species (Orchidaceae)

“…However, high transferability of microsatellite markers and allele difference are not always compatible. It is common for amplification to fail in several loci in cross-amplification tests (e.g., G. flavilabella and its related species, Tsai et al, 2014), and even if amplified well, similar-sized alleles are observed among taxa (e.g., Livistona rigida and its related species, Kaneko et al, 2011;Stachyurus macrocarpus var. macrocarpus and var.…”

Molecular characterization of twenty polymorphic microsatellite markers in the polyploid fruit tree species Syzygium samarangense (Myrtaceae)

“…Microsatellite loci were isolated using the modified AFLP and magnetic bead enrichment method (Ho et al, 2014;Tsai et al, 2014). Genomic DNA from S. samarangense 'Pink' was digested using MseI (Promega, Madison, Wisconsin, USA) and separated by 1.2% agarose gel electrophoresis using a Tris-boric acid-EDTA buffer system.…”