Development of microsatellite markers based on expressed sequence tags in Asparagus cochinchinensis (Asparagaceae)

Abstract

Premise of the study:Transcriptome-derived simple sequence repeat (SSR) markers were developed in Asparagus cochinchinensis (Asparagaceae). Due to its application in traditional medicine, its wild populations are threatened by over-collection even in protected areas, requiring immediate conservation efforts.Methods and Results:Based on transcriptome data of A. cochinchinensis, 96 primer pairs with two to seven alleles per locus were selected for initial validation; of those, 27 primer pairs amplified across all samples, resulting in 15 polymorphic and 12 monomorphic microsatellite markers. The usefulness of these markers was assessed in 60 individuals representing three populations of A. cochinchinensis. Observed and expected heterozygosity values ranged from 0.050 to 0.950 and 0.049 to 0.626, respectively. Cross-species amplification of the 27 markers was tested in the related species A. rigidulus and A. schoberioides.Conclusions:These polymorphic, transcriptome-derived SSR markers can be used as molecular markers to study population genetics and ecological conservation in A. cochinchinensis and related taxa.

An unexpected genetic diversity pattern and a complex demographic history of a rare medicinal herb, Chinese asparagus (Asparagus cochinchinensis) in Korea

“…One of the two loci (AC069; see Kim et al . 2017 for detailed information about the marker loci) 21 appeared to have null alleles present in all eight populations while null alleles were present in only two populations for the other locus (AC079). A significant departure from Hardy-Weinberg Equilibrium (HWE) was shown in locus 3 (AC014, high heterozygosity) and locus 8 (AC069; an excess of homozygotes with null allele present).…”

“…PCR amplification for 13 microsatellite markers (nrSSR) was conducted to genotype all 158 individuals using primer sets developed by Kim et al . 21 . PCR reactions were performed in a 25 μl volume containing 2.5 μL of 10× Ex Taq buffer (TaKaRa Bio, Otsu, Japan), 2 μL of 2.5 mM dNTPs, 0.01 μM of each of the forward and reverse primers, 0.1 μL of Ex Taq DNA polymerase (5 units/μL) (TaKaRa Bio), 5–10 ng of template DNA, and distilled water (Sigma-Aldrich Co., St. Louis, Missouri, USA).…”