Dataset Information

Development of microsatellite markers for Cypripedium tibeticum (Orchidaceae) and their applicability to two related species.

ABSTRACT: Premise of the study:To investigate genetic diversity and structure, microsatellite markers were developed and characterized for Cypripedium tibeticum, an endangered orchid species, and their utility tested in two relatives: C. flavum and C. bardolphianum. Methods and Results:Candidate microsatellite loci were isolated based on next-generation sequencing. We identified 20 polymorphic loci with di- or trinucleotide repeats in three populations of C. tibeticum. Genotyping results showed the total number of alleles per locus varied from two to 21, and the observed and expected heterozygosity ranged from 0.261 to 0.967 and 0.441 to 0.960, respectively. Cross-species amplification showed most of the markers were applicable to C. flavum and C. bardolphianum. Conclusions:The 20 polymorphic microsatellite markers developed in this study are useful tools for studying the conservation genetics and phylogeography of C. tibeticum and its related species.

SUBMITTER: Li J

PROVIDER: S-EPMC5749819 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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Development of microsatellite markers for <i>Cypripedium tibeticum</i> (Orchidaceae) and their applicability to two related species.

Li Jing J Luo Yibo Y Xu Lingling L

Applications in plant sciences 20171221 12

<h4>Premise of the study</h4>To investigate genetic diversity and structure, microsatellite markers were developed and characterized for <i>Cypripedium tibeticum</i>, an endangered orchid species, and their utility tested in two relatives: <i>C. flavum</i> and <i>C. bardolphianum</i>.<h4>Methods and results</h4>Candidate microsatellite loci were isolated based on next-generation sequencing. We identified 20 polymorphic loci with di- or trinucleotide repeats in three populations of <i>C. tibeticu ...[more]

PMID: 29299395

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Project description:BACKGROUND: Amorphophallus is a genus of perennial plants widely distributed in the tropics or subtropics of West Africa and South Asia. Its corms contain a high level of water-soluble glucomannan; therefore, it has long been used as a medicinal herb and food source. Genetic studies of Amorphophallus have been hindered by a lack of genetic markers. A large number of molecular markers are required for genetic diversity study and improving disease resistance in Amorphophallus. Here, we report large scale of transcriptome sequencing of two species: Amorphophallus konjac and Amorphophallus bulbifer using deep sequencing technology, and microsatellite (SSR) markers were identified based on these transcriptome sequences. RESULTS: cDNAs of A. konjac and A. bulbifer were sequenced using Illumina HiSeq™ 2000 sequencing technology. A total of 135,822 non-redundant unigenes were assembled from about 9.66 gigabases, and 19,596 SSRs were identified in 16,027 non-redundant unigenes. Di-nucleotide SSRs were the most abundant motif (61.6%), followed by tri- (30.3%), tetra- (5.6%), penta- (1.5%), and hexa-nucleotides (1%) repeats. The top di- and tri-nucleotide repeat motifs included AG/CT (45.2%) and AGG/CCT (7.1%), respectively. A total of 10,754 primer pairs were designed for marker development. Of these, 320 primers were synthesized and used for validation of amplification and assessment of polymorphisms in 25 individual plants. The total of 275 primer pairs yielded PCR amplification products, of which 205 were polymorphic. The number of alleles ranged from 2 to 14 and the polymorphism information content valued ranged from 0.10 to 0.90. Genetic diversity analysis was done using 177 highly polymorphic SSR markers. A phenogram based on Jaccard's similarity coefficients was constructed, which showed a distinct cluster of 25 Amorphophallus individuals. CONCLUSION: A total of 10,754 SSR markers have been identified in Amorphophallus using transcriptome sequencing. One hundred and seventy-seven polymorphic markers were successfully validated in 25 individuals. The large number of genetic markers developed in the present study should contribute greatly to research into genetic diversity and germplasm characterization in Amorphophallus.

Dataset Information

Development of microsatellite markers for Cypripedium tibeticum (Orchidaceae) and their applicability to two related species.

Publications

Development of microsatellite markers for <i>Cypripedium tibeticum</i> (Orchidaceae) and their applicability to two related species.

Similar Datasets

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