Browse
Submit Data
Databases
API
Help

Dataset Information

38 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development and characterisation of nine polymorphic microsatellite markers for Tephrosia calophylla Bedd. (Fabaceae).

ABSTRACT: Tephrosia calophylla Bedd. (Fabaceae) is an endangered tropical plant endemic to southwestern Ghats, India. The objective of this study was to contribute to the characterisation of the diversity of this rare species, which is necessary for its future conservation. Accordingly, microsatellite markers were designed, and their ability to detect polymorphisms was determined. Nine microsatellite markers were developed using genomic libraries, and all of the markers were successfully amplified in 42 individuals. Three to nine alleles per locus were observed, and the heterozygosity of the loci ranged from 0.381 to 0.905. The nine newly developed polymorphic markers recognise a sufficient number of varying loci to perform further studies on the conservation and breeding of this medicinal cultivar.

SUBMITTER: Parine NR

PROVIDER: S-EPMC4336440 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Development and characterisation of nine polymorphic microsatellite markers for Tephrosia calophylla Bedd. (Fabaceae).

Parine Narasimha Reddy NR Lakshmi P P Kumar Devinder D Shaik Jilani P JP Alanazi Mohammed M Pathan Akbar Ali Khan AA

Saudi journal of biological sciences 20141222 2

Tephrosia calophylla Bedd. (Fabaceae) is an endangered tropical plant endemic to southwestern Ghats, India. The objective of this study was to contribute to the characterisation of the diversity of this rare species, which is necessary for its future conservation. Accordingly, microsatellite markers were designed, and their ability to detect polymorphisms was determined. Nine microsatellite markers were developed using genomic libraries, and all of the markers were successfully amplified in 42 i ...[more]

PMID: 25737647

Similar Datasets

Characterisation of nine new polymorphic microsatellite loci in the reticulated glass frog Hyalinobatrachium valerioi (Centrolenidae).

Project description:Here we document the development of thirteen novel microsatellite markers for the reticulated glass frog Hyalinobatrachium valerioi (Centrolenidae). Nine of those markers were polymorphic and contained between 4 and 34 alleles per locus (mean = 20.3) in 138 individuals (91 males, 47 females) from the field site 'La Gamba', Costa Rica. Average observed heterozygosity was 0.76. Two loci (Hyval19 and Hyval21) significantly deviated from Hardy-Weinberg equilibrium. We did not find evidence for linkage disequilibrium among any of the loci. These markers will serve to identify the genetic mating system in H. valerioi, investigate gene flow between local populations, and reconstruct parent-offspring relationships for studies on individual mating and reproductive success. Therefore, these markers will serve to answer a wide range of scientific questions in conservation, behavioural ecology, and also evolutionary biology.

| S-EPMC4122515 | biostudies-literature

Development and characterization of microsatellite markers for Piptadenia gonoacantha (Fabaceae).

Project description:• Microsatellite primers were designed for Piptadenia gonoacantha (Fabaceae) and characterized to estimate genetic diversity parameters. The species is a native tree from the Atlantic Forest biome commonly used in forest restoration; it has medicinal potential and the wood is economically useful. • Twenty-eight microsatellite loci were identified from an enriched genomic library. Fifteen loci resulted in successful amplifications and were characterized in a natural population of 94 individuals. Twelve loci were polymorphic, with allele numbers ranging from three to 15 per locus, and expected and observed heterozygosities ranging from 0.2142 to 0.8325 and 0.190 to 0.769, respectively. • The developed markers will be used in further studies of population genetics of P. gonoacantha, aimed at conservation and management of the species in natural populations and in forest restoration projects.

| S-EPMC4332145 | biostudies-literature

Development of 23 polymorphic microsatellite loci in invasive silver wattle, Acacia dealbata (Fabaceae).

Project description:Microsatellite markers were developed for silver wattle, Acacia dealbata (Fabaceae), which is both an ornamental and an invasive weed species. It is native to southeastern Australia and invasive in Europe, Africa, Asia, and the Americas. The pyrosequencing of a microsatellite-enriched genomic DNA library of A. dealbata produced 33,290 sequences and allowed the isolation of 201 loci with a minimum of seven repeats of microsatellite motifs. Amplification tests led to the setup of two multiplex PCR mixes allowing the amplification of 21 loci. The polymorphism of these markers was evaluated on a sample of 32 individuals collected in southeastern Australia. The number of alleles and the expected heterozygosity varied between two and 11, and between 0.11 and 0.88, respectively. The level of polymorphism of this set of 23 microsatellites is large enough to provide valuable information on the genetic structure and the invasion history of A. dealbata.

| S-EPMC4435469 | biostudies-literature

Development and characterization of 14 microsatellite markers for Indigofera pseudotinctoria (Fabaceae).

Project description:PREMISE OF THE STUDY:Microsatellite markers can be used to evaluate population structure and genetic diversity in native populations of Indigofera pseudotinctoria (Fabaceae) and assess genetic disturbance caused by nonnative plants of the same species. METHODS AND RESULTS:We developed 14 markers for I. pseudotinctoria using next-generation sequencing and applied them to test two native populations, totaling 77 individuals, and a transplanted population, imported from a foreign country, of 17 individuals. The mean number of alleles was 3.310, observed heterozygosity was 0.242, and expected heterozygosity was 0.346. The fixation index in the transplanted population was 0.469, which was higher than in the native populations (0.154 and 0.158). In addition, the transplanted population contains one allele that is not shared by the native population. CONCLUSIONS:Microsatellite markers can be useful for evaluating genetic diversity within and between populations and for studying population genetics in I. pseudotinctoria and related species.

| S-EPMC4850052 | biostudies-literature

Development of 16 microsatellite markers for the Korean endemic Vicia hirticalycina (Fabaceae).

Project description:Premise of the Study:Vicia hirticalycina (Fabaceae) is a narrowly endemic species restricted to mountain valleys of southern Korea. To investigate its fine-scale genetic diversity and differentiation in Korea, we developed polymorphic microsatellite markers. Methods and Results:Sixteen polymorphic microsatellite markers were developed from Illumina MiSeq data. In 74 individual plants from four populations, one to seven alleles were expressed for each locus. The levels of observed and expected heterozygosity ranged from 0.000 to 0.778 and from 0.000 to 0.738, respectively. Cross-amplification was conducted with three related species and seven to 11 markers were successfully amplified. Conclusions:These new microsatellite markers will be useful in future studies on the population genetics of V. hirticalycina.

| S-EPMC6055556 | biostudies-literature

Development of 15 polymorphic microsatellite markers for Ficus virens (Moraceae).

Project description:PREMISE OF THE STUDY:Ficus virens (Moraceae) is distributed widely in South and Southeast Asia, Melanesia, and northern Australia, and it is also cultivated outside its original northern range limit in southwestern China. Therefore, the species is well suited to explore the mechanism of range limits of Ficus species. However, little is known about its genetic background. METHODS AND RESULTS:Fifteen polymorphic microsatellite markers were developed using the biotin-streptavidin capture method. Polymorphism was tested in 85 F. virens individuals sampled from three populations. The number of alleles ranged from three to 17. The observed and expected heterozygosity of each population varied from 0.0667 to 0.9286 and 0.0650 to 0.8890, respectively. Cross-species amplification was also carried out in eight other Ficus species. CONCLUSIONS:These 15 markers will be valuable for studying the genetic variation and population structure of F. virens and related Ficus species.

| S-EPMC5231912 | biostudies-literature

Polymorphic microsatellite markers for Microbotryum saponariae

Project description:Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing.

| PRJEB11435 | ENA

Microsatellite markers for the yam bean Pachyrhizus (Fabaceae).

Project description:UNLABELLED: PREMISE OF THE STUDY:Microsatellite loci were developed for the understudied root crop yam bean (Pachyrhizus spp.) to investigate intraspecific diversity and interspecific relationships within the genus Pachyrhizus. • METHODS AND RESULTS:Seventeen nuclear simple sequence repeat (SSR) markers with perfect di- and trinucleotide repeats were developed from 454 pyrosequencing of SSR-enriched genomic libraries. Loci were characterized in P. ahipa and wild and cultivated populations of four closely related species. All loci successfully cross-amplified and showed high levels of polymorphism, with number of alleles ranging from three to 12 and expected heterozygosity ranging from 0.095 to 0.831 across the genus. • CONCLUSIONS:By enabling rapid assessment of genetic diversity in three native neotropical crops, P. ahipa, P. erosus, and P. tuberosus, and two wild relatives, P. ferrugineus and P. panamensis, these markers will allow exploration of the genetic diversity and evolutionary history of the genus Pachyrhizus.

| S-EPMC4103131 | biostudies-literature

Development of microsatellite markers in Cratylia mollis and their transferability to C. argentea (Fabaceae).

Project description:This work aimed to develop microsatellite markers for Cratylia mollis as tools to assess its genetic diversity and structure and to evaluate their potential cross-amplification in related species. • Microsatellite markers were developed using a microsatellite-enriched library and an intersimple sequence repeat library. From a set of 19 markers, 12 microsatellite loci were polymorphic and presented considerable variation in allele number (2-11), expected heterozygosity (0.226-0.883), and polymorphism information content per locus (0.212-0.870). Cross-amplification in C. argentea was successful in 16 loci, 12 of which were polymorphic (2-10 alleles). • The polymorphism of this set of microsatellite markers for C. mollis, as well as their successful cross-amplification in C. intermedia and C. bahiensis and their transferability to C. argentea, supports their use in future comparative studies to understand the mechanism involved in population divergence and speciation in the genus.

| S-EPMC4103464 | biostudies-literature

Development of polymorphic microsatellite markers for the Killarney Fern (Vandenboschia speciosa, Hymenophyllaceae).

Project description:We characterize 10 microsatellite loci in the endangered fern Vandenboschia speciosa (Hymenophyllaceae), enabling studies on the genetic population structure of this Macaronesian-European species using DNA hypervariable markers. Ten primer sets were developed and tested on 47 individuals in a total of two Iberian populations of V. speciosa. The primers amplified di- and hexanucelotide repeats. The number of alleles ranged from two to eight, and the expected heterozygosity ranged from 0.107 to 0.807 among the populations analyzed. The 10 microsatellite markers developed will be useful in characterizing the genetic diversity of V. speciosa and understanding its population structure (including the possible structure between sporophyte and gametophyte phases) and biogeographic history, and will provide important genetic data for the conservation of this species.

| S-EPMC4651631 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data