Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development and characterization of EST-SSR markers for Begonia luzhaiensis (Begoniaceae).

ABSTRACT: PREMISE OF THE STUDY:Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure. METHODS AND RESULTS:Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.804 with averages of 0.370 and 0.404, respectively. Five loci could be successfully amplified in B. leprosa. CONCLUSIONS:The expressed sequence tag-simple sequence repeat markers are the first specifically developed for B. luzhaiensis and the first developed in Begonia sect. Coelocentrum. These markers will be useful for future studies of the genetic structure and phylogeography of B. luzhaiensis.

SUBMITTER: Tseng YH

PROVIDER: S-EPMC5435407 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Development and characterization of EST-SSR markers for <i>Begonia luzhaiensis</i> (Begoniaceae).

Tseng Yu-Hsin YH Huang Han-Yau HY Xu Wei-Bin WB Yang Hsun-An HA Liu Yan Y Peng Ching-I CI Chung Kuo-Fang KF

Applications in plant sciences 20170508 5

<h4>Premise of the study</h4>Microsatellite primers were developed for <i>Begonia luzhaiensis</i> (Begoniaceae) to assess genetic diversity and population genetic structure.<h4>Methods and results</h4>Based on the transcriptome data of <i>B. luzhaiensis</i>, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity r ...[more]

PMID: 28529834

Similar Datasets

Development and characterization of microsatellite markers for Central American Begonia sect. Gireoudia (Begoniaceae).

Project description:Transcriptome sequence data were used to design microsatellite primers for two widespread Central American Begonia species, B. heracleifolia and B. nelumbiifolia, to investigate population structure and hybridization. • The transcriptome from vegetative meristem tissue from the related B. plebeja was mined for microsatellite loci, and 31 primer pairs amplified in the target species. Fifteen primer pairs were combined in two multiplex PCR reactions, which amplified an average of four alleles per locus. • The markers developed will be a valuable genetic resource for medium-throughput genotyping of Central American species of Begonia sect. Gireoudia. A subset of these markers have perfect sequence matches to Asian B. venusta, and are promising for studies in other Begonia sections.

| S-EPMC4105041 | biostudies-literature

Development and characterization of EST-SSR markers in Ostryopsis (Betulaceae).

Project description:A set of expressed sequence tag (EST) microsatellite markers were developed and characterized using next-generation sequencing technology for the Chinese genus Ostryopsis (Betulaceae). • A total of 38 high-quality simple sequence repeat (SSR) primers were identified, of which 15 could be successfully amplified. Subsequently, we selected 80 individuals to represent the three species of the genus to evaluate the efficacy of these markers for examining genetic diversity of each species in the future. We found that the number of alleles per locus ranged from one to nine, with an average of 3.8. The expected heterozygosity and observed heterozygosity per locus varied from 0 to 0.829 and from 0 to 1, respectively, with their respective mean values as 0.483 and 0.416. • These EST-SSR markers will be useful for evaluating the range-wide genetic diversity of each species and examining genetic divergence and gene flow between the three species.

| S-EPMC4103604 | biostudies-literature

Development and characterization of EST-SSR markers in Bombax ceiba (Malvaceae).

Project description:PREMISE OF THE STUDY:Bombax ceiba (Malvaceae), commonly known as silk cotton tree, is a multipurpose tree species of tropical forests. Novel expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized for the species using transcriptome analysis. METHODS AND RESULTS:A total of 33 new EST-SSR markers were developed for B. ceiba, of which 13 showed polymorphisms across the 24 individuals from four distant populations tested in the study. The results showed that the number of alleles per polymorphic locus ranged from two to four, and the expected heterozygosity and observed heterozygosity per locus varied from 0.043 to 0.654 and from 0 to 0.609, respectively. CONCLUSIONS:These newly developed EST-SSR markers can be used in phylogeographic and population genetic studies to investigate the origin of B. ceiba populations. Furthermore, these EST-SSR markers could also greatly promote the development of molecular breeding studies pertaining to silk cotton tree.

| S-EPMC4406838 | biostudies-literature

Development and characterization of EST-SSR markers for Catalpa bungei (Bignoniaceae).

Project description:Premise of the studyCatalpa bungei (Bignoniaceae) is a deciduous tree native to China. We developed microsatellite markers for C. bungei to investigate its population genetics.Methods and resultsOne hundred seventy-seven expressed sequence tag (EST)-simple sequence repeat (SSR) primer pairs were isolated and characterized using next-generation sequencing. Thirty of these primer pairs were polymorphic loci in 52 individuals of C. bungei. The number of alleles ranged from two to 18 with observed and expected heterozygosity values of 0.05-1.00 and 0.18-0.95, respectively. The fixation index ranged from -1.00 to 1.00 with an average of 0.32. No linkage disequilibrium was detected in any pair of loci. All markers showed good amplification results in four species (C. bungei, C. fargesii, C. duclouxii, and C. ovata) except three loci.ConclusionsThese polymorphic markers are expected to be helpful in further studies on the systematics and phylogeography of C. bungei and related species.

| S-EPMC4850053 | biostudies-literature

Development and characterization of EST-SSR markers in Stipa breviflora (Poaceae).

Project description:Stipa breviflora (Poaceae) is one of the dominant species of the desert steppe in the eastern Eurasian grasslands. Simple sequence repeat (SSR) markers were developed for use in genetic diversity studies of this species. A total of 1954 potentially polymorphic loci were obtained by comparing transcriptome data of eight different S. breviflora individuals. We selected 81 loci to verify polymorphism and 63 loci amplified, of which 21 loci exhibited polymorphism. The number of alleles per locus varied from two to 24, the observed heterozygosity ranged from 0.083 to 0.958, and the expected heterozygosity ranged from 0.396 to 0.738. These newly identified SSR loci can be used for population genetic and landscape genetic studies of S. breviflora. In addition, 14 loci also amplified in six related Stipa species (S. grandis, S. krylovii, S. bungeana, S. aliena, S. gobica, and S. purpurea).

| S-EPMC5400433 | biostudies-literature

Development and characterization of EST-SSR markers for Artocarpus hypargyreus (Moraceae).

Project description:Polymorphic microsatellite markers were developed for Artocarpus hypargyreus (Moraceae), a threatened species endemic to China, to investigate the genetic diversity and structure of the species. Based on the transcriptome data of A. hypargyreus, 63 primer pairs were preliminarily designed and tested, of which 34 were successfully amplified and 10 displayed clear polymorphisms across the 67 individuals from four populations of A. hypargyreus. The results showed the number of alleles per locus ranged from three to 10, and the observed heterozygosity and expected heterozygosity per locus varied from 0.000 to 0.706 and from 0.328 to 0.807, respectively. These microsatellite markers will be useful in exploring genetic diversity and structure of A. hypargyreus. Furthermore, most loci were successfully cross-amplified in A. nitidus and A. heterophyllus, indicating that they will be of great value for genetic study across this genus.

| S-EPMC5238703 | biostudies-literature

Development and characterization of EST-SSR markers for <i>Camellia reticulata</i>.

Project description:PremiseCamellia reticulata, which is native to southwestern China, is an economically important plant belonging to the family Theaceae. We developed expressed sequence tag-simple sequence repeat (EST-SSR) markers for C. reticulata, which can be used to investigate its genetic diversity, population structure, and evolutionary history.Methods and resultsWe detected 4780 SSRs in C. reticulata from Camellia RNA-Seq data deposited in the National Center for Biotechnology Information's expressed sequence tags database (dbEST). Primer pairs for 70 SSR loci were designed and used for PCR amplification using 90 individuals from four populations of C. reticulata. Of these loci, 50 microsatellite markers were successfully identified, including 11 polymorphic markers. The allele number per locus ranged from two to seven (mean = 4.182), and the levels of observed and expected heterozygosity ranged from 0.044 to 0.567 and from 0.166 to 0.642, respectively. Eleven primer pairs amplified PCR products in three other species of Camellia (C. saluenensis, C. pitardii, and C. yunnanensis).ConclusionsThe set of microsatellite markers developed here can be used to study the genetic variation and population structure of C. reticulata and related species and thereby help to develop conservation strategies for this species.

| S-EPMC7249272 | biostudies-literature

Development and characterization of novel EST-SSR markers for Speranskia tuberculata (Euphorbiaceae).

Project description:The first set of expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized for Speranskia tuberculata (Euphorbiaceae), a traditional medicinal plant endemic to northern China, to explore the effects of recent habitat fragmentation on the genetic diversity and structure of this species. In this study, a total of 18 novel polymorphic microsatellite (EST-SSR) markers were developed for S. tuberculata using high-throughput transcriptome sequencing. Analysis of 24 individuals of S. tuberculata from four natural populations revealed their robust polymorphic reliability. The number of alleles per locus ranged from two to 11, while the expected and observed heterozygosity per marker varied from 0.187 to 0.827 and 0.042 to 0.917, respectively. Of these markers, 13 showed good amplification results in the closely related species S. cantonensis. These newly generated SSR markers are expected to provide novel tools for genetic studies of S. tuberculata, which will contribute to the conservation and sustainable use of the species' wild genetic resources.

| S-EPMC5077283 | biostudies-literature

Characterization and development of EST-derived SSR markers in Sinowilsonia henryi (Hamamelidaceae).

Project description:Polymorphic microsatellite markers were developed to reveal the genetic diversity of extant populations and the mating system of Sinowilsonia henryi (Hamamelidaceae). In this study, nuclear simple sequence repeat (SSR) markers were developed using the Illumina high-throughput sequencing technique (RNA-Seq). The de novo-assembled transcriptome generated a total of 64,694 unique sequences with an average length of 601 bp. A total of 2941 microsatellite loci were detected. Of the 121 tested loci, 13 loci were polymorphic and eight were monomorphic among 72 individuals representing three natural populations of the species. The number of alleles per locus ranged from one to four, and the observed and expected heterozygosity at population level were 0.00-1.00 and 0.10-0.66, respectively. The developed expressed sequence tag (EST)-SSRs will be useful for studying genetic diversity of S. henryi as well as assessing the mating system among Sinowilsonia species.

| S-EPMC5703181 | biostudies-literature

Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley.

Project description:Tibetan annual wild barley is rich in genetic variation. This study was aimed at the exploitation of new SSRs for the genetic diversity and phylogenetic analysis of wild barley by data mining. We developed 49 novel EST-SSRs and confirmed 20 genomic SSRs for 80 Tibetan annual wild barley and 16 cultivated barley accessions. A total of 213 alleles were generated from 69 loci with an average of 3.14 alleles per locus. The trimeric repeats were the most abundant motifs (40.82%) among the EST-SSRs, while the majority of the genomic SSRs were di-nuleotide repeats. The polymorphic information content (PIC) ranged from 0.08 to 0.75 with a mean of 0.46. Besides this, the expected heterozygosity (He) ranged from 0.0854 to 0.7842 with an average of 0.5279. Overall, the polymorphism of genomic SSRs was higher than that of EST-SSRs. Furthermore, the number of alleles and the PIC of wild barley were both higher than that of cultivated barley, being 3.12 vs 2.59 and 0.44 vs 0.37. Indicating more polymorphism existed in the Tibetan wild barley than in cultivated barley. The 96 accessions were divided into eight subpopulations based on 69 SSR markers, and the cultivated genotypes can be clearly separated from wild barleys. A total of 47 SSR-containing EST unigenes showed significant similarities to the known genes. These EST-SSR markers have potential for application in germplasm appraisal, genetic diversity and population structure analysis, facilitating marker-assisted breeding and crop improvement in barley.

| S-EPMC3988095 | 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