scholarly journals Development and characterization of polymorphic microsatellite markers in taro (Colocasia esculenta)

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 823-832 ◽  
Author(s):  
Emma S Mace ◽  
Ian D Godwin
Keyword(s):  
Genomic Library ◽  
Genome Mapping ◽  
Colocasia Esculenta ◽  
Germplasm Management ◽  
Ca Repeat ◽  
Genomic Libraries ◽  
Expected Size Range ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Microsatellite-containing sequences were isolated from enriched genomic libraries of taro (Colocasia esculenta (L.) Schott). The sequencing of 269 clones yielded 77 inserts containing repeat motifs. The majority of these (81.7%) were dinucleotide or trinucleotide repeats. The GT/CA repeat motif was the most common, accounting for 42% of all repeat types. From a total of 43 primer pairs designed, 41 produced markers within the expected size range. Sixteen (39%) were polymorphic when screened against a restricted set of taro genotypes from Southeast Asia and Oceania, with an average of 3.2 alleles detected on each locus. These markers represent a useful resource for taro germplasm management, genome mapping, and marker-assisted selection.Key words: Colocasia esculenta, microsatellite-enriched genomic library, simple sequence repeats, germplasm characterization.

scholarly journals Development and characterization of microsatellite loci for Cedrela fissilis Vell (Meliaceae), an endangered tropical tree species

2014 ◽  
Vol 63 (1-6) ◽  
pp. 240-243 ◽  
Author(s):  
F. B. Gandara ◽  
E. V. Tambarussi ◽  
Alexandre Magno Sebbenn ◽  
E. M. Ferraz ◽  
M. A. Moreno ◽  
...  
Keyword(s):  
Genomic Library ◽  
Population Level ◽  
Fixation Index ◽  
Allele Number ◽  
Neotropical Tree ◽  
Expected Heterozygosity ◽  
Adult Trees ◽  
Ssr Loci ◽  
Polymorphic Microsatellite

Abstract The timber of the Neotropical tree Cedrela fissilis is used in construction, shipbuilding, carpentry and for medical purposes. In this study, polymorphic microsatellite (SSR) markers derived from an enriched genomic library were characterized using 120 adult trees from four different C. fissilis populations. No substantial genotypic linkage disequilibrium was detected among all possible pairs of SSR loci. The number of alleles per locus ranged from 2 to 20, the average allele number ranged from 8 to 9.7, depending on the population. The observed heterozygosity among the different SSR loci varied from 0.0 to 1.00 , the expected heterozygosity varied from 0.07 to 0.95 On the population level, the average observed and expected heterozygosities ranged from 0.50 to 0.63 and from 0.64 to 0.70, respectively. The average fixation index among populations ranged from 0.09 to 0.24. Thus, the SSR loci revealed high poly - morphism rates and can be used to study the genetic diversity,structure, mating system, and gene flow in C. fissilis.

Development and characterization of microsatellite markers from tropical forage Stylosanthes species and analysis of genetic variability and cross-species transferability

Genome ◽  
2011 ◽  
Vol 54 (12) ◽  
pp. 1016-1028 ◽  
Author(s):  
Amaresh Chandra ◽  
K.K. Tiwari ◽  
D. Nagaich ◽  
N. Dubey ◽  
S. Kumar ◽  
...  
Keyword(s):  
Genetic Improvement ◽  
Expressed Sequence Tag ◽  
Intraspecific Diversity ◽  
Genomic Libraries ◽  
Tropical Forage ◽  
Genomic Ssr ◽  
Functional Molecular Markers ◽  
Expressed Sequence ◽  
Simple Sequence

A limited number of functional molecular markers has slowed the desired genetic improvement of Stylosanthes species. Hence, in an attempt to develop simple sequence repeat (SSR) markers, genomic libraries from Stylosanthes seabrana B.L. Maass & ’t Mannetje (2n = 2x = 20) using 5′ anchored degenerate microsatellite primers were constructed. Of the 76 new microsatellites, 21 functional primer pairs were designed. Because of the small number of primer pairs designed, 428 expressed sequence tag (EST) sequences from seven Stylosanthes species were also examined for SSR detection. Approximately 10% of sequences delivered functional primer pairs, and after redundancy elimination, 57 microsatellite repeats were selected. Tetranucleotides followed by trinucleotides were the major repeated sequences in Stylosanthes ESTs. In total, a robust set of 21 genomic–SSR (gSSR) and 20 EST–SSR (eSSR) markers were developed. These markers were analyzed for intraspecific diversity within 20 S. seabrana accessions and for their cross-species transferability. Mean expected (He) and observed (Ho) heterozygosity values with gSSR markers were 0.64 and 0.372, respectively, whereas with eSSR markers these were 0.297 and 0.214, respectively. Dendrograms having moderate bootstrap value (23%–94%) were able to distinguish all accessions of S. seabrana with gSSR markers, whereas eSSR markers showed 100% similarities between few accessions. The set of 21 gSSRs, from S. seabrana, and 20 eSSRs, from selected Stylosanthes species, with their high cross-species transferability (45% with gSSRs, 86% with eSSRs) will facilitate genetic improvement of Stylosanthes species globally.

scholarly journals Metagenomic Profiling: Microarray Analysis of an Environmental Genomic Library

2003 ◽  
Vol 69 (8) ◽  
pp. 4927-4934 ◽  
Author(s):  
Jonathan L. Sebat ◽  
Frederick S. Colwell ◽  
Ronald L. Crawford
Keyword(s):  
Genomic Dna ◽  
Genomic Library ◽  
Hydrogen Oxidation ◽  
Metagenomic Library ◽  
Environmental Dna ◽  
Cosmid Library ◽  
Genomic Libraries ◽  
Novel Approach ◽  
Ecological Importance

ABSTRACT Genomic libraries derived from environmental DNA (metagenomic libraries) are useful for characterizing uncultured microorganisms. However, conventional library-screening techniques permit characterization of relatively few environmental clones. Here we describe a novel approach for characterization of a metagenomic library by hybridizing the library with DNA from a set of groundwater isolates, reference strains, and communities. A cosmid library derived from a microcosm of groundwater microorganisms was used to construct a microarray (COSMO) containing ∼1-kb PCR products amplified from the inserts of 672 cosmids plus a set of 16S ribosomal DNA controls. COSMO was hybridized with Cy5-labeled genomic DNA from each bacterial strain, and the results were compared with the results for a common Cy3-labeled reference DNA sample consisting of a composite of genomic DNA from multiple species. The accuracy of the results was confirmed by the preferential hybridization of each strain to its corresponding rDNA probe. Cosmid clones were identified that hybridized specifically to each of 10 microcosm isolates, and other clones produced positive results with multiple related species, which is indicative of conserved genes. Many clones did not hybridize to any microcosm isolate; however, some of these clones hybridized to community genomic DNA, suggesting that they were derived from microbes that we failed to isolate in pure culture. Based on identification of genes by end sequencing of 17 such clones, DNA could be assigned to functions that have potential ecological importance, including hydrogen oxidation, nitrate reduction, and transposition. Metagenomic profiling offers an effective approach for rapidly characterizing many clones and identifying the clones corresponding to unidentified species of microorganisms.

Development and characterization of 248 novel microsatellite markers in turbot (Scophthalmus maximus)

Genome ◽  
2007 ◽  
Vol 50 (3) ◽  
pp. 329-332 ◽  
Author(s):  
B.G. Pardo ◽  
C. Fernández ◽  
M. Hermida ◽  
A. Vázquez-López ◽  
M. Pérez ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Scophthalmus Maximus ◽  
Marine Aquaculture ◽  
Genomic Libraries ◽  
Polymorphic Microsatellites ◽  
Great Relevance ◽  
Trait Locus ◽  
Turbot Scophthalmus Maximus ◽  
Simple Sequence

The turbot is a flatfish species of great relevance to marine aquaculture in Europe. Only a limited number of microsatellites have been isolated to date in this species. To increase the number of potentially useful mapping markers, we screened simple sequence repeat (SSR) - enriched genomic libraries obtained from several di-, tri-, and tetranucleotide tandem repeat motifs. A total of 248 new polymorphic microsatellites were successfully optimized. The efficiency of the protocol applied (6.4%) was higher than that in other studies of fish that used the same method. Dinucleotide and perfect microsatellites were predominant in this species; the (AC)n motif was the most frequent class of repeat. Polymorphism and structural properties at these loci, together with 30 variable loci previously reported in turbot, were evaluated in 6 wild individuals. The number of alleles per locus ranged from 2 to 10, with an average of 4.046. The microsatellite markers characterized in this study will contribute to the development of the turbot genetic map, which can be used for quantitative trait locus (QTL) identification, marker-assisted selection programs, and other applications to improve its culture.

scholarly journals Isolation and Characterization of 10 Polymorphic Microsatellite Loci in Paphiopedilum concolor (Batem.) Pfitzer (Orchidaceae) and Cross-species Amplification

HortScience ◽  
2010 ◽  
Vol 45 (8) ◽  
pp. 1286-1287 ◽  
Author(s):  
Long-na Li ◽  
Songjun Zeng ◽  
Feng Zheng ◽  
Zhi-lin Chen ◽  
Kun-lin Wu ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Microsatellite Locus ◽  
Microsatellite Loci ◽  
Genomic Library ◽  
Enriched Genomic Library ◽  
Relationship Patterns ◽  
Isolation And Characterization ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite

Ten polymorphic microsatellite loci were isolated and characterized from an enriched genomic library of Paphiopedilum concolor (Batem.) Pfitzer. The number of alleles per microsatellite locus ranged from three to 11 with an average of 6.4 in a sample of 30 individuals from three populations. The observed and expected heterozygosity ranged from 0.200 to 0.800 and from 0.544 to 0.827, respectively. These microsatellites can be used as tools to investigate the genetic structure of P. concolor populations and relationship patterns with closely related taxa.

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