ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2007
Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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85 citing papers in PubMed, 243 citations in OpenAlex.
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- Development of EST-SSR markers based on transcriptome sequencing for germplasm evaluation of 65 lilies (Lilium).Molecular biology reports · 2023Article
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- Occurrence of simple sequence repeats in cDNA sequences of safflower (Frontiers in plant science · 2022Article
- Development of a new set of genic SSR markers in the genus3 Biotech · 2021Article
- Development of EST-SSR markers forPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinense germplasm based on low-coverage whole genome sequencing.Biological research · 2020Article
- Genetic structure and diversity analysis of tall fescue populations by EST-SSR and ISSR markers.Molecular biology reports · 2020Article
- Advancements in molecular marker technologies and their applications in diversity studies.Journal of biosciences · 2020Review
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- De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweedPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Population structure and genetic relationships between Ethiopian and Brazilian Coffea arabica genotypes revealed by SSR markers.Genetica · 2019Article
25 more citing papers are in PubMed but not listed here.
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6 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Genic microsatellites or EST-SSRs derived from expressed sequence tags (ESTs) are desired because these are inexpensive to develop, represent transcribed genes, and often a putative function can be assigned to them. In this study we investigated 2,553 coffee ESTs (461 from the public domain and 2,092 in-house generated ESTs) for identification and development of genic microsatellite markers. Of these, 2,458 ESTs (all >100 bp in size) were searched for SSRs using MISA--search module followed by stackPACK clustering that revealed a total of 425 microsatellites in 331 (13.5%) non-redundant ESTs/consensus sequences suggesting an approximate frequency of 1 SSR/2.16 kb of the analysed coffee transcriptome. Identified microsatellites mainly comprised of di-/tri-nucleotide repeats, of which repeat motifs AG and AAG were the most abundant. A total of 224 primer pairs could be designed from the non-redundant SSR-positive ESTs (excluding those with only mononucleotide repeats) for possible use as potential genic markers. Of this set, a total of 24 (10%) primer pairs were tested and 18 could be validated as usable markers. Sixteen of these markers revealed moderate to high polymorphism information content (PIC) across 23 genotypes of C. arabica and C. canephora, while 2 markers were found to be monomorphic. All the markers also showed robust cross-species amplifications across 14 Coffea and 4 Psilanthus species. The apparent broad cross-species/genera transferability was further confirmed by cloning and sequencing of the amplified alleles. Thus, the study provides an insight about the frequency and distribution of SSRs in coffee transcriptome, and also demonstrates the successful development of genic-SSRs. It is expected that the potential markers described here would add to the repertoire of DNA markers needed for genetic studies in cultivated coffee and also related taxa that constitute the important secondary genepool for coffee improvement.
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