ArticleMolecular genetics and genomics : MGG2006
SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus.
Article in Molecular genetics and genomics : MGG, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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66 citing papers in PubMed.
- Liberica Coffee (Molecules (Basel, Switzerland) · 2026Review
- Genome-wide identification and characterization of NAC transcription factor-derived microsatellites in wheat (Triticum aestivum L.).Journal of applied genetics · 2026Article
- Assessing Genetic Variability and Population Structure ofPlants (Basel, Switzerland) · 2024Article
- Analysis of the genetic diversity and population structure of Monochasma savatieri Franch. ex Maxim using novel EST-SSR markers.BMC genomics · 2022Article
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- Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L.Plant biotechnology journal · 2019Article
- Generation and classification of transcriptomes in twoPlant diversity · 2018Article
- Mining and comparative survey of EST-SSR markers among members of Euphorbiaceae family.Molecular biology reports · 2018Article
- Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.Molecules (Basel, Switzerland) · 2018Review
- Transcriptome sequence analysis and mining of SSRs in Jhar Ber (Ziziphus nummularia (Burm.f.) Wight & Arn) under drought stress.Scientific reports · 2018Article
- Mining and characterization of EST-SSR markers forPhysiology and molecular biology of plants : an international journal of functional plant biology · 2017Article
- Systemic Identification ofJournal of nucleic acids · 2017Article
- Selection and Validation of Reference Genes for Accurate RT-qPCR Data Normalization inFrontiers in plant science · 2017Article
- Article
- In silico search, characterization and validation of new EST-SSR markers in the genus Prunus.BMC research notes · 2016Article
- Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species.Ecology and evolution · 2016Article
- Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars.BMC plant biology · 2016Article
- Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits.Molecular genetics and genomics : MGG · 2016Article
- Genetic linkage map construction and QTL mapping of seedling height, basal diameter and crown width of Taxodium 'Zhongshanshan 302' × T. mucronatum.SpringerPlus · 2016Article
6 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
Expressed sequence tags (ESTs) from Coffea canephora leaves and fruits were used to search for types and frequencies of simple sequence repeats (EST-SSRs) with a motif length of 1-6 bp. From a non-redundant (NR) EST set of 5,534 potential unigenes, 6.8% SSR-containing sequences were identified, with an average density of one SSR every 7.73 kb of EST sequences. Trinucleotide repeats were found to be the most abundant (34.34%), followed by di- (25.75%) and hexa-nucleotide (22.04%) motifs. The development of unique genic SSR markers was optimized by a computational approach which allowed us to eliminate redundancy in the original EST set and also to test the specificity of each pair of designed primers. Twenty-five EST-SSRs were developed and used to evaluate cross-species transferability in the Coffea genus. The orthology was supported by the amplicon sequence similarity and the amplification patterns. The >94% identity of flanking sequences revealed high sequence conservation across the Coffea genus. A high level of polymorphic loci was obtained regardless of the species considered (from 75% for C. liberica to 86% for C. canephora). Moreover, the polymorphism revealed by EST-SSR was similar to that exposed by genomic SSR. It is concluded that Coffea ESTs are a valuable resource for microsatellite mining. EST-SSR markers developed from C. canephora sequences can be easily transferred to other Coffea species for which very little molecular information is available. They constitute a set of conserved orthologous markers, which would be ideal for assessing genetic diversity in coffee trees as well as for cross-referencing transcribed sequences in comparative genomics studies.
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