ArticleBMC research notes2016
In silico search, characterization and validation of new EST-SSR markers in the genus Prunus.
Article in BMC research notes, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Generation and characterization of novel transcriptome-derived SSR markers for genetic applications in blueberry.Scientific reports · 2025Article
- Development of novel InDel markers by whole-genome sequence comparison and genetic diversity assessment of Thailand rice blast fungus populations.Stress biology · 2025Article
- Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species.Scientific reports · 2023Article
- Development of a new set of genic SSR markers in the genus3 Biotech · 2021Article
- Development and characterization of genic SSR-FDM for stem gall disease resistance in coriander (Coriandrum sativum L.) and its cross species transferability.Molecular biology reports · 2021Article
- Development of EST-SSR markers forPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSimple sequence repeats (SSRs) are defined as sequence repeat units between 1 and 6 bp that occur in both coding and non-coding regions abundant in eukaryotic genomes, which may affect the expression of genes. In this study, expressed sequence tags (ESTs) of eight Prunus species were analyzed for in silico mining of EST-SSRs, protein annotation, and open reading frames (ORFs), and the identification of codon repetitions.
resultsA total of 316 SSRs were identified using MISA software. Dinucleotide SSR motifs (26.31 %) were found to be the most abundant type of repeats, followed by tri- (14.58 %), tetra- (0.53 %), and penta- (0.27 %) nucleotide motifs. An attempt was made to design primer pairs for 316 identified SSRs but these were successful for only 175 SSR sequences. The positions of SSRs with respect to ORFs were detected, and annotation of sequences containing SSRs was performed to assign function to each sequence. SSRs were also characterized (in terms of position in the reference genome and associated gene) using the two available Prunus reference genomes (mei and peach). Finally, 38 SSR markers were validated across peach, almond, plum, and apricot genotypes. This validation showed a higher transferability level of EST-SSR developed in P. mume (mei) in comparison with the rest of species analyzed.
conclusionsFindings will aid analysis of functionally important molecular markers and facilitate the analysis of genetic diversity.
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