ArticleBMC plant biology2011
In silico comparative analysis of SSR markers in plants.
Article in BMC plant biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Transcriptome analysis of mulberry (Morus alba L.) leaves to identify differentially expressed genes associated with post-harvest shelf-life elongation.Scientific reports · 2022Article
- An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants?Functional & integrative genomics · 2022Article
- Development ofFrontiers in genetics · 2022Article
- Development of a new set of genic SSR markers in the genus3 Biotech · 2021Article
- Transcriptome characterization and generation of marker resource for Himalayan vulnerable species, Ulmus wallichiana.Molecular biology reports · 2021Article
- Deciphering the SSR incidences across viral members of Coronaviridae family.Chemico-biological interactions · 2020Article
- The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development.Scientific reports · 2020Article
- EST-SSR marker development based on RNA-sequencing of E. sibiricus and its application for phylogenetic relationships analysis of seventeen Elymus species.BMC plant biology · 2019Article
- Generation and characterization of expressed sequence tags (ESTs) from coralloid root cDNA library ofPlant diversity · 2018Article
- Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes.Scientific reports · 2018Article
- Mining and comparative survey of EST-SSR markers among members of Euphorbiaceae family.Molecular biology reports · 2018Article
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- Molecular Resources from Transcriptomes in the Brassicaceae Family.Frontiers in plant science · 2017Article
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- Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis.Genetics research international · 2016Article
- Assessment of genetic diversity in Nordic timothy (Hereditas · 2016Article
- PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers.Frontiers in plant science · 2016Article
- Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda).BMC genetics · 2015Article
- Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants.BMC genomics · 2015Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes.
resultsIn this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using the SSRLocator software in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools.
conclusionsThe comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.
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