ArticlePloS one2013
Exploiting the transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to develop and characterize new EST-SSR markers and construct an EST-SSR database.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 40 citations in OpenAlex.
- Population Genetics ofGenes · 2025Article
- Twelve newly assembled jasmine chloroplast genomes: unveiling genomic diversity, phylogenetic relationships and evolutionary patterns among Oleaceae and Jasminum species.BMC plant biology · 2024Article
- Review
- Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea.Plants (Basel, Switzerland) · 2021Article
- Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia.Scientific reports · 2021Article
- Development of Novel Polymorphic EST-SSR Markers from the Cranberry Fruit Transcriptome.Iranian journal of biotechnology · 2021Article
- Variation of Chromosome Composition in a Full-Sib Population Derived From 2x × 3x Interploidy Cross ofFrontiers in plant science · 2021Article
- Article
- Report on the development of putative functional SSR and SNP markers in passion fruits.BMC research notes · 2017Article
- Development of microsatellite markers for Fargesia denudata (Poaceae), the staple-food bamboo of the giant panda.Applications in plant sciences · 2016Article
- Application of Microsatellite Loci for Molecular Identification of Elite Genotypes, Analysis of Clonality, and Genetic Diversity in Aspen Populus tremula L. (Salicaceae).International journal of plant genomics · 2015Article
- Article
- Barcoding poplars (Populus L.) from western China.PloS one · 2013Article
- FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research.PloS one · 2013Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicrosatellite markers or Simple Sequence Repeats (SSRs) are the most popular markers in population/conservation genetics. However, the development of novel microsatellite markers has been impeded by high costs, a lack of available sequence data and technical difficulties. New species-specific microsatellite markers were required to investigate the evolutionary history of the Euphratica tree, Populus euphratica, the only tree species found in the desert regions of Western China and adjacent Central Asian countries. METHODOLOGY/PRINCIPAL
findingsA total of 94,090 non-redundant Expressed Sequence Tags (ESTs) from P. euphratica comprising around 63 Mb of sequence data were searched for SSRs. 4,202 SSRs were found in 3,839 ESTs, with 311 ESTs containing multiple SSRs. The most common motif types were trinucleotides (37%) and hexanucleotides (33%) repeats. We developed primer pairs for all of the identified EST-SSRs (eSSRs) and selected 673 of these pairs at random for further validation. 575 pairs (85%) gave successful amplification, of which, 464 (80.7%) were polymorphic in six to 24 individuals from natural populations across Northern China. We also tested the transferability of the polymorphic eSSRs to nine other Populus species. In addition, to facilitate the use of these new eSSR markers by other researchers, we mapped them onto Populus trichocarpa scaffolds in silico and compiled our data into a web-based database (http://202.205.131.253:8080/poplar/resources/static_page/index.html).
conclusionsThe large set of validated eSSRs identified in this work will have many potential applications in studies on P. euphratica and other poplar species, in fields such as population genetics, comparative genomics, linkage mapping, QTL, and marker-assisted breeding. Their use will be facilitated by their incorporation into a user-friendly web-based database.
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