ArticleApplications in plant sciences2018
Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for
Article in Applications in plant sciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 26 citations in OpenAlex.
- Article
- Carob Tree: A Review of Traditional Uses, Medicinal Properties, and Future Perspectives in Sustainable Forestry.Life (Basel, Switzerland) · 2026Review
- Comprehensive Genetic and Morphological Analysis of Algerian Carob (Plants (Basel, Switzerland) · 2025Article
- Phenotypic and genetic characterization of anFrontiers in plant science · 2023Article
- Article
- Genome-wide footprints in the carob tree (Ceratonia siliqua) unveil a new domestication pattern of a fruit tree in the Mediterranean.Molecular ecology · 2022Article
- Microsatellite marker development in the crop wild relativeApplications in plant sciences · 2020Article
- Pod Morphology, Primary and Secondary Metabolite Profiles in Non-grafted and Grafted Carob Germplasm Are Configured by Agro-Environmental Zone, Genotype, and Growing Season.Frontiers in plant science · 2020Article
- Article
- Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods forApplications in plant sciences · 2018Article
Corrections and comments
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Authors and funding
12 authors at 7 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premise of the studySimple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected.
methodsIn this study, we implemented a next-generation sequencing-based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree,
resultsThe analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single-nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates. DISCUSSION: Next-generation sequencing allows the detection and scoring of SSRs, single-nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.