ArticleNucleic acids research2017
An accurate and efficient method for large-scale SSR genotyping and applications.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- EST-SSR based genetic polymorphism among Lablab (Lablab purpureus L. Sweet) accessions contrasting for drought stress at seedling stage.Scientific reports · 2026Article
- Elite donors and stable marker-trait associations for grain iron and zinc biofortification in rice under organic and inorganic production systems.Frontiers in plant science · 2026Article
- Integrative Analysis ofEcology and evolution · 2025Article
- MGV-seq: a sensitive and culture-independent method for detecting microbial genetic variation.Frontiers in microbiology · 2025Article
- The Whole Mitochondrial Genome Sequence ofGenes · 2024Article
- GenoBaits®WheatplusEE: a targeted capture sequencing panel for quick and accurate identification of wheat-Thinopyrum derivatives.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources.Plants (Basel, Switzerland) · 2023Article
- Carryover Contamination-Controlled Amplicon Sequencing Workflow for Accurate Qualitative and Quantitative Detection of Pathogens: a Case Study on SARS-CoV-2.Microbiology spectrum · 2023Article
- Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom (Journal of fungi (Basel, Switzerland) · 2023Article
- Genetic diversity analysis and variety identification using SSR and SNP markers in melon.BMC plant biology · 2023Article
- Feature Compression Applications of Genetic Algorithm.Frontiers in genetics · 2022Article
- An integrated strategy for target SSR genotyping with toleration of nucleotide variations in the SSRs and flanking regions.BMC bioinformatics · 2021Article
- De novo identification and targeted sequencing of SSRs efficiently fingerprints Sorghum bicolor sub-population identity.PloS one · 2021Article
- Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli (Frontiers in plant science · 2021Article
- Integration of advanced technologies for plant variety and cultivar identification.Journal of biosciences · 2021Review
- Dissection of Molecular Processes and Genetic Architecture Underlying Iron and Zinc Homeostasis for Biofortification: From Model Plants to Common Wheat.International journal of molecular sciences · 2020Review
- Article
- MultiplexSSR: A pipeline for developing multiplex SSR-PCR assays from resequencing data.Ecology and evolution · 2020Article
- Article
- Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties.BMC plant biology · 2019Article
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Authors and funding
12 authors.
Funding
Abstract
Accurate and efficient genotyping of simple sequence repeats (SSRs) constitutes the basis of SSRs as an effective genetic marker with various applications. However, the existing methods for SSR genotyping suffer from low sensitivity, low accuracy, low efficiency and high cost. In order to fully exploit the potential of SSRs as genetic marker, we developed a novel method for SSR genotyping, named as AmpSeq-SSR, which combines multiplexing polymerase chain reaction (PCR), targeted deep sequencing and comprehensive analysis. AmpSeq-SSR is able to genotype potentially more than a million SSRs at once using the current sequencing techniques. In the current study, we simultaneously genotyped 3105 SSRs in eight rice varieties, which were further validated experimentally. The results showed that the accuracies of AmpSeq-SSR were nearly 100 and 94% with a single base resolution for homozygous and heterozygous samples, respectively. To demonstrate the power of AmpSeq-SSR, we adopted it in two applications. The first was to construct discriminative fingerprints of the rice varieties using 3105 SSRs, which offer much greater discriminative power than the 48 SSRs commonly used for rice. The second was to map Xa21, a gene that confers persistent resistance to rice bacterial blight. We demonstrated that genome-scale fingerprints of an organism can be efficiently constructed and candidate genes, such as Xa21 in rice, can be accurately and efficiently mapped using an innovative strategy consisting of multiplexing PCR, targeted sequencing and computational analysis. While the work we present focused on rice, AmpSeq-SSR can be readily extended to animals and micro-organisms.
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