ArticleFrontiers in plant science2019
Target SSR-Seq: A Novel SSR Genotyping Technology Associate With Perfect SSRs in Genetic Analysis of Cucumber Varieties.
Article in Frontiers in plant science, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
- Upscaling Genotyping by Amplicon Sequencing With GBAS-GUI.Molecular ecology resources · 2026Article
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- Estimating asian elephant abundance: a comparative analysis of dung counts and genetic SECR in a known population of Kodagu, Karnataka, India.BMC ecology and evolution · 2025Article
- Plastome structure, evolution and diversity of Frankincense-producing Boswellia genus.Functional & integrative genomics · 2025Article
- Development of SNP panel for genetic diversity assessment, fingerprinting identification and backcross breeding inMolecular breeding : new strategies in plant improvement · 2025Article
- Construction of SNP Fingerprinting and Genetic Diversity Analysis of Eggplant Based on KASP Technology.International journal of molecular sciences · 2025Article
- An updated reference genome of Barbatula barbatula (Linnaeus, 1758).Scientific data · 2025Article
- Establishment of Novel Simple Sequence Repeat (SSR) Markers fromPlants (Basel, Switzerland) · 2024Article
- Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes.International journal of molecular sciences · 2024Article
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- Exploring horticultural traits and disease resistance in Capsicum baccatum through segmental introgression lines.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Preliminary Investigation of Essentially Derived Variety of Tea Tree and Development of SNP Markers.Plants (Basel, Switzerland) · 2023Article
- Screening and identification of multiple abiotic stress responsive candidate genes based on hybrid-sequencing inHeliyon · 2023Article
- Genetic Diversity Analysis and Core Germplasm Collection Construction of Radish Cultivars Based on Structure Variation Markers.International journal of molecular sciences · 2023Article
- Genetic diversity analysis and variety identification using SSR and SNP markers in melon.BMC plant biology · 2023Article
- The complete chloroplast genome of the medical plant Huperzia crispata from the Huperziaceae family: structure, comparative analysis, and phylogenetic relationships.Molecular biology reports · 2022Article
- Targeted Identification of Rice Grain-Associated Gene Allelic Variation Through Mutation Induction, Targeted Sequencing, and Whole Genome Sequencing Combined with a Mixed-Samples Strategy.Rice (New York, N.Y.) · 2022Article
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11 authors.
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Abstract
Simple sequence repeats (SSR) - also known as microsatellites - have been used extensively in genetic analysis, fine mapping, quantitative trait locus (QTL) mapping, as well as marker-assisted selection (MAS) breeding and other techniques. Despite a plethora of studies reporting that perfect SSRs with stable motifs and flanking sequences are more efficient for genetic research, the lack of a high throughput technology for SSR genotyping has limited their use as genetic targets in many crops. In this study, we developed a technology called Target SSR-seq that combined the multiplexed amplification of perfect SSRs with high throughput sequencing. This method can genotype plenty of SSR loci in hundreds of samples with highly accurate results, due to the substantial coverage afforded by high throughput sequencing. We also detected 844 perfect SSRs based on 182 resequencing datasets in cucumber, of which 91 SSRs were selected for Target SSR-seq. Finally, 122 SSRs, including 31 SSRs for varieties identification, were used to genotype 382 key cucumber varieties readily available in Chinese markets using our Target SSR-seq method. Libraries of PCR products were constructed and then sequenced on the Illumina HiSeq X Ten platform. Bioinformatics analysis revealed that 111 filtered SSRs were accurately genotyped with an average coverage of 1289× at an extremely low cost; furthermore, 398 alleles were observed in 382 cucumber cultivars. Genetic analysis identified four populations: northern China type, southern China type, European type, and Xishuangbanna type. Moreover, we acquired a set of 16 core SSRs for the identification of 382 cucumber varieties, of which 42 were isolated as backbone cucumber varieties. This study demonstrated that Target SSR-seq is a novel and efficient method for genetic research.
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