ArticleScientific reports2020
A new SNP genotyping technology Target SNP-seq and its application in genetic analysis of cucumber varieties.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 61 papers.
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61 citing papers in PubMed, 141 citations in OpenAlex.
- Approaches to Thoroughbred Horse Identification in Diverse Sample Types Using Multiplexed SNP-PCR Sequencing Panels.Animal genetics · 2026Article
- Genetic Diversity and SNP-Based Fingerprinting of 94 Pumpkin Cultivars: Database Establishment and Population Analysis.Plants (Basel, Switzerland) · 2026Article
- A PCA-random forest pipeline for high-resolution SNP-based cultivar discrimination in Leymus chinensis.BMC plant biology · 2026Article
- A comprehensive analysis of two Chinese cucumber genomes and a mutant population as resources for precision breeding.Horticulture research · 2026Article
- Genetic Diversity Analysis of Cotton Cultivars Using a 40K Liquid Chip in Northern Xinjiang.International journal of molecular sciences · 2026Article
- Development and application of core collection, KASP markers and SNP-based DNA fingerprinting inFrontiers in plant science · 2026Article
- Comprehensive analysis of non-synonymous single-nucleotide polymorphism of human TSC1 and TSC2 genes: An in silico approach.PloS one · 2026Article
- Development of KASP molecular markers and construction of fingerprinting for cowpea (Vigna unguiculata (L.) Walp.) based on ddRAD-Seq.PloS one · 2026Article
- Genome-wide association study of agronomic traits in winter wheat (Triticum aestivum L.) using a custom SNP marker set.BMC plant biology · 2025Article
- Advances in Functional Genomics for Exploring Abiotic Stress Tolerance Mechanisms in Cereals.Plants (Basel, Switzerland) · 2025Review
- Development of SNP panel for genetic diversity assessment, fingerprinting identification and backcross breeding inMolecular breeding : new strategies in plant improvement · 2025Article
- Genetic Structure, Selective Signatures, and Single Nucleotide Polymorphism Fingerprints of Blue Tilapia (International journal of molecular sciences · 2025Article
- Litchi40K v1.0: a cost-effective, flexible, and versatile liquid SNP chip for genetic analysis and digitalization of germplasm resources in litchi.Horticulture research · 2025Article
- Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars.BMC genomics · 2025Article
- Screening of a core SNP set for the seedling identification of Saccharina japonica cultivars in northern China.PloS one · 2025Article
- An initial exploration of core collection construction and DNA fingerprinting inFrontiers in plant science · 2025Article
- SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.).BMC genomics · 2024Article
- Precision Agriculture and Water Conservation Strategies for Sustainable Crop Production in Arid Regions.Plants (Basel, Switzerland) · 2024Review
- Parental Reconstruction from a Half-Sib Population of Stoneless JujubePlants (Basel, Switzerland) · 2024Article
- Development and verification of a 10K liquid chip for Hainan black goat based on genotyping by pinpoint sequencing of liquid captured targets.BMC genomic data · 2024Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To facilitate the utility of SNP-based genotyping, we developed a new method called target SNP-seq which combines the advantages of multiplex PCR amplification and high throughput sequencing. Compared with KASP, Microarrays, GBS and other SNP genotyping methods, target SNP-seq is flexible both in SNPs and samples, yields high accuracy, especially when genotyping genome wide perfect SNPs with high polymorphism and conserved flanking sequences, and is cost-effective, requiring 3 days and $7 for per DNA sample to genotype hundreds of SNP loci. The present study established a DNA fingerprint of 261 cucumber varieties by target SNP-seq with 163 perfect SNPs from 4,612,350 SNPs based on 182 cucumber resequencing datasets. Four distinct subpopulations were found in 261 Chinese cucumber varieties: the north China type, the south China type, the Europe type, and the Xishuangbanna type. The north China type and Xishuangbanna type harbored lower genetic diversity, indicating greater risk of genetic erosion in these two subpopulations. Furthermore, a core set of 24 SNPs was able to distinguish 99% of the 261 cucumber varieties. 29 core cucumber backbone varieties in China were identified. Therefore, target SNP-seq provides a new way to screen out core SNP loci from the whole genome for DNA fingerprinting of crop varieties. The high efficiency and low cost of target SNP-seq is more competitive than the current SNP genotyping methods, and it has excellent application prospects in genetic research, as well as in promoting plant breeding processes in the near future.
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