ArticleBiology2012
Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNP.
Article in Biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
34 citing papers in PubMed.
- Genome-wide assessment of genetic diversity and selective signatures in sunflower (Helianthus annuus L.) using a 10 K SNP array.Scientific reports · 2026Article
- Genetic diversity and population structure analysis of cotton (Gossypium hirsutum L.) genotypes using DArTseq technology.BMC genomics · 2026Article
- Future of durum wheat research and breeding: Insights from early career researchers.The plant genome · 2025Review
- A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology.Nature plants · 2023Article
- Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 ofPathogens (Basel, Switzerland) · 2023Article
- Article
- Candidate Rlm6 resistance genes against Leptosphaeria. maculans identified through a genome-wide association study in Brassica juncea (L.) Czern.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Skim sequencing: an advanced NGS technology for crop improvement.Journal of genetics · 2021Review
- Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding.G3 (Bethesda, Md.) · 2020Article
- Characterization of genetic diversity and population structure in wheat using array based SNP markers.Molecular biology reports · 2020Article
- Wild Origins of Macadamia Domestication Identified Through Intraspecific Chloroplast Genome Sequencing.Frontiers in plant science · 2019Article
- Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references.PloS one · 2019Article
- Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping.Plant biotechnology journal · 2018Article
- DNA sequence-based re-assessment of archived Cronobacter sakazakii strains isolated from dairy products imported into China between 2005 and 2006.BMC genomics · 2018Article
- Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data.Frontiers in plant science · 2018Article
- Assembly and comparison of two closely related Brassica napus genomes.Plant biotechnology journal · 2017Article
- High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis.Functional & integrative genomics · 2017Article
- Review
- SNP-based association analysis for seedling traits in durum wheat (Breeding science · 2017Article
- Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application.Plant biotechnology journal · 2017Review
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide polymorphisms (SNPs) are becoming the dominant form of molecular marker for genetic and genomic analysis. The advances in second generation DNA sequencing provide opportunities to identify very large numbers of SNPs in a range of species. However, SNP identification remains a challenge for large and polyploid genomes due to their size and complexity. We have developed a pipeline for the robust identification of SNPs in large and complex genomes using Illumina second generation DNA sequence data and demonstrated this by the discovery of SNPs in the hexaploid wheat genome. We have developed a SNP discovery pipeline called SGSautoSNP (Second-Generation Sequencing AutoSNP) and applied this to discover more than 800,000 SNPs between four hexaploid wheat cultivars across chromosomes 7A, 7B and 7D. All SNPs are presented for download and viewing within a public GBrowse database. Validation suggests an accuracy of greater than 93% of SNPs represent polymorphisms between wheat cultivars and hence are valuable for detailed diversity analysis, marker assisted selection and genotyping by sequencing. The pipeline produces output in GFF3, VCF, Flapjack or Illumina Infinium design format for further genotyping diverse populations. As well as providing an unprecedented resource for wheat diversity analysis, the method establishes a foundation for high resolution SNP discovery in other large and complex genomes.
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Registered trials
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.