ArticleMolecules and cells2014
Genome-wide SNP calling using next generation sequencing data in tomato.
Article in Molecules and cells, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Genome-wide SNP analysis reveals genetic diversity and structure of wild and cultivated olives (Olea europaea L.) in Oman.Scientific reports · 2026Article
- Development and application of SNP markers to discriminate Korean Perilla (Perilla frutescens) varieties using genomic sequence variations.Scientific reports · 2025Article
- Three distinct genetic lineages of Trichonephila clavata based on mitochondrial COI and genome-wide SNPs on the Korean Peninsula.Scientific reports · 2025Article
- The landscape of sequence variations between resistant and susceptible hot peppers to predict functional candidate genes against bacterial wilt disease.BMC plant biology · 2024Article
- Genotyping-by-Sequencing Analysis Reveals Associations between Agronomic and Oil Traits in Gamma Ray-Derived Mutant Rapeseed (Plants (Basel, Switzerland) · 2024Article
- Genome-Wide Association Study for Agronomic Traits in Gamma-Ray-Derived Mutant Kenaf (Plants (Basel, Switzerland) · 2024Article
- Comparative transcriptome analysis of persimmon somatic mutants (Frontiers in plant science · 2024Article
- Development of a Gene-Based Marker Set for Orange-Colored Watermelon Flesh with a High β-Carotene Content.International journal of molecular sciences · 2023Article
- Development of an SNP marker set for marker-assisted backcrossing using genotyping-by-sequencing in tetraploid perilla.Molecular genetics and genomics : MGG · 2023Article
- A Comprehensive Genome-Wide Association Study of Carotenoid and Capsaicinoid Contents inInternational journal of molecular sciences · 2023Article
- Age-Dependent Growth-Related QTL Variations in Pacific Abalone,International journal of molecular sciences · 2023Article
- Genome-wide association study of resistance to anthracnose in pepper (Capsicum chinense) germplasm.BMC plant biology · 2023Article
- Genome-Wide Association Study of Phenolic Content and Antioxidant Properties in Eggplant Germplasm.Genes · 2023Article
- Population Genetic Analysis in Persimmons (Plants (Basel, Switzerland) · 2023Article
- Genetic diversity assessment and genome-wide association study reveal candidate genes associated with component traits in sweet potato (Ipomoea batatas (L.) Lam).Molecular genetics and genomics : MGG · 2023Article
- Article
- A GBS-based genetic linkage map and quantitative trait loci (QTL) associated with resistance toFrontiers in plant science · 2023Article
- Genome-Wide Association Study for Agro-Morphological Traits in Eggplant Core Collection.Plants (Basel, Switzerland) · 2022Article
- Next-Generation Sequencing of Local Romanian Tomato Varieties and Bioinformatics Analysis of theInternational journal of molecular sciences · 2022Article
- QTL Mapping for Resistance to Bacterial Wilt Caused by Two Isolates ofPlants (Basel, Switzerland) · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The tomato (Solanum lycopersicum L.) is a model plant for genome research in Solanaceae, as well as for studying crop breeding. Genome-wide single nucleotide polymorphisms (SNPs) are a valuable resource in genetic research and breeding. However, to do discovery of genome-wide SNPs, most methods require expensive high-depth sequencing. Here, we describe a method for SNP calling using a modified version of SAMtools that improved its sensitivity. We analyzed 90 Gb of raw sequence data from next-generation sequencing of two resequencing and seven transcriptome data sets from several tomato accessions. Our study identified 4,812,432 non-redundant SNPs. Moreover, the workflow of SNP calling was improved by aligning the reference genome with its own raw data. Using this approach, 131,785 SNPs were discovered from transcriptome data of seven accessions. In addition, 4,680,647 SNPs were identified from the genome of S. pimpinellifolium, which are 60 times more than 71,637 of the PI212816 transcriptome. SNP distribution was compared between the whole genome and transcriptome of S. pimpinellifolium. Moreover, we surveyed the location of SNPs within genic and intergenic regions. Our results indicated that the sufficient genome-wide SNP markers and very sensitive SNP calling method allow for application of marker assisted breeding and genome-wide association studies.
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