ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2013
Genome-wide SNP genotyping to infer the effects on gene functions in tomato.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- An advanced 10K SNP panel for genotyping tomato (Frontiers in plant science · 2025Article
- Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum).DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Polymorphisms of an oncogenic gene, mesothelin, predict the risk and prognosis of gastric cancer in a Chinese Han population.Archives of toxicology · 2022Article
- Whole-genome sequencing of a year-round fruiting jackfruit (Frontiers in plant science · 2022Article
- Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function.Scientific reports · 2020Article
- Review
- Applications and Trends of Machine Learning in Genomics and Phenomics for Next-Generation Breeding.Plants (Basel, Switzerland) · 2019Review
- Characterization and Expression Analysis of the CaPlants (Basel, Switzerland) · 2019Article
- Article
- Article
- New insights into tomato microRNAs.Scientific reports · 2018Article
- Role of genomics in promoting the utilization of plant genetic resources in genebanks.Briefings in functional genomics · 2018Review
- Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina).Plant molecular biology · 2018Article
- Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial FTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations.Scientific reports · 2016Article
- Rapid identification of causal mutations in tomato EMS populations via mapping-by-sequencing.Nature protocols · 2016Article
- Article
- Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- A simulation-based breeding design that uses whole-genome prediction in tomato.Scientific reports · 2016Article
- Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique.Applied and environmental microbiology · 2016Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genotype data of 7054 single nucleotide polymorphism (SNP) loci in 40 tomato lines, including inbred lines, F1 hybrids, and wild relatives, were collected using Illumina's Infinium and GoldenGate assay platforms, the latter of which was utilized in our previous study. The dendrogram based on the genotype data corresponded well to the breeding types of tomato and wild relatives. The SNPs were classified into six categories according to their positions in the genes predicted on the tomato genome sequence. The genes with SNPs were annotated by homology searches against the nucleotide and protein databases, as well as by domain searches, and they were classified into the functional categories defined by the NCBI's eukaryotic orthologous groups (KOG). To infer the SNPs' effects on the gene functions, the three-dimensional structures of the 843 proteins that were encoded by the genes with SNPs causing missense mutations were constructed by homology modelling, and 200 of these proteins were considered to carry non-synonymous amino acid substitutions in the predicted functional sites. The SNP information obtained in this study is available at the Kazusa Tomato Genomics Database (http://plant1.kazusa.or.jp/tomato/).
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