ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2013
Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated 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 44 papers.
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44 citing papers in PubMed, 83 citations in OpenAlex.
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- Genome-wide meta-QTL approach identifies consensus loci associated with agriculturally important tomato fruit traits.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- An advanced 10K SNP panel for genotyping tomato (Frontiers in plant science · 2025Article
- Advances in single-cell sequencing technology in microbiome research.Genes & diseases · 2024Review
- Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach.PLoS computational biology · 2022Article
- Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato.Computational and structural biotechnology journal · 2022Review
- Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects.International journal of molecular sciences · 2021Review
- Genome-Wide Association Study to Map Genomic Regions Related to the Initiation Time of Four Growth Stage Traits in Soybean.Frontiers in genetics · 2021Article
- Article
- Advances and Challenges in Bacterial Spot Resistance Breeding in Tomato (International journal of molecular sciences · 2020Review
- 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
- Article
- Mutation Breeding in Tomato: Advances, Applicability and Challenges.Plants (Basel, Switzerland) · 2019Review
- Identification of Loci and Candidate Genes Responsible for Pod Dehiscence in Soybean via Genome-Wide Association Analysis Across Multiple Environments.Frontiers in plant science · 2019Article
- Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Genetic Loci Controlling Carotenoid Biosynthesis in Diverse Tropical Maize Lines.G3 (Bethesda, Md.) · 2018Article
- An InDel in the Promoter ofThe Plant cell · 2017Article
- Genetic dissection of adventitious shoot regeneration in roses by employing genome-wide association studies.Plant cell reports · 2017Article
- 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
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the aim of understanding relationship between genetic and phenotypic variations in cultivated tomato, single nucleotide polymorphism (SNP) markers covering the whole genome of cultivated tomato were developed and genome-wide association studies (GWAS) were performed. The whole genomes of six tomato lines were sequenced with the ABI-5500xl SOLiD sequencer. Sequence reads covering ~13.7× of the genome for each line were obtained, and mapped onto tomato reference genomes (SL2.40) to detect ~1.5 million SNP candidates. Of the identified SNPs, 1.5% were considered to confer gene functions. In the subsequent Illumina GoldenGate assay for 1536 SNPs, 1293 SNPs were successfully genotyped, and 1248 showed polymorphisms among 663 tomato accessions. The whole-genome linkage disequilibrium (LD) analysis detected highly biased LD decays between euchromatic (58 kb) and heterochromatic regions (13.8 Mb). Subsequent GWAS identified SNPs that were significantly associated with agronomical traits, with SNP loci located near genes that were previously reported as candidates for these traits. This study demonstrates that attractive loci can be identified by performing GWAS with a large number of SNPs obtained from re-sequencing analysis.
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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.