title: Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato.
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.
authors.affiliation: 1 Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Kenta
authors.initials: K
authors.lastname: Shirasawa
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Fukuoka
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Matsunaga
authors.forename: Yuhko
authors.initials: Y
authors.lastname: Kobayashi
authors.forename: Issei
authors.initials: I
authors.lastname: Kobayashi
authors.forename: Hideki
authors.initials: H
authors.lastname: Hirakawa
authors.forename: Sachiko
authors.initials: S
authors.lastname: Isobe
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics; D056426:Genetic Loci; D005819:Genetic Markers / Q000502:physiology; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D015810:Linkage Disequilibrium; D018551:Solanum lycopersicum / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers
keywords: genome-wide association studies; linkage disequilibrium; single nucleotide polymorphism; tomato; whole-genome re-sequencing
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