Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato

DNA Res. 2013 Dec;20(6):593-603. doi: 10.1093/dnares/dst033. Epub 2013 Jul 31.


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.

Keywords: genome-wide association studies; linkage disequilibrium; single nucleotide polymorphism; tomato; whole-genome re-sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crops, Agricultural / genetics
  • Genetic Loci
  • Genetic Markers / physiology
  • Genome, Plant*
  • Genome-Wide Association Study
  • Genotype
  • Linkage Disequilibrium
  • Lycopersicon esculentum / genetics*
  • Polymorphism, Single Nucleotide*
  • Sequence Analysis, DNA


  • Genetic Markers