Genome-wide SNP genotyping to infer the effects on gene functions in tomato

DNA Res. 2013 Jun;20(3):221-33. doi: 10.1093/dnares/dst005. Epub 2013 Mar 12.

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/).

Keywords: Solanum lycopersicum; goldengate assay; homology modelling; infinium assay; single nucleotide polymorphism (SNP).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breeding
  • Chimera
  • Genes, Plant*
  • Genome-Wide Association Study
  • Genotype
  • Lycopersicon esculentum / genetics*
  • Mutation, Missense
  • Polymorphism, Single Nucleotide*
  • Sequence Homology