Identification of an SNP variation of elite tomato (Solanum lycopersicum L.) lines using genome resequencing analysis

Abstract

The completion of the tomato genome sequence and recent advances in DNA sequencing technology allow in-depth characterization of genetic variation present in the tomato genome. Cultivated tomato lines show low molecular but high phenotypic diversity. We resequenced the genomes of four elite tomato lines with an Illumina HiSeq 2000 sequencer. We generated, on average, 84 million 100-bp paired-end reads per line. Mapped reads covered 89.0-93.4% of the mapped S. lycopersicum reference genome (782 Mb). On average, 0.42 single nucleotide polymorphisms (SNPs)/kb and 0.05 short insertions and deletions (InDels)/kb were found in the four elite lines. The highest number of SNPs was 558,526 found in tomato line 13-1084. We identified many SNPs and InDels, derived from 1012 genes, in region 7-62 Mb of chromosome 5 in the four elite lines. The same pattern of multiple SNPs was detected on chromosome 5 in lines 13-1151 and 10-3321, deriving from genes in region 0-2 Mb, and many homozygous SNPs and InDels were detected on chromosome 1 of these two lines. The same pattern of multiple SNPs and InDels derived from genes located between regions 53-60 Mb of chromosomes 4 and 11 was found in the four elite lines. The SNPs and InDels identified in this resequencing study will serve as useful genetic tools and candidate polymorphisms in the search for DNA variations associated with valuable phenotypic diversity.