High-Throughput, Genome-Wide Tomato Genotyping Using Targeted Sequencing

The diversity of the tomato genome has been shaped by a complex history of intensive breeding that narrowed genetic variation, coupled with recent efforts to introgress regions of interest from wild species. The composition of modern tomato is expected to reflect this complex breeding history. Much work has been done in characterizing the genome, however, the scientific community still lacks a genotyping tool for high-throughput and genome-wide characterization of the genetic variation along the genome. Here we developed a new genotyping platform based on sequence-capture and next-generation sequencing of 78,000 distinct regions distributed every 10Kbp in the genome. We evaluated the approach in 19 varieties of Solanum lycopersicum, including several heirloom varieties, 2 varieties of S. lycopersicum var. cerasiforme and one S. pimpinellifolium. The sequences were compared to the S. lycopersicum reference genome and 31,619 SNPs were identified. The SNPs were well distributed across the whole genome and revealed different introgression blocks in the genotypes. On average, the 20 varieties had 5% heterozygosity, excluding the species S. pimpinellifolium, which had 24%. In addition, 1568 probes were designed to capture the gene sequence of 31 candidate flavor genes, out of which 949 SNPs were identified. Phylogenetic patterns were generated for each of the candidate genes using Maximum-likelihood and reflect the breeding history of the different varieties. This pilot demonstrated the feasibility of this genotyping platform for tomato. Its flexibility and high-throughput allows its use for a broad range of genomic applications such as QTL mapping, population genetic studies and genomic selection.