S01 - Session P1 - Tunable genotyping-by-sequencing (tGBS) of a tomato (Solanum lycopersicum) collection

Authors: Amol Nankar *, Gancho Pasev, Dimitrina Kostova, Vesela Radeva-Ivanova, Valentina Ivanova, Stanislava Grozeva, Daniela Ganeva, Ivanka Tringovska, Zoran Nikoloski

Tomatoes are one of the most widely grown vegetables in Bulgaria and they are known for their good taste and unique fruit features. The objective of this study was to sequence the current tomato collection and identify SNPs sites for association mapping. A total of 192 tomato accessions were genotyped using tunable genotyping-by-sequencing (tGBS ® ) technology conducted with the restriction enzyme Bsp1286I. Each accession sample was sequenced using an Illumina HiSeq X instrument, and reads were aligned to the Solanum lycopersicum Version 4.0 reference genome after debarcoding and quality trimming of reads using GSNAP. The sequencing of the accessions generated several sets of SNPs within the population. The first set, termed "ALL SNPs", generated a set of 415,959 SNP sites, which were less stringent and low quality. The second set, referred to as MCR50 SNPs, generated 281,558 stringent and high quality SNP sites, and was genotyped in at least 50% of the samples. Each of these SNPs was supported on average by 34 tGBS reads/SNP/genotyped sample. Finally for each genotype, imputation was performed on the chromosome-based MCR50 SNPs, such that those SNP sites that lacked a sufficient number of reads to call a genotype, were filled in. The SNP information is being utilized to develop GWAS models and to identify QTLs related to agronomic and fruit quality traits that could be introgressed into elite breeding materia