Whole Genome Sequencing Reveals Introgressions and Structural Variations in the Pedigree of a Tomato Line Bred for Resistance to Multiple Species of Xanthomonas

Tomato variety improvement has a 100 year history of introducing resistance from wild relatives.  Introduced resistances are often accompanied by large chromosomal fragments referred to as introgressions.  Our goal was to quantify the size of introgressions introduced through breeding and to identify structural variations (SV) within these regions.  The processing tomato line OH7663 integrates resistance which is effective against different Xanthomonas species causing bacterial spot.  The pedigree of OH7663 has four potential wild donors of resistance.  We used resequencing of the pedigree to identify introgressions.  Four analytical approaches were used: (1) comparison of single nucleotide polymorphism (SNP) density, (2) phylogenetic analysis, (3) alignment against an alternative genome and (4) analysis of SV.  The sequences averaged 12-fold depth and were aligned to the SL2.50 (Solanum lycopersicum) and the LA 1589 (S. pimpinellifolium) references.  A statistical comparison of SNP density and phylogenetic analysis defined 12 introgressions ranging from 0.1 to 37.3 Mb.  Deletions and inversions were identified across the genome, with a large number mapping to chromosome 1, 5, 10, 11 and 12.  These regions represent portions of the genome that differentiate the pedigree from the Heinz reference due to fresh-market or wild species introgressions.  In addition, 31% and 25% of sequences that did not map to SL2.50, mapped to chromosome 5 and 11 of LA1589, consistent with the occurrence of SV in these regions.  The detection of structural variation associated with introgressions highlights the need for more than one reference genome in order to interpret non-linear genome organization in re-sequencing analysis.