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Highlights • Resequencing of "Caimanta" and "LA0722" reveals polymorphisms across the tomato genome. • Multiple sequence comparisons revealed several features relevant for breeding goals. • Development of DNA markers for easily accessed genotyping platforms. • Linkage map construction as genetic reference for QTL detection and resource for MAS. Abstract Next generation sequencing technologies have become affordable for most plant breeding programs. In this study we sequenced the entire genome of the Solanum lycopersicum L. cultivar Caimanta and S. pimpinellifolium L. accession LA0722 with assembly relative to the Heinz 1706 reference version SL2.50. We present 1) analysis of the amount and distribution of polymorphism in "Caimanta" and "LA0722", 2) examination of alleles in candidate genes affecting disease resistance, fruit shape, fruit weight and fruit quality and 3) development of molecular markers to construct a genetic linkage map based on a F 2 population. A total of 1,397,518 polymorphisms were detected in the comparison between "Caimanta" and "LA0722". A resistant allele for Rx4/ Xv3 was detected by sequence, and confirmed through inoculation. - We developed a set of insertion/deletion (InDel) DNA markers that can be multiplexed and scored using easily accessed genotyping platforms. These markers were used to construct a genetic linkage map. We demonstrate that the whole genome sequencing of parental lines can be successfully used to reveal phenotypes and characterize a reference population through easily accessed genotyping strategies. [ABSTRACT FROM AUTHOR]

Highlights: [•] QTLs for fruit quality traits segregated in a tomato interspecific backcross. [•] Some QTLs were consistent across several backcross generations. [•] QTLs with recessive effects from S. pimpinellifolium LA722 prolonged shelf life. [•] New genetic resources for tomato quality breeding programs are reported. [ABSTRACT FROM AUTHOR]

Abstract: The tomato fruit quality results of biochemical and physiological changes that occur during the ripening process. Although, the pericarp total protein profiles are less polymorphic than DNA-based markers the polymorphism in those could be directly associated with fruit quality traits. The aim of this work was to identify associations between polymorphic polypeptides from fruit pericarp at two ripening stages and fruit quality traits evaluated in two segregating populations of tomato. A cross between a normal ripening cultivar of Solanum lycopersicum (C, Caimanta) and a genotype carrying the nor (non ripening) gene (N) as well as a cross between Caimanta and a cherry type tomato of S. lycopersicum var. cerasiforme (Ce) showed genetic variance for several fruit quality traits such as fruit weight, shape, solids soluble content, acidity, color and fruit shelf life. The quantitative variations observed at phenotypic level had correspondence with the polymorphism detected in the protein profiles. Indeed, the polymophic polypeptides associated with quality fruit traits and fruit shelf life would be useful to assist tomato breeding programs as protein molecular markers. [Copyright &y& Elsevier]