Fruit weight (FW) and shelf life (SL) are important traits in commercial fresh market tomatoes. A tomato RIL population was developed by antagonistic and divergent selection for both traits from an interspecific cross between the Solanum lycopersicum L. cv. “Caimanta” and the S. pimpinellifolium L. accession “LA0722”. The objective of this work was to evaluate phenotypic and genetic components for FW and SL. Phenotypic data from RILs were collected during 3-year trials. Sixteen SSR, 62 InDels developed based on the genome sequences of “Caimanta” and “LA0722”, and four functional markers for fruit size genes were used. FW and SL had a significant genetic variability, and both traits showed a genotype by year interaction. Genome-wide molecular characterization of the population demonstrated that is genetically structured according to FW. Marker data was used to study changes on allelic frequencies at loci between the phenotypic extreme group of RILs for FW and SL. Twenty four markers were associated to FW, the LC gene in chromosome 2 and other six markers in chromosomes 1, 2, 6, and 11 presented the most significant associations. Finally, we reported three new genomic regions located on chromosomes 9, 10 and 12 that underlie SL in tomato.

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 F2 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.