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.

The elucidation of the ripening pathways of climacteric fruits helps to reduce postharvest losses and improve fruit quality. Here, we report an integrative study on tomato ripening for two near-isogenic lines (NIL115 and NIL080) with Solanum pimpinellifolium LA0722 introgressions. A comprehensive analysis using phenotyping, molecular, transcript, and protein data were performed. Both NILs show improved fruit firmness and NIL115 also has longer shelf life compared to the cultivated parent. NIL115 differentially expressed a transcript from the APETALA2 ethylene response transcription factor family (AP2/ERF) with a potential role in fruit ripening. E4, another ERF, showed an upregulated expression in NIL115 as well as in the wild parent, and it was located physically close to a wild introgression. Other proteins whose expression levels changed significantly during ripening were identified, including an ethylene biosynthetic enzyme (ACO3) and a pectate lyase (PL) in NIL115, and an alpha-1,4 glucan phosphorylase (Pho1a) in NIL080. In this study, we provide insights into the effects of several genes underlying tomato ripening with potential impact on fruit shelf life. Data integration contributed to unraveling ripening-related genes, providing opportunities for assisted breeding.

The goal of this study was to estimate the single and joint effect of the basal region of chromosome 2 and centromeric region of chromosome 8 on morphological and fruit quality traits in tomato (Solanum lycopersicum). The analysis was performed in a population derived from a cross between Rio Grande of S. lycopersicum and LA1589 of S. pimpinellifolium that segregates for both genomic regions. Four major QTLs were found on chromosome 2 and three on chromosome 8, all of them related with morphological traits. QTLs for fruit shape index, proximal fruit end angle and distal fruit end protrusion showed epistatic interaction. Both genomic regions (fs2.1 and fs8.1) explained 62, 47 and 46 % of the phenotypic variability for fruit shape index, proximal fruit end angle and distal fruit end protrusion respectively. Minor QTLs were detected for other morphological and quality traits such as color, pH and fruit shelf life on chromosomes 2 and 8. Only single genomic region effects were found for quality trait. On the other hand, fs2.1 and fs8.1 regions control several fruit morphology attributes following a digenic linear additive model with epistatic interactions.