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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. [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]

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]

• Reciprocal hybrids showed the highest transcriptomic differences. • Reciprocal effect and heterosis were found among differentially expressed genes. • Correlations of multi-omics data differentiate homozygous vs heterozygous genotypes. • Tomato fruit metabolites correlated with genes with similar gene action. • Cross-direction is important in the F1's performance. External and internal attributes of fleshy fruits can be affected by phenomena like reciprocal effect and heterosis. The aim of this work is to study the genetic and molecular differences between two parental lines and their reciprocal hybrids, as well as the presence of heterosis and reciprocal effects. The tomato cultivars Querubín FCA and Gema FCA were selected as parental genotypes because this cross showed a high presence of heterosis and reciprocal effect. A combined investigation of the gene actions involved in gene expression profile and metabolic content was performed by analysing transcriptomic data and its integration with previously reported metabolic data. The reciprocal hybrids showed the most significant differences at the transcript levels (157 out of 200). Several transcripts which encode transcription factors were found, suggesting that ripe red fruits still have a highly regulated transcriptome. Furthermore, 41 differentially expressed genes connected to 11 metabolites were identified. Afterwards, transcript and metabolite gene actions were calculated. The results showed that the metabolic phenotypes of the parental genotypes are mainly explained by transcripts showing an additive gene action. In contrast, transcripts with non-additive gene actions mainly explained the heterotic metabolic phenotype in the hybrids. This work contributes to a deeper understanding of the molecular basis of reciprocal effect and heterosis in plant crops. [ABSTRACT FROM AUTHOR]