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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]

The domestication process of tomato (Solanum lycopersium L.) resulted in very low variability for most agronomic interesting traits. In this work we explore the variability present in an unusual segregating population obtained by selfing a second cycle hybrid to identify and mapping novel Quantitative Trait Loci (QTL) for fruit quality traits. With this aim, a molecular characterization of the population by 130 single nucleotide polymorphism designed from genome sequencing of the parental lines was performed, which resulted in a genetic map and the location of seven novel QTL associated with the inheritance of the fruit quality traits: fruit diameter (R2 ranging from 0.179 to 0.207), fruit weight (R2 = 0.171) and fruit shape index (R2 ranging from 0.179 to 0.341). The analysis through the G-statistic allowed to define the consistence of the novel QTL identified, especially those associated to fruit shape index and fruit diameter. This approach has also led to the identification of new codominant molecular markers flanking the QTL which will be useful in future genetic breeding programs. [ABSTRACT FROM AUTHOR]

Key message: Reciprocal effects were found for tomato fruit quality and DNA methylation. The epigenetic identity of reciprocal hybrids indicates that DNA methylation might be one of the mechanisms involved in POEs. Crosses between different genotypes and even between different species are commonly used in plant breeding programs. Reciprocal hybrids are obtained by changing the cross direction (or the sexual role) of parental genotypes in a cross. Phenotypic differences between these hybrids constitute reciprocal effects (REs). The aim of this study was to evaluate phenotypic differences in tomato fruit traits and DNA methylation profiles in three inter- and intraspecific reciprocal crosses. REs were detected for 13 of the 16 fruit traits analyzed. The number of traits with REs was the lowest in the interspecific cross, whereas the highest was found in the cross between recombinant inbred lines (RILs) derived from the same interspecific cross. An extension of gene action analysis was proposed to incorporate parent-of-origin effects (POEs). Maternal and paternal dominance were found in four fruit traits. REs and paternal inheritance were found for epiloci located at coding and non-coding regions. The epigenetic identity displayed by the reciprocal hybrids accounts for the phenotypic differences among them, indicating that DNA methylation might be one of the mechanisms involved in POEs. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The introgression of genes from the wild species S. pimpinellifolium has the potential to improve tomato commercial varieties for numerous fruit quality traits. One of particular interest for fresh-market tomatoes is long shelf life (SL). Twenty-two near isogenic lines (NILs) were developed in three to four backcrosses using S. pimpinellifolium accession LA0722 as the donor parent, based on phenotypic selection for long SL and using a set of 28 SSRs for marker assisted selection. A total of 30 QTLs for fruit quality were found and 18 were subsequently validated in previous generations. A two year trial of the NILs homozygous for the LA0722 introgressions showed several novel QTLs. Fruit quality QTLs revealed an increased effect promoted by LA0722 alleles. A SL QTL was found on chromosome 9 and was consistent both years. A wild introgression on chromosome 3 showed a stable QTL for increased firmness and for yellow fruits. Therefore, the wild introgressions provide a source of variation with positive effects in fruit traits of commercial value. While obtaining new varieties, this strategy provided an effective method that integrates the QTL analysis and the prediction of positive alleles in wild germplasm. [ABSTRACT FROM AUTHOR]

Plant varieties are named and released based on distinct, unique and stable characteristics but may be maintained separately by genebanks or stock centers under separate accession identification numbers. Genetic heterogeneity of the original variety, genetic drift, failure to exclude cross pollination, and propagation error may erode the integrity of genetic resources. The availability of resequencing and genotyping data for duplicate samples enables an analysis to clarify the relationship between specific varieties or independently curated accessions of the same variety while also assessing the fidelity of germplasm maintenance. We accessed both Single Nucleotide Polymorphism (SNP) array genotypes and resequencing data for two important tomato varieties 'UC 82'and 'M82' that have been maintained as separate accessions in collections as important resources for the research and breeding communities. Our analysis of these data suggests that polymorphism rates from resequencing of cultivated tomato are overestimated in the literature due to heterozygous calls caused by either sequence error or coalignment of repetitive sequences. We defined a set of 32,352 robust SNPs from a file containing data for all samples and we compared the distribution of data with SNPs called from a genotyping array. For both analyses, intravariety variation was found in haplotype blocks, with the same haplotypes identified using SNPs detected from array and sequence data. The distribution pattern of variation across the entire genome sequence was similar for both 'UC 82'and 'M82'. Overall, the differences between distinct accessions of a variety were nearly as great as the differences between 'UC 82'and 'M82'. The similarities between 'UC82' and 'M82' range from 99.33% to 99.74% and are highly consistent with a common pedigree and shared selection from partially inbred progeny. The data also suggest that these tomato genetic resources have been propagated with high fidelity. [ABSTRACT FROM AUTHOR]