Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools. In order to identify QTLs controlling fruit quality, a recombinant inbred line population was developed using two commercial cultivars as parental lines: “Védrantais”, from the cantalupensis group, and “Piel de Sapo”, from the inodorus group. Both have desirable quality traits for the market, but their fruits differ in traits such as rind and flesh color, sugar content, ripening behavior, size and shape. We used a genotyping-by-sequencing strategy to construct a dense genetic map, which included around five thousand variants distributed in 824 bins. The RIL population was phenotyped for quality and morphology traits, and we mapped 33 stable QTLs involved in sugar and carotenoid content, fruit and seed morphology and major loci controlling external color of immature fruit and mottled rind. The median confidence interval of the QTLs was 942 kb, suggesting that the high density of the genetic map helped in increasing the mapping resolution. Some of these intervals contained less than a hundred annotated genes, and an integrative strategy combining gene expression and resequencing data enabled identification of candidate genes for some of these traits. Several QTLs controlling fruit quality traits in melon were identified and delimited to narrow genomic intervals, using a RIL population and a GBS-based genetic map.

Genome Wide Association Studies (GWAS) have been recently used to dissect complex quantitative traits and identify candidate genes affecting phenotype variation of polygenic traits. In order to map loci controlling variation in tomato marketable and nutritional fruit traits, we used a collection of 96 cultivated genotypes, including Italian, Latin American, and other worldwide-spread landraces and varieties. Phenotyping was carried out by measuring ten quality traits and metabolites in red ripe fruits. In parallel, genotyping was carried out by using the Illumina Infinium SolCAP array, which allows data to be collected from 7,720 single nucleotide polymorphism (SNP) markers. The Mixed Linear Model used to detect associations between markers and traits allowed population structure and relatedness to be evidenced within our collection, which have been taken into consideration for association analysis. GWAS identified 20 SNPs that were significantly associated with seven out of ten traits considered. In particular, our analysis revealed two markers associated with phenolic compounds, three with ascorbic acid, β-carotene and trans-lycopene, six with titratable acidity, and only one with pH and fresh weight. Co-localization of a group of associated loci with candidate genes/QTLs previously reported in other studies validated the approach. Moreover, 19 putative genes in linkage disequilibrium with markers were found. These genes might be involved in the biosynthetic pathways of the traits analyzed or might be implied in their transcriptional regulation. Finally, favourable allelic combinations between associated loci were identified that could be pyramided to obtain new improved genotypes. Our results led to the identification of promising candidate loci controlling fruit quality that, in the future, might be transferred into tomato genotypes by Marker Assisted Selection or genetic engineering, and highlighted that intraspecific variability might be still exploited for enhancing tomato fruit quality.

During its evolution and domestication Solanum lycopersicum has undergone various genetic ‘bottlenecks’ and extreme inbreeding of limited genotypes. In Europe the tomato found a secondary centre for diversification, which resulted in a wide array of fruit shape variation given rise to a range of landraces that have been cultivated for centuries. Landraces represent a reservoir of genetic diversity especially for traits such as abiotic stress resistance and high fruit quality. Information about the variation present among tomato landrace populations is still limited. A collection of 123 genotypes from different geographical areas was established with the aim of capturing a wide diversity. Eighteen morphological traits were evaluated, mainly related to the fruit. About 45% of morphological variation was attributed to fruit shape, as estimated by the principal component analysis, and the dendrogram of relatedness divided the population in subgroups mainly on the basis of fruit weight and locule number. Genotyping was carried out using the tomato array platform SolCAP able to interrogate 7,720 SNPs. In the whole collection 87.1% markers were polymorphic but they decreased to 44–54% when considering groups of genotypes with different origin. The neighbour-joining tree analysis clustered the 123 genotypes into two main branches. The STRUCTURE analysis with K = 3 also divided the population on the basis of fruit size. A genomic-wide association strategy revealed 36 novel markers associated to the variation of 15 traits. The markers were mapped on the tomato chromosomes together with 98 candidate genes for the traits analyzed. Six regions were evidenced in which candidate genes co-localized with 19 associated SNPs. In addition, 17 associated SNPs were localized in genomic regions lacking candidate genes. The identification of these markers demonstrated that novel variability was captured in our germoplasm collection. They might also provide a viable indirect selection tool in future practical breeding programs.

High temperature is one of the most detrimental abiotic stresses in tomatoes. Many studies highlighted that even small increases in temperature can alter the plant reproductive system, causing a significant reduction in tomato yield. The aim of this study was to exploit the phenotypic and genomic variations of a tomato landrace collection grown at high temperatures. Fifteen genotypes were selected as the best performing in two experimental fields. The selection was based on six yield-related traits, including flower earliness, number of flowers per inflorescence, fruit set, number of fruit per plant, fruit weight and yield per plant. In order to identify markers targeting traits that could be highly influenced by adverse climate conditions, such as flowering and fruit setting, an association mapping approach was undertaken exploiting a tomato high-throughput genomic array. The phenotypic variability observed allowed us to identify a total of 15 common markers associated with the studied traits. In particular, the most relevant associations co-localized with genes involved in the floral structure development, such as the style2.1 gene, or with genes directly involved in the response to abiotic stresses. These promising candidate genes will be functionally validated and transferred to a cultivated tomato to improve its performance under high temperatures.

Increased interest towards traditional tomato varieties is fueled by the need to rescue desirable organoleptic traits and to improve the quality of fresh and processed tomatoes in the market. In addition, the phenotypic and genetic variation preserved in tomato landraces represents a means to understand the genetic basis of traits related to health and organoleptic aspects and improve them in modern varieties. To establish a framework for this approach, we studied the content of several metabolites in a panel of Italian tomato landraces categorized into three broad fruit type classes (flattened/ribbed, pear/oxheart, round/elongate). Three modern hybrids, corresponding to the three fruit shape typologies, were included as reference. Red ripe fruits were morphologically characterized and biochemically analyzed for their content in glycoalkaloids, phenols, amino acids and Amadori products. The round/elongate types showed a higher content in glycoalkaloids, whereas flattened types had higher levels of phenolic compounds. Flattened tomatoes were also rich in total amino acids and in particular in glutamic acid. Multivariate analysis of amino acid content clearly separated the three classes of fruit types. Making allowance of the very low number of genotypes, phenotype-marker relationships were analyzed after retrieving single nucleotide polymorphisms (SNPs) among the landraces available in the literature. Sixty-six markers were significantly associated with the studied traits. The positions of several of these SNPs showed correspondence with already described genomic regions and QTLs supporting the reliability of the association. Overall the data indicated that significant changes in quality-related metabolites occur depending on the genetic background in traditional tomato germplasm, frequently according to specific fruit shape categories. Such a variability is suitable to harness association mapping for metabolic quality traits using this germplasm as an experimental population, paving the way for investigating their genetic/molecular basis and facilitating breeding for quality-related compounds in tomato fruits.

Melon (Cucumis melo L.) is one of the most important horticultural species, which includes several taxonomic groups. With the advent of next-generation sequencing, single nucleotide polymorphism (SNP) markers are widely used in the study of genetic diversity and genomics. We report the first successful application of genotyping-by-sequencing (GBS) technology in melon. We detected 25,422 SNPs by the analysis of 72 accessions collected in Apulia, a secondary centre of diversity in Southern Italy. Analyses of genetic structure, principal components, and hierarchical clustering support the identification of three distinct subpopulations. One of them includes accessions known with the folk name of ‘carosello’, referable to the chate taxonomic group. This is one of the oldest domesticated forms of C. melo, once widespread in Europe and now exposed to the risk of genetic erosion. The second subpopulation contains landraces of ‘barattiere’, a regional vegetable production that was never characterized at the DNA level and we show was erroneously considered another form of chate melon. The third subpopulation includes genotypes of winter melon (C. melo var. inodorus). Genetic analysis within each subpopulation revealed patterns of diversity associated with fruit phenotype and geographical origin. We used SNP data to describe, for each subpopulation, the average linkage disequilibrium (LD) decay, and to highlight genomic regions possibly resulting from directional selection and associated with phenotypic variation. We used GBS to characterize patterns of genetic diversity and genomic features within C. melo. We provide useful information to preserve endangered gene pools and to guide the use of germplasm in breeding. Finally, our findings lay a foundation for molecular breeding approaches and the identification of genes underlying phenotypic traits.