Dataset Information

Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits.

ABSTRACT: Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65.8?M and 56.4?M of 30-150?bp paired-end reads, respectively. New contigs including reads that could not be mapped to the tomato reference genome were assembled, and a total of 43, 054 and 44, 579 gene loci were annotated in COR and LUC. Both genomes showed novel regions with similarity to Solanum pimpinellifolium and Solanum pennellii. In addition to small deletions and insertions, 2, 000 and 1, 700 single nucleotide polymorphisms (SNPs) could exert potentially disruptive effects on 1, 371 and 1, 201 genes in COR and LUC, respectively. A detailed survey of the SNPs occurring in fruit quality, shelf life and stress tolerance related-genes identified several candidates of potential relevance. Variations in ethylene response components may concur in determining peculiar phenotypes of COR and LUC.

SUBMITTER: Tranchida-Lombardo V

PROVIDER: S-EPMC5909465 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits.

Tranchida-Lombardo Valentina V Aiese Cigliano Riccardo R Anzar Irantzu I Landi Simone S Palombieri Samuela S Colantuono Chiara C Bostan Hamed H Termolino Pasquale P Aversano Riccardo R Batelli Giorgia G Cammareri Maria M Carputo Domenico D Chiusano Maria Luisa ML Conicella Clara C Consiglio Federica F D'Agostino Nunzio N De Palma Monica M Di Matteo Antonio A Grandillo Silvana S Sanseverino Walter W Tucci Marina M Grillo Stefania S

DNA research : an international journal for rapid publication of reports on genes and genomes 20180401 2

Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences ...[more]

PMID: 29149280

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Project description:Increased interest toward 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.

Project description:The conservation and characterization of landraces have key roles in the safeguarding and valorization of agrobiodiversity. Indeed, these plant genetic resources represent an important crop heritage with quality and sensory characteristics that can be of great use to consumers and industry. In addition, the preservation of genetic resources from the risk of progressive genetic erosion, and the enhancement of their potential can contribute to food security and improve the nutritional value of food. Accordingly, this study aimed to investigate a collection of Sardinian tomato landraces for parameters that have determinant roles in evaluating their responses to conservation, and therefore to consumer acceptance. Six Sardinian landraces and two commercial varieties were cultivated in a two-years off-season trial, harvested at two different maturity stages (turning, red-ripe) and characterized using 14 fruit-related quality parameters that define the marketability, nutritional value, and flavor of the fruit. Data were collected at intervals of 10 days, starting from the harvest date and over 30 days of storage under refrigeration. The simultaneous analysis of all the qualitative characteristics for the different genotypes allowed to clearly differentiate the local varieties from the commercial varieties and a few landraces emerged for their satisfactory performances, e.g. "Tamatta kaki" ad "Tamatta groga de appiccai". In particular, the "Tamatta groga de appiccai" showed satisfactory lycopene content at marketable stages (average 5.65 mg 100g-1 FF), a peculiar orange-pink color with the highest hue angle values (range: H°T0 = 72.55-H°T30 = 48.26), and the highest firmness among the landraces of the red-ripe group (range: EpT0 = 1.64-EpT30 = 0.54 N mm-1). These results highlight the potential of some of the Sardinian tomato landraces for developing new varieties or promoting their direct valorization in local markets and could considerably increase the effectiveness and efficiency of agrobiodiversity conservation strategies.

Project description: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.

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Dataset Information

Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits.

Publications

Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits.

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