Articolo in rivista, 2018, ENG, 10.1093/dnares/dsx045

Whole-genome re-sequencing of two Italian tomato landraces

Tranchida-Lombardo V., Aiese Cigliano R., Anzar i., Landi S., Palombieri S., Colantuono C., Bostan H., Termolino P., Aversano R., Batelli G., Cammareri M., Carputo D.,Chiusano ML. Conicella C., Consiglio F., D'Agostino N., De Palma M., Di Matteo A., Grandillo S., Sanseverino W., Tucci M., Grillo S.

National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Universita` 133, 80055 Portici, Italy, Sequentia Biotech Calle Comte D'Urgel 240, 08036 Barcelona, Spain, Department of Agricultural Sciences, University of Naples Federico II, Via Universita' 100, 80055 Portici, Italy, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro Di Ricerca Orticultura e Florovivaismo (CREAOF), Via Cavalleggeri, 25, 84098 Pontecagnano Faiano SA, Italy

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 65.8M and 56.4M of 30-150bp 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.

DNA research 25 (4), pp. 149–160

Keywords

traditional varieties, SNPs, next generation sequencing, genomic platform

CNR authors

Tranchida Lombardo Valentina, Palombieri Samuela, Landi Simone, Tucci Marina, Grandillo Silvana, Grillo Maria Stefania, Consiglio Maria Federica, Cammareri Maria, De Palma Monica, Batelli Giorgia, Termolino Pasquale, Conicella Clara

CNR institutes

IBBR – Istituto di Bioscienze e Biorisorse