Cucurbigene: New genomic tools for Squash (Cucurbita spp.) breeding: transcriptome, genetic map, SNP collections and high throughput genotyping platforms applied to the competitive development of new cultivars, with improve fruit quality and disease resistance.
Cucurbita spp (Cucurbitaceae), include squashes, gourds and pumpkins. This genus contains some of the earliest domesticated plant species. The “Zucchini” types of C. pepo rank among the highest valued vegetables world-wide, and other C. pepo and related Cucurbita spp., mostly C. maxima and C. moschata, are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding.
The main focus of CUCURBIGENE is developing genomic tools to facilitate the competitive development of new Cucurbita cultivars. Part of the activities of this project has been funded by the Spanish government through two INIA projects (RTA2008-00035-C02-02 and RTA2011-00044-C02-02), cofunded with FEDER funds, started in 2008. It involves two groups of the COMAV-Polytechnic University of Valencia (COMAV-UPV), the Cucurbits Breeding Group and the Genomics and Bioinformatics group. In these INIA projects a research group from IFAPA (área de Mejora y Biotecnología de cultivos) is also participating, collaborating with COMAV in some mapping activities and in the development of a new RILs mapping population. Both groups (COMAV and IFAPA) provided RNA from different tissues of Cucurbita, mainly fruits subjected to various pre and postharvest treatments, to generate an improved version of the Cucurbita transcriptome. The research group "Genetics of Vegetable crops", at the University of Almería (UAL), has also participated in the generation of the new transcriptome v2, providing RNA from different fruit tissues and conditions (financed through grant AGL2011-30568-C02-02/ALI).
The genomic tools developed and available at this database are (i) the first transcriptome of the genus and its annotation v1 (ii) A new improved version of these transcriptome enriched in fruit transcripts and its annotation v2 (iii) the first massive SSR and SNP collection, variable within and between cultivars, subspecies, and species (iv) the use of these resources to produce the first SNP-based genetic map (v) and the first high –throughput golden gate genotyping platform.
All these tools are being essential to assist a competitive breeding process in the species obtaining varieties with resistance to pests and diseases and with improved fruit quality
PLEASE READ BEFORE ACCESSING THE DATA
As a public service, the sequence data from the CucurGene project generated by COMAV are being made available before scientific publication. These pre-publication data are preliminary and may contain errors. COMAV provides these data in good faith, but makes no warranty, expressed or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used.
This data is made available before its publication with the understanding that users will respect the rights of those who contributed to produce it. The users are allowed to use it, but they are not allowed to publish it without the authorization of the owners of this web site.
The data may be freely downloaded and used by all who respect the restrictions in the previous paragraphs. While still in waiting period status, the data should not be redistributed or repackaged without permission from COMAV.
- Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). José Blanca, Joaquín Cañizares, Cristina Roig, Pello Ziarsolo, Fernando Nuez and Belén Picó/. BMC Genomics 2011, 12:104 doi:10.1186/1471-2164-12-104.
- High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping. Cristina Esteras, Pedro Gomez, Antonio J Monforte, Jose Blanca, Nelly Vicente-Dolera, Cristina Roig, Fernando Nuez and Belen Pico. BMC Genomics 2012, 13:80 doi:10.1186/1471-2164-13-80