New Genomic Tools For Breeding Cucurbita spp

The genus Cucurbita is one of the most variable within the Cucurbitaceae family, comprising five cultivated and many wild species. The “Zucchini” type of C. pepo ranks among the highest valued vegetables worldwide, and other Cucurbita spp (pumpkins and squashes) are rich sources of fat and vitamins and economically important as rootstocks. Despite their agricultural and biological importance, the lack of genomic resources has severely hampered molecular breeding in these species.

To overcome this limitation, we obtained the first transcriptome of C. pepo by 454 sequencing. The assembly of approximately 500.000 ESTs from multi-tissue libraries of two main commercial genotypes (Zucchini, subsp. pepo, and Scallop, subsp. ovifera) yielded 49.610 unigenes. Currently, we have substantially improved this transcriptome by pair-end Illumina sequencing of transcripts from fruit tissues, yielding a total of 103,635 unigenes longer than 500 bp. Transcriptome sequencing in these genotypes with contrasting phenotypes allowed the identification of a large set of SNPs. High throughput genotyping with this SNP array has facilitate the construction of two genetic maps used to map QTLs involved in flowering and fruit quality traits. Genotyping arrays are also accelerating the development of new mapping populations such as RILs and ILs.

New SNPs collections are being generated by re-sequencing several pools of C. pepo genotypes, of cultivars and landraces of the related species C. moschata, a reservoir of resistance and quality genes, and also of pools of wild Cucurbita species. Most of this information is available at http://cucurbigene.net. These new genomic tools will enhance Cucurbita breeding efficiency.