Abstract
BackgroundCucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL).ResultsWe herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations.ConclusionOur results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in the coding regions of genes involved in different physiological processes. The platform will also be useful for future mapping and diversity studies, and will be essential in order to accelerate the process of breeding new and better-adapted squash varieties.
Highlights
Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae
Design of the 384-Single Nucleotide Polymorphisms (SNP) GoldenGate genotyping platform Of the 19,980 SNP identified in silico [20], 9,043 were monomorphic within and polymorphic between the two parents of the map (Zucchini MU-CU-16 and Scallop Universitat Politècnica de València (UPV)-196) (Figure 1) and were not located in highly variable regions
The Illumina scores and annotation details of the corresponding unigenes are described in Additional File 3: “Annotation data and map position of the 384 loci included in the GoldenGate platform”
Summary
Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. There are few genomic tools available for Cucurbita, unlike other cucurbits, such as watermelon (Citrullus lanatus (Thunb.) Matsum & Nakai), cucumbers (Cucumis sativus L.) and melons (Cucumis melo L.), for which new mapping populations, dense genetic maps [4,5,6,7], microarrays [8,9], reverse genetics platforms [10,11], transcriptomes [12,13] and even whole genome sequences have already been generated [14,15,16]. SSR, continue to be widely used in studies with no need for automation due to their co-dominant and multiallelic nature
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