title: High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping.
abstract: BACKGROUND
  Cucurbita 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).
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  Our 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.
authors.affiliation: Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Esteras
authors.forename: Pedro
authors.initials: P
authors.lastname: Gómez
authors.forename: Antonio J
authors.initials: AJ
authors.lastname: Monforte
authors.forename: José
authors.initials: J
authors.lastname: Blanca
authors.forename: Nelly
authors.initials: N
authors.lastname: Vicente-Dólera
authors.forename: Cristina
authors.initials: C
authors.lastname: Roig
authors.forename: Fernando
authors.initials: F
authors.lastname: Nuez
authors.forename: Belén
authors.initials: B
authors.lastname: Picó
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping / Q000379:methods*; D018553:Cucumis sativus / Q000235:genetics; D028464:Cucurbita / Q000033:anatomy & histology / Q000235:genetics*; D020224:Expressed Sequence Tags / Q000378:metabolism; D035264:Flowers / Q000033:anatomy & histology / Q000235:genetics; D005638:Fruit / Q000033:anatomy & histology / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D060005:Genotyping Techniques / Q000379:methods*; D006824:Hybridization, Genetic; D018895:Microsatellite Repeats / Q000235:genetics; D010858:Pigmentation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*; D026801:Synteny / Q000235:genetics
chemical_list: D005819:Genetic Markers