title: An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing.
abstract: Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species.
  
  
  
  We report the Genotyping-by-sequencing analysis of a RIL population developed from the inter subspecific cross Zucchini x Scallop (ssp. pepo x ssp. ovifera). Several thousands of SNP markers were identified and genotyped, followed by the construction of a high-density linkage map based on 7,718 SNPs (average of 386 markers/linkage group) covering 2,817.6 cM of the whole genome, which is a great improvement with respect to previous maps. A QTL analysis was performed using phenotypic data obtained from the RIL population from three environments. In total, 48 consistent QTLs for vine, flowering and fruit quality traits were detected on the basis of a multiple-environment analysis, distributed in 33 independent positions in 15 LGs, and each QTL explained 1.5-62.9% of the phenotypic variance. Eight major QTLs, which could explain greater than 20% of the phenotypic variation were detected and the underlying candidate genes identified.
  
  
  
  Here we report the first SNP saturated map in the species, anchored to the physical map. Additionally, several consistent QTLs related to early flowering, fruit shape and length, and rind and flesh color are reported as well as candidate genes for them. This information will enhance molecular breeding in C. pepo and will assist the gene cloning underlying the studied QTLs, helping to reveal the genetic basis of the studied processes in squash.
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: Javier
authors.initials: J
authors.lastname: Montero-Pau
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: José
authors.initials: J
authors.lastname: Blanca
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.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: Eva Ma
authors.initials: EM
authors.lastname: Martínez-Pérez
authors.affiliation: Instituto de Investigación y Formación Agraria y Pesquera (IFAPA). Área de Mejora y Biotecnología de cultivos. Camino San Nicolás 1, 04745, La Mojonera, Almería, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Gómez
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ciudad Politécnica de la Innovación (CPI), Ed. 8E, C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain.
authors.forename: Antonio J
authors.initials: AJ
authors.lastname: Monforte
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. jcanizares@upv.es.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Cañizares
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. mpicosi@btc.upv.es.
authors.forename: Belén
authors.initials: B
authors.lastname: Picó
mesh_terms: D002874:Chromosome Mapping; D028464:Cucurbita / Q000235:genetics* / Q000254:growth & development; D035264:Flowers / Q000254:growth & development; D005638:Fruit / Q000235:genetics* / Q000378:metabolism; D023281:Genomics; D060005:Genotyping Techniques; D010641:Phenotype; D010858:Pigmentation; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D017421:Sequence Analysis
keywords: Candidate genes; Cartography; Cucurbita pepo; GBS; Phenotyping; RIL