title: SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium.
abstract: Novel sequencing technologies were recently used to generate sequences from multiple melon (Cucumis melo L.) genotypes, enabling the in silico identification of large single nucleotide polymorphism (SNP) collections. In order to optimize the use of these markers, SNP validation and large-scale genotyping are necessary. In this paper, we present the first validated design for a genotyping array with 768 SNPs that are evenly distributed throughout the melon genome. This customized Illumina GoldenGate assay was used to genotype a collection of 74 accessions, representing most of the botanical groups of the species. Of the assayed loci, 91 % were successfully genotyped. The array provided a large number of polymorphic SNPs within and across accessions. This set of SNPs detected high levels of variation in accessions from this crop's center of origin as well as from several other areas of melon diversification. Allele distribution throughout the genome revealed regions that distinguished between the two main groups of cultivated accessions (inodorus and cantalupensis). Population structure analysis showed a subdivision into five subpopulations, reflecting the history of the crop. A considerably low level of LD was detected, which decayed rapidly within a few kilobases. Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in melon. Since many of the genotyped accessions are currently being used as the parents of breeding populations in various programs, this set of mapped markers could be used for future mapping and breeding efforts.
authors: COMAV, Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitat Politècnica de València (UPV), Camino de Vera s/n, 46022 Valencia, Spain.
authors: Cristina
authors: C
authors: Esteras
authors: Gelsomina
authors: G
authors: Formisano
authors: Cristina
authors: C
authors: Roig
authors: Aurora
authors: A
authors: Díaz
authors: José
authors: J
authors: Blanca
authors: Jordi
authors: J
authors: Garcia-Mas
authors: María Luisa
authors: ML
authors: Gómez-Guillamón
authors: Ana Isabel
authors: AI
authors: López-Sesé
authors: Almudena
authors: A
authors: Lázaro
authors: Antonio J
authors: AJ
authors: Monforte
authors: Belén
authors: B
authors: Picó
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis; D002874:Chromosome Mapping; D019662:Cucurbitaceae / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D005828:Genetics, Population; D018745:Genome, Plant; D005838:Genotype; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
chemical_list: D018744:DNA, Plant
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