title: Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pools.
abstract: Melon (Cucumis melo L.) is one of the most important horticultural species, which includes several taxonomic groups. With the advent of next-generation sequencing, single nucleotide polymorphism (SNP) markers are widely used in the study of genetic diversity and genomics.
  
  
  
  We report the first successful application of genotyping-by-sequencing (GBS) technology in melon. We detected 25,422 SNPs by the analysis of 72 accessions collected in Apulia, a secondary centre of diversity in Southern Italy. Analyses of genetic structure, principal components, and hierarchical clustering support the identification of three distinct subpopulations. One of them includes accessions known with the folk name of 'carosello', referable to the chate taxonomic group. This is one of the oldest domesticated forms of C. melo, once widespread in Europe and now exposed to the risk of genetic erosion. The second subpopulation contains landraces of 'barattiere', a regional vegetable production that was never characterized at the DNA level and we show was erroneously considered another form of chate melon. The third subpopulation includes genotypes of winter melon (C. melo var. inodorus). Genetic analysis within each subpopulation revealed patterns of diversity associated with fruit phenotype and geographical origin. We used SNP data to describe, for each subpopulation, the average linkage disequilibrium (LD) decay, and to highlight genomic regions possibly resulting from directional selection and associated with phenotypic variation.
  
  
  
  We used GBS to characterize patterns of genetic diversity and genomic features within C. melo. We provide useful information to preserve endangered gene pools and to guide the use of germplasm in breeding. Finally, our findings lay a foundation for molecular breeding approaches and the identification of genes underlying phenotypic traits.
authors.affiliation: Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy. stefano.pavan@uniba.it.
authors.forename: Stefano
authors.identifier: 0000-0002-3666-7291
authors.initials: S
authors.lastname: Pavan
authors.affiliation: Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy.
authors.forename: Angelo Raffaele
authors.initials: AR
authors.lastname: Marcotrigiano
authors.affiliation: Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Ciani
authors.affiliation: Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy.
authors.forename: Rosa
authors.initials: R
authors.lastname: Mazzeo
authors.affiliation: Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy.
authors.forename: Vito
authors.initials: V
authors.lastname: Zonno
authors.affiliation: Sequentia Biotech, Barcelona, Spain.
authors.forename: Valentino
authors.initials: V
authors.lastname: Ruggieri
authors.affiliation: Department of the Sciences of Agriculture, Food and Environment, University of Foggia, via Napoli 25, I-71100, Foggia, Italy.
authors.forename: Concetta
authors.initials: C
authors.lastname: Lotti
authors.affiliation: Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Ricciardi
mesh_terms: D028463:Cucumis melo / Q000235:genetics*; D005788:Gene Pool; D055106:Genome-Wide Association Study; D060005:Genotyping Techniques; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: Cucumis melo; Genetic diversity; Genomics; Genotyping-by-sequencing; Molecular breeding