title: Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh).
abstract: High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Bianco
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cestaro
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
authors.forename: Daniel James
authors.initials: DJ
authors.lastname: Sargent
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Banchi
authors.affiliation: CNAG - Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona, Spain.
authors.forename: Sophia
authors.initials: S
authors.lastname: Derdak
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy; Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands.
authors.forename: Mario
authors.initials: M
authors.lastname: Di Guardo
authors.affiliation: DipSA - University of Bologna, Bologna, Italy.
authors.forename: Silvio
authors.initials: S
authors.lastname: Salvi
authors.affiliation: Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands.
authors.forename: Johannes
authors.initials: J
authors.lastname: Jansen
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Viola
authors.affiliation: CNAG - Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona, Spain.
authors.forename: Ivo
authors.initials: I
authors.lastname: Gut
authors.affiliation: INRA, UMR1345 Institut de Recherche en Horticulture and Semences, Beaucouzé, France.
authors.forename: Francois
authors.initials: F
authors.lastname: Laurens
authors.affiliation: Plant & Food Research, Palmerston North Research Centre, Palmerston North, New Zealand.
authors.forename: David
authors.initials: D
authors.lastname: Chagné
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands.
authors.forename: Eric
authors.initials: E
authors.lastname: van de Weg
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
authors.forename: Michela
authors.initials: M
authors.lastname: Troggio
mesh_terms: D019295:Computational Biology / Q000379:methods; D005819:Genetic Markers; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D027845:Malus / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results
chemical_list: D005819:Genetic Markers