title: Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa).
abstract: Cultivated strawberry (Fragaria × ananassa) is a genetically complex allo-octoploid crop with 28 pairs of chromosomes (2n = 8x = 56) for which a genome sequence is not yet available. The diploid Fragaria vesca is considered the donor species of one of the octoploid sub-genomes and its available genome sequence can be used as a reference for genomic studies. A wide number of strawberry cultivars are stored in ex situ germplasm collections world-wide but a number of previous studies have addressed the genetic diversity present within a limited number of these collections. Here, we report the development and application of two platforms based on the implementation of Diversity Array Technology (DArT) markers for high-throughput genotyping in strawberry. The first DArT microarray was used to evaluate the genetic diversity of 62 strawberry cultivars that represent a wide range of variation based on phenotype, geographical and temporal origin and pedigrees. A total of 603 DArT markers were used to evaluate the diversity and structure of the population and their cluster analyses revealed that these markers were highly efficient in classifying the accessions in groups based on historical, geographical and pedigree-based cues. The second DArTseq platform took benefit of the complexity reduction method optimized for strawberry and the development of next generation sequencing technologies. The strawberry DArTseq was used to generate a total of 9,386 SNP markers in the previously developed '232' × '1392' mapping population, of which, 4,242 high quality markers were further selected to saturate this map after several filtering steps. The high-throughput platforms here developed for genotyping strawberry will facilitate genome-wide characterizations of large accessions sets and complement other available options.
authors.affiliation: Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140, Málaga, Spain.
authors.forename: José F
authors.initials: JF
authors.lastname: Sánchez-Sevilla
authors.affiliation: INRA, UMR 1332 BFP, F-33140 Villenave d'Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d'Ornon, France.
authors.forename: Aniko
authors.initials: A
authors.lastname: Horvath
authors.affiliation: Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC), Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, 29071, Málaga, Spain.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Botella
authors.affiliation: INRA, UMR 1332 BFP, F-33140 Villenave d'Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d'Ornon, France.
authors.forename: Amèlia
authors.initials: A
authors.lastname: Gaston
authors.affiliation: University of Florida, Horticultural Sciences Department, Gainesville, Florida, 32611, United States of America.
authors.forename: Kevin
authors.initials: K
authors.lastname: Folta
authors.affiliation: Diversity Arrays Technology Pty Ltd, Building 3, University of Canberra, Bruce, ACT 2617, Australia.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kilian
authors.affiliation: INRA, UMR 1332 BFP, F-33140 Villenave d'Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d'Ornon, France.
authors.forename: Beatrice
authors.initials: B
authors.lastname: Denoyes
authors.affiliation: Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140, Málaga, Spain.|University of Florida, Horticultural Sciences Department, Gainesville, Florida, 32611, United States of America.
authors.forename: Iraida
authors.initials: I
authors.lastname: Amaya
mesh_terms: D002874:Chromosome Mapping; D016000:Cluster Analysis; D004171:Diploidy; D031985:Fragaria / Q000235:genetics*; D008040:Genetic Linkage; D014644:Genetic Variation; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy