Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa)

Publication Overview
TitleDiversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa)
AuthorsSánchez-Sevilla JF, Horvath A, Botella MA, Gaston A, Folta K, Kilian A, Denoyes B, Amaya I
TypeJournal Article
Journal NamePloS one
Volume10
Issue12
Year2015
Page(s)e0144960
CitationSánchez-Sevilla JF, Horvath A, Botella MA, Gaston A, Folta K, Kilian A, Denoyes B, Amaya I. Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa). PloS one. 2015; 10(12):e0144960.

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.

Features
This publication contains information about 1,798 features:
Feature NameUniquenameType
F15847-8:G>TF15847-8:G>Tgenetic_marker
F15890-61:A>C-F15890-61:A>C-genetic_marker
F15893-39:C>TF15893-39:C>Tgenetic_marker
F15914-66:C>TF15914-66:C>Tgenetic_marker
F16196-51:T>A-F16196-51:T>A-genetic_marker
F16208-36:T>C-F16208-36:T>C-genetic_marker
F16215-36:T>CF16215-36:T>Cgenetic_marker
F16224-59:A>CF16224-59:A>Cgenetic_marker
F16242-6:T>AF16242-6:T>Agenetic_marker
F16288-49:A>T-F16288-49:A>T-genetic_marker
F16313-48:T>GF16313-48:T>Ggenetic_marker
F16320-23:T>AF16320-23:T>Agenetic_marker
F16356-66:A>GF16356-66:A>Ggenetic_marker
F16656-16:C>TF16656-16:C>Tgenetic_marker
F16662-43:T>CF16662-43:T>Cgenetic_marker
F16684-35:T>G-F16684-35:T>G-genetic_marker
F16737-24:T>CF16737-24:T>Cgenetic_marker
F16749-52:G>CF16749-52:G>Cgenetic_marker
F16766-57:A>G-F16766-57:A>G-genetic_marker
F16832-46:G>AF16832-46:G>Agenetic_marker
F16981-44:C>TF16981-44:C>Tgenetic_marker
F17043-39:C>TF17043-39:C>Tgenetic_marker
F17083-34:G>AF17083-34:G>Agenetic_marker
F17108-24:T>AF17108-24:T>Agenetic_marker
F17126-15:T>CF17126-15:T>Cgenetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
Strawberry-232x1392-F1-2015
Stocks
This publication contains information about 3 stocks:
Stock NameUniquenameType
232232accession
13921392accession
232_x_1392232_x_1392population