title: Large SNP arrays for genotyping in crop plants.
abstract: Genotyping with large numbers of molecular markers is now an indispensable tool within plant genetics and breeding. Especially through the identification of large numbers of single nucleotide polymorphism (SNP) markers using the novel high-throughput sequencing technologies, it is now possible to reliably identify many thousands of SNPs at many different loci in a given plant genome. For a number of important crop plants, SNP markers are now being used to design genotyping arrays containing thousands of markers spread over the entire genome and to analyse large numbers of samples. In this article, we discuss aspects that should be considered during the design of such large genotyping arrays and the analysis of individuals. The fact that crop plants are also often autopolyploid or allopolyploid is given due consideration. Furthermore, we outline some potential applications of large genotyping arrays including  high-density genetic mapping, characterization (fingerprinting) of genetic material and breeding-related aspects such as  association studies and genomic selection.
authors.affiliation: TraitGenetics GmbH, Am Schwabeplan 1b, D-06466 Gatersleben, Germany. ganal@traitgenetics.de
authors.forename: Martin W
authors.initials: MW
authors.lastname: Ganal
authors.forename: Andreas
authors.initials: A
authors.lastname: Polley
authors.forename: Eva-Maria
authors.initials: EM
authors.lastname: Graner
authors.forename: Joerg
authors.initials: J
authors.lastname: Plieske
authors.forename: Ralf
authors.initials: R
authors.lastname: Wieseke
authors.forename: Hartmut
authors.initials: H
authors.lastname: Luerssen
authors.forename: Gregor
authors.initials: G
authors.lastname: Durstewitz
mesh_terms: D001483:Base Sequence; D001947:Breeding; D002874:Chromosome Mapping; D018556:Crops, Agricultural / Q000235:genetics*; D005819:Genetic Markers; D018745:Genome, Plant; D060005:Genotyping Techniques; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D011003:Ploidies; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic
chemical_list: D005819:Genetic Markers