New technologies for ultra-high throughput genotyping in plants

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88 Citations (Scopus)


Molecular genetic markers represent one of the most powerful tools for the analysis of plant genomes and the association of heritable traits with underlying genetic variation. Molecular marker technology has developed rapidly over the last decade, with the development of high-throughput genotyping methods. Two forms of sequence-based marker, simple sequence repeats (SSRs), also known as microsatellites and single nucleotide polymorphisms (SNPs) now predominate applications in modern plant genetic analysis, along the anonymous marker systems such as amplified fragment length polymorphisms (AFLPs) and diversity array technology (DArT). The reducing cost of DNA sequencing and increasing availability of large sequence data sets permits the mining of this data for large numbers of SSRs and SNPs. These may then be used in applications such as genetic linkage analysis and trait mapping, diversity analysis, association studies and marker-assisted selection. Here, we describe automated methods for the discovery of molecular markers and new technologies for high-throughput, low-cost molecular marker genotyping. Genotyping examples include multiplexing of SSRs using Multiplex-Ready® marker technology (MRT); DArT genotyping; SNP genotyping using the Invader® assay, the single base extension (SBE), oligonucleotide ligation assay (OLA) SNPlex™ system, and Illumina GoldenGate™ and Infinium® methods.

Original languageEnglish
Title of host publicationPlant Genomics
Subtitle of host publicationMethods and Protocols
EditorsDaryl Somers, Perry Gustafson, Peter Langridge
PublisherHumana Press
Number of pages21
ISBN (Print)9781588299970
Publication statusPublished - 1 Dec 2009
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


Cite this

Appleby, N., Edwards, D., & Batley, J. (2009). New technologies for ultra-high throughput genotyping in plants. In D. Somers, P. Gustafson, & P. Langridge (Eds.), Plant Genomics: Methods and Protocols (pp. 19-39). (Methods in Molecular Biology; Vol. 513). Humana Press.