Plant Genomics

Volume 513 of the series Methods in Molecular Biology™ pp 19-39


New Technologies for Ultra-High Throughput Genotyping in Plants

  • Nikki Appleby
  • , David Edwards
  • , Jacqueline BatleyAffiliated withARC Centre for Integrated Legume Research, University of Queensland Email author 

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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.


Diversity array technology DArT GoldenGate® Infinium® Invader® Multiplex-Ready® marker technology, MRT Oligonucleotide ligation assay, OLA Simple sequence repeat, SSR Single Base Extension, SBE Single Nucleotide Polymorphism, SNP SNPlex®