TY - JOUR
T1 - New technologies for ultra-high throughput genotyping in plants
AU - Appleby, Nikki
AU - Edwards, David
AU - Batley, Jacqueline
PY - 2009/12/1
Y1 - 2009/12/1
N2 - 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.
AB - 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.
KW - DArT
KW - Diversity array technology
KW - GoldenGate®
KW - Infinium®
KW - Invader®
KW - Multiplex-Ready® marker technology, MRT
KW - Oligonucleotide ligation assay, OLA
KW - Simple sequence repeat, SSR
KW - Single Base Extension, SBE
KW - Single Nucleotide Polymorphism, SNP
KW - SNPlex®
UR - http://www.scopus.com/inward/record.url?scp=65349159741&partnerID=8YFLogxK
U2 - 10.1007/978-1-59745-427-8_2
DO - 10.1007/978-1-59745-427-8_2
M3 - Article
C2 - 19347650
AN - SCOPUS:65349159741
SP - 19
EP - 39
JO - Methods in Molecular Biology
JF - Methods in Molecular Biology
SN - 1064-3745
ER -