A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats

Batley, J., Mogg, R., Edwards, D., O'Sullivan, H. and Edwards, K. J. (2003) A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats. Molecular Breeding, 11 2: 111-120.


Author Batley, J.
Mogg, R.
Edwards, D.
O'Sullivan, H.
Edwards, K. J.
Title A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats
Journal name Molecular Breeding  (ERA 2012 Listed)    (ERA 2010 Rank B)   Check publisher's open access policy
Publication date 2003-02
Sub-type Article
DOI 10.1023/A:1022446021230
Volume number 11
Issue number 2
ISSN 1380-3743 (Print); 1572-9788 (Online)
Start page 111
End page 120
Total pages 10
Place of publication Netherlands
Publisher Springer
Language eng
Abstract Information on genetic relationships among individuals is of importance to maize breeders for line and hybrid development. Estimates on the genetic similarity of breeding materials is best obtained using DNA markers. Single Nucleotide Polymorphisms and small insertions/deletions are both emerging as a new generation of markers, due to their abundance and amenability to fully automated genotyping. Application of SNPs, for example in genetic mapping projects or breeding programs, involves the analysis of a large number of samples, and therefore requires rapid, inexpensive, and highly automated methods to genotype the sequence variants. Towards this, we have applied a high throughput Single Nucleotide Primer Extension assay to assess 23 polymorphic base variations at five microsatellite loci in 22 inbred maize lines, as well as in a mapping population of two of the inbred lines. Using a MegaBACE automated genotyper, we are able to assay more than 1248 (96 x 13) samples in a single 75 minute run. The SNuPE method successfully genotyped the base pair variations of interest in all maize lines. It was also found that primers containing polymorphisms themselves could be used to genotype the samples. This technique allows the rapid production of valuable high throughput information on genetic relationships among maize varieties. We further demonstrate the utility of this method, using it to successfully map one of the microsatellite loci.
Keyword Agronomy
Biotechnology & Applied Microbiology
Plant Sciences
Horticulture
capillary electrophoresis
indel
maize
Microsatellites
SNPs
SNuPE
Single Nucleotide Polymorphisms
Microsatellite Markers
Null Alleles
Dna
Population
Hybrids
Base
Loci
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article
Collections: Excellence in Research Australia (ERA) - Collection
School of Agriculture and Food Sciences
 
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Created: Wed, 19 Sep 2007, 15:16:30 EST