A high-throughput assay for rapid and simultaneous analysis of perfect markers for important quality and agronomic traits in rice using multiplexed MALDI-TOF mass spectrometry

Masouleh, Ardashir K., Waters, Daniel L. E., Reinke, Russel F. and Henry, Robert J. (2009) A high-throughput assay for rapid and simultaneous analysis of perfect markers for important quality and agronomic traits in rice using multiplexed MALDI-TOF mass spectrometry. Plant Biotechnology Journal, 7 4: 355-363. doi:10.1111/j.1467-7652.2009.00411.x


 
Dataset relationships
 
Author Masouleh, Ardashir K.
Waters, Daniel L. E.
Reinke, Russel F.
Henry, Robert J.
Title A high-throughput assay for rapid and simultaneous analysis of perfect markers for important quality and agronomic traits in rice using multiplexed MALDI-TOF mass spectrometry
Journal name Plant Biotechnology Journal   Check publisher's open access policy
ISSN 1467-7644
1467-7652
Publication date 2009-05
Sub-type Article (original research)
DOI 10.1111/j.1467-7652.2009.00411.x
Volume 7
Issue 4
Start page 355
End page 363
Total pages 9
Place of publication Oxford, England, U.K.
Publisher Wiley-Blackwell Publishing
Language eng
Formatted abstract Summary The application of single nucleotide polymorphisms (SNPs) in plant breeding involves the analysis of a large number of samples, and therefore requires rapid, inexpensive and highly automated multiplex methods to genotype the sequence variants. We have optimized a high-throughput multiplexed SNP assay for eight polymorphisms which explain two agronomic and three grain quality traits in rice. Gene fragments coding for the agronomic traits plant height (semi-dwarf, sd-1) and blast disease resistance (Pi-ta) and the quality traits amylose content (waxy), gelatinization temperature (alk) and fragrance (fgr) were amplified in a multiplex polymerase chain reaction. A single base extension reaction carried out at the polymorphism responsible for each of these phenotypes within these genes generated extension products which were quantified by a matrix-assisted laser desorption ionization-time of flight system. The assay detects both SNPs and indels and is co-dominant, simultaneously detecting both homozygous and heterozygous samples in a multiplex system. This assay analyses eight functional polymorphisms in one 5 μL reaction, demonstrating the high-throughput and cost-effective capability of this system. At this conservative level of multiplexing, 3072 assays can be performed in a single 384-well microtitre plate, allowing the rapid production of valuable information for selection in rice breeding. © 2009 Blackwell Publishing Ltd.
Keyword Matrix-assisted Laser Desorption Ionization-time Of Flight (maldi-tof)
Multiplex Perfect Markers
Rice
Single Nucleotide Polymorphism
Single-nucleotide Polymorphisms
Starch-synthase-iia
Map-based Cloning
Gene Pi-ta
Green-revolution
Resistance Gene
Oryza-sativa
Waxy Gene
Gelatinization Temperature
Gibberellin-synthesis
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
ERA 2012 Admin Only
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 10 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 13 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Access Statistics: 45 Abstract Views  -  Detailed Statistics
Created: Mon, 07 Mar 2011, 16:11:51 EST