Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Open Badges Methodology article

Multiplex-Ready PCR: A new method for multiplexed SSR and SNP genotyping

Matthew J Hayden12*, Thao M Nguyen12, Amanda Waterman2 and Kenneth J Chalmers12

Author Affiliations

1 Molecular Plant Breeding CRC, PMB 1, Glen Osmond, SA, 5064, Australia

2 School of Agriculture, Food and Wine, Adelaide University, Waite Campus, Urrbrae, 5064, Australia

For all author emails, please log on.

BMC Genomics 2008, 9:80  doi:10.1186/1471-2164-9-80

Published: 18 February 2008



Microsatellite (SSR) and single nucleotide polymorphism (SNP) markers are widely used in plant breeding and genomic research. Thus, methods to improve the speed and efficiency of SSR and SNP genotyping are highly desirable. Here we describe a new method for multiplex PCR that facilitates fluorescence-based SSR genotyping and the multiplexed preparation of DNA templates for SNP assays.


We show that multiplex-ready PCR can achieve a high (92%) success rate for the amplification of published sequences under standardised reaction conditions, with a PCR specificity comparable to that of conventional PCR methods. We also demonstrate that multiplex-ready PCR supports an improved level of multiplexing in plant genomes of varying size and ploidy, without the need to carefully optimize assay conditions. Several advantages of multiplex-ready PCR for SSR and SNP genotyping are demonstrated and discussed. These include the uniform amplification of target sequences within multiplexed reactions and between independent assays, and the ability to label amplicons during PCR with specialised moieties such fluorescent dyes and biotin.


Multiplex-ready PCR provides several technological advantages that can facilitate fluorescence-based SSR genotyping and the multiplexed preparation of DNA templates for SNP assays. These advantages can be captured at several points in the genotyping process, and offer considerable cost and labour savings. Multiplex-ready PCR is broadly applicable to plant genomics and marker assisted breeding, and should be transferable to any animal or plant species.