High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing

Sanzhen Liu, Hsin D. Chen, Irina Makarevitch, Rebecca Shirmer, Scott J. Emrich, Charles R. Dietrich, W. Brad Barbazuk, Nathan M. Springer, Patrick S. Schnable

Research output: Contribution to journalArticlepeer-review

51 Scopus citations


Advances in next-generation sequencing technology have facilitated the discovery of single nucleotide polymorphisms (SNPs). Sequenom-based SNP-typing assays were developed for 1359 maize SNPs identified via comparative next-generation transcriptomic sequencing. Approximately 75% of these SNPs were successfully converted into genetic markers that can be scored reliably and used to generate a SNPbased genetic map by genotyping recombinant inbred lines from the intermated B73 X Mo17 population. The quantitative nature of Sequenom-based SNP assays led to the development of a time- and costefficient strategy to genetically map mutants via quantitative bulked segregant analysis. This strategy was used to rapidly map the loci associated with several dozen recessive mutants. Because a mutant can be mapped using as few as eight multiplexed sets of SNP assays on a bulk of as few as 20 mutant F2 individuals, this strategy is expected to be widely adopted for mapping in many species.

Original languageEnglish (US)
Pages (from-to)19-26
Number of pages8
Issue number1
StatePublished - Jan 2010

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