Simultaneous mutation detection of three homoeologous genes in wheat by High Resolution Melting analysis and Mutation Surveyor®

Chongmei Dong,Peter Sharp,Kate Vincent

doi:10.1186/1471-2229-9-143

Abstract

BackgroundTILLING (Targeting Induced Local Lesions IN Genomes) is a powerful tool for reverse genetics, combining traditional chemical mutagenesis with high-throughput PCR-based mutation detection to discover induced mutations that alter protein function. The most popular mutation detection method for TILLING is a mismatch cleavage assay using the endonuclease CelI. For this method, locus-specific PCR is essential. Most wheat genes are present as three similar sequences with high homology in exons and low homology in introns. Locus-specific primers can usually be designed in introns. However, it is sometimes difficult to design locus-specific PCR primers in a conserved region with high homology among the three homoeologous genes, or in a gene lacking introns, or if information on introns is not available. Here we describe a mutation detection method which combines High Resolution Melting (HRM) analysis of mixed PCR amplicons containing three homoeologous gene fragments and sequence analysis using Mutation Surveyor® software, aimed at simultaneous detection of mutations in three homoeologous genes.ResultsWe demonstrate that High Resolution Melting (HRM) analysis can be used in mutation scans in mixed PCR amplicons containing three homoeologous gene fragments. Combining HRM scanning with sequence analysis using Mutation Surveyor® is sensitive enough to detect a single nucleotide mutation in the heterozygous state in a mixed PCR amplicon containing three homoeoloci. The method was tested and validated in an EMS (ethylmethane sulfonate)-treated wheat TILLING population, screening mutations in the carboxyl terminal domain of the Starch Synthase II (SSII) gene. Selected identified mutations of interest can be further analysed by cloning to confirm the mutation and determine the genomic origin of the mutation.ConclusionPolyploidy is common in plants. Conserved regions of a gene often represent functional domains and have high sequence similarity between homoeologous loci. The method described here is a useful alternative to locus-specific based methods for screening mutations in conserved functional domains of homoeologous genes. This method can also be used for SNP (single nucleotide polymorphism) marker development and eco-TILLING in polyploid species.

Highlights

TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful tool for reverse genetics, combining traditional chemical mutagenesis with high-throughput PCR-based mutation detection to discover induced mutations that alter protein function
TILLING has proven to be a valuable methodology for reverse genetics, combining traditional chemical mutagenesis with high-throughput PCR-based mutation detection
For TILLING in soybean, a recent allotetraploid species [10], a restriction enzyme digestion of the genomic DNA before PCR was added to the method in an attempt to reduce the homoeologous complexity [11], but this method would not work without a locus-specific restriction site

Summary

Introduction

TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful tool for reverse genetics, combining traditional chemical mutagenesis with high-throughput PCR-based mutation detection to discover induced mutations that alter protein function. The most popular mutation detection method for TILLING is a mismatch cleavage assay using the endonuclease CelI. For this method, locus-specific PCR is essential. TILLING has proven to be a valuable methodology for reverse genetics, combining traditional chemical mutagenesis with high-throughput PCR-based mutation detection. PCR reactions for heteroduplex assay are performed using gene-specific primers at high stringency. These conditions are sometime difficult to achieve when TILLING a polyploid species. For TILLING in soybean, a recent allotetraploid species [10], a restriction enzyme digestion of the genomic DNA before PCR was added to the method in an attempt to reduce the homoeologous complexity [11], but this method would not work without a locus-specific restriction site

Methods

Results

Discussion

Conclusion