Strategies for Mutation Discovery and Characterization for Plant Functional Genomics

Mutagenized populations are crucial tools for plant functional genomics. They create a wide range of variation in otherwise homogeneous backgrounds and can be used both for forward and reverse genetic approaches to investigating gene function. In clonally-propagated crops, mutant populations can be created with novel genotypes (e.g. aneuploids) even if they can not be maintained through sexual reproduction. They offer the advantage of providing new variation, which can potentially be directly incorporated into breeding programs. The characterization of mutant populations has historically been difficult due to the challenges inherent to mutation detection. With the advent of the new sequencing technologies, it is now possible to more efficiently detect, catalog and exploit mutations induced by chemical or physical agents. Here we discuss different approaches used to create and characterize mutant populations depending on the characteristics of the crop or model system at hand. Specifically, we discuss the power of next-generation sequencing to catalog both large-scale dosage variation and point mutations in various mutant populations. The power of exome capture compared to whole genome sequencing will also be discussed as a strategy for mutation discovery. In many cases, the availability of thousands of mutations within well-characterized genomes is unprecedented and allows for investigations of the potential preferential targeting of specific sequences by various mutagens.