Forward Genetics in Setaria viridis

Abstract

Forward genetics is a powerful approach to identify mutations and genes underlying traits of interest. Typically, screens begin with chemical mutagenesis of seed or pollen to generate a collection of novel alleles. Dominant or semidominant mutants can be identified in screens of M1 plants and recessive mutants identified in screens of M2 families following self-pollination of the M1. During the last few years, the low cost of next-generation sequencing (NGS) has enabled mapping by sequencing, greatly accelerating the process of gene discovery. As an alternative to mutagenesis, quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) are powerful tools to explore natural variation. In this chapter, we describe the development of a Setaria viridis NMU-mutagenized population using the sequenced reference line A10.1. Strategies for screening mutant populations are described as techniques using bulked segregant analysis by sequencing or direct sequencing of the mutant lines to identify causative lesions underlying mutant phenotypes. We will also discuss strategies to develop recombinant inbred lines (RILs) and MAGIC mapping populations in Setaria viridis.