Sequencing Trait-Associated Mutations (STAM) to Clone Rust Resistance Genes

Sequencing trait-associated mutations (STAM) is a simple and straightforward gene cloning method that was developed in wheat. It uses full-length isoform sequencing (Iso-Seq) of the wild type as the reference and employs transcriptome sequencing of multiple, independently derived mutants for gene cloning. The STAM method eliminates the need for fine-mapping or a high-quality whole genome assembly of a specific wheat cultivar, and it could also be used in other plant species with complex genomes. Detailed, bioinformatic analysis protocol and tips for STAM are provided in this chapter.