Nonhost resistance in plants - part II

In addition to analyzing the natural genetic diversity of Brachypodium to wheat stem rust resistance, I also investigated Brachypodium mutants that showed compromised resistance compared to their respective resistant wild type. After sequencing resistant and susceptible pools of plants from a cross between Bd21 (resistant) and a Bd21-derived mutant (susceptible), I start digging into the Brachy genome to find the causative mutation. Since I didn't find any major deviation in allele frequencies of SNPs from resistant and susceptible pools, I called structural variants (i.e., deletions, insertions, duplications, inversions, and translocations) using three different bioinformatics tools. After analyzing this data, I found a 1 base pair deletion present only in the sequenced susceptible plants, introducing a premature stop codon in the gene Bradi1g24100. This gene is a homolog of the Arabidopsis thaliana gene TIME FOR COFFEE (TIC), a circadian clock regulator that has also been shown to increase susceptibility to the bacterial pathogen Pseudomonas syringae.