Genomic analysis of the Stagonospora nodorum toxin sensitivity locus Snn1 in wheat

The pathogen Stagonospora nodorum produces multiple host-selective toxins (HSTs) that induce cell death and necrosis in sensitive wheat genotypes. One such HST is SnTox1, which interacts with the host gene Snn1 on wheat chromosome arm 1BS to cause necrosis, leading to disease susceptibility. Toward the positional cloning of Snn1, the region containing Snn1 was saturated with 54 markers consisting of RFLPs, SSRs, and bin-mapped ESTs. We also determined colinearity between the region spanning Snn1 and rice by aligning EST and RFLP probe sequences to the rice genome. Overall, colinearity was poorly conserved due to numerous complex chromosomal rearrangements. However, 12 of the wheat EST/RFLP sequences had similarity to sequences on rice chromosome 5 and were in a colinear arrangement with only a few exceptions, including an inversion of the markers flanking Snn1. High-resolution mapping of the Snn1 delimited the gene to a 0.46-cM interval, and we found two EST-derived markers that cosegregated with Snn1. We also assembled a 595-kb physical BAC contig at the Snn1 locus. Recombination along the contig was highly variable with all recombination events occurring within the first 54-kb of the contig, and the remaining 541-kb was void of recombination. By BAC clone sequencing and sequence annotation, we identified eight putative genes in the chromosome segment cosegregating with Snn1, indicating a gene density of 1 gene per 67-kb. Genes that cosegregated with Snn1 had homology to genes involved in disease resistance and defense response, including NBS-LRR-like genes, receptor kinases, and a wall-associated kinase, which may be considered potential candidates for Snn1.