Genomic Analysis of the Snn1 Locus on Wheat Chromosome Arm 1BS and the Identification of Candidate Genes

The pathogen Stagonospora nodorum produces multiple host-selective toxins (HSTs) that induce cell death and necrosis in sensitive wheat (Triticum sp.) 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, we developed saturated and high-resolution maps of the Snn1 locus and evaluated colinearity of the region with rice (Oryza sativa L.). An F-2 population of 120 individuals derived from 'Chinese Spring' (CS) and the CS-T. dicoccoides chromosome 1B disomic substitution line was used to map 54 markers consisting of restriction fragment length polymorphisms (RFLPs), simple sequence repeats, and bin mapped expressed sequence tags (ESTs). Colinearity between wheat 1BS and rice was determined by aligning EST and RFLP probe sequences to the rice genome. Overall, colinearity was poorly conserved due to numerous complex chromosomal rearrangements, and of 48 wheat EST-RFLP sequences mapped, 30 had significant similarity to sequences on nine different rice chromosomes. However, 12 of the wheat 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 locus in 8510 gametes delineated the gene to a 0.46-cM interval. Two EST-derived markers that cosegregated with Snn1 were found to share homology to nucleotide binding site-leucine rich repeat-like genes and are considered potential candidates for Snn1.