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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #224398

Title: Genomic analysis of the Snn1 locus on wheat chromosome arm 1BS and the identification of candidate genes

item Friesen, Timothy
item Chao, Shiaoman
item Faris, Justin

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/13/2008
Publication Date: 7/16/2008
Citation: Reedy, L., Friesen, T.L., Meinhardt, S.W., Chao, S., Faris, J.D. 2008. Genomic analysis of the Snn1 locus on wheat chromosome arm 1BS and the identification of candidate genes. The Plant Genome. 1:55-66

Interpretive Summary: The wheat fungal pathogen Stagonospora nodorum causes the disease Stagonospora nodorum blotch (SNB) on leaves and heads of susceptible wheat lines. The fungus produces numerous toxins, which aid in its ability to cause disease. One of these toxins is known as SnTox1. Sensitivity of wheat to SnTox1 is governed by the gene designated Snn1, which is on the short arm of chromosome 1B. Toward the goal of isolating Snn1, we developed saturated and high-resolution linkage maps of the Snn1 genomic region, and we evaluated the level of conservation between the wheat region harboring Snn1 and the rice genome. Overall, conservation with rice was poor, which indicates that information from rice will be of little use for isolating Snn1 from wheat. High-resolution mapping of the Snn1 region resulted in the delineation of the locus to small genetic interval, and two genes with resistance gene-like features were identified as candidates for the Snn1 gene. The isolation of the Snn1 gene will provide knowledge of the Snn1-SnTox1 interaction, insights as to how the pathogen causes disease, and lead to novel methods of creating SNB resistant wheat.

Technical Abstract: 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, we developed saturated and high-resolution maps of the Snn1 locus and evaluated colinearity of the region with rice. An F2 population of 120 individuals derived from Chinese Spring (CS) and the CS – Triticum dicoccoides chromosome 1B disomic substitution line (CS-DIC 1B) was used to map 54 markers consisting of RFLPs, SSRs, and bin mapped ESTs. Colinearity between the region spanning Snn1 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 9 different rice chromosomes. However, twelve 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 locus in 8,510 gametes delineated the gene to a 0.46 cM interval. Two EST-derived markers that cosegregated with Snn1 were found to share homology to NBS-LRR like genes and are considered potential candidates for Snn1.