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Marker development, saturation mapping, and high-resolution mapping of the Septoria nodorum blotch susceptibility gene Snn3-B1 in wheat


Septoria nodorum blotch (SNB), caused by Parastagonospora nodorum, is a severe foliar and glume disease on durum and common wheat. Pathogen-produced necrotrophic effectors (NEs) are the major determinants for SNB on leaves. One such NE is SnTox3, which evokes programmed cell death and leads to disease when recognized by the wheat Snn3-B1 gene. Here, we developed saturated genetic linkage maps of the Snn3-B1 region using two F2 populations derived from the SnTox3-sensitive line Sumai 3 crossed with different SnTox3-insensitive lines. Markers were identified and/or developed from various resources including previously mapped simple sequence repeats, bin-mapped expressed sequence tags, single nucleotide polymorphisms, and whole genome survey sequences. Subsequent high-resolution mapping of the Snn3-B1 locus in 5600 gametes delineated the gene to a 1.5 cM interval. Analysis of micro-colinearity of the Snn3-B1 region indicated that it was highly disrupted compared to rice and Brachypodium distachyon. The screening of a collection of durum and common wheat cultivars with tightly linked markers indicated they are not diagnostic for the presence of Snn3-B1, but can be useful for marker-assisted selection if the SnTox3 reactions of lines are first determined. Finally, we developed an ethyl methanesulfonate-induced mutant population of Sumai 3 where the screening of 408 M2 families led to the identification of 17 SnTox3-insensitive mutants. These mutants along with the markers and high-resolution map developed in this research provide a strong foundation for the map-based cloning of Snn3-B1, which will broaden our understanding of the wheat-P. nodorum system and plant-necrotrophic pathogen interactions in general.

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This research was supported by USDA-Agricultural Research Service CRIS project 5442-22000-037-00D.

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Correspondence to Justin D. Faris.

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Gongjun Shi declares that he has no conflict of interest. Zengcui Zhang declares that she has no conflict of interest. Timothy Friesen declares that he has no conflict of interest. Urmil Bansal declares that she has no conflict of interest. Sylvie Cloutier declares that she has no conflict of interest. Thomas Wicker declares that he has no conflict of interest. Jack Rasmussen declares that he has no conflict of interest. Justin Faris declares that he has no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.

Communicated by B. Yang.

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Shi, G., Zhang, Z., Friesen, T.L. et al. Marker development, saturation mapping, and high-resolution mapping of the Septoria nodorum blotch susceptibility gene Snn3-B1 in wheat. Mol Genet Genomics 291, 107–119 (2016).

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  • Wheat
  • Necrotrophic pathogen
  • Disease resistance
  • Map-based cloning
  • Molecular marker
  • Host-selective toxin