Skip to main content
ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #399503

Research Project: Improvement of Biotic Stress Resistance in Durum and Hard Red Spring Wheat Using Genetics and Genomics

Location: Cereal Crops Research

Title: Genetic diversity and marker-assisted elimination of the Snn1 gene in wheat

item SENEVIRATNE, SUDESHI - North Dakota State University
item SHI, GONGJUN - North Dakota State University
item SZABO-HEVER, AGNES - Oak Ridge Institute For Science And Education (ORISE)
item Zhang, Zengcui
item PETERS HAUGRUD, AMANDA - Oak Ridge Institute For Science And Education (ORISE)
item RUNNING, KATHERINE - North Dakota State University
item SINGH, GURMINDER - North Dakota State University
item Nandety, Raja Sekhar
item Fiedler, Jason
item Xu, Steven
item Friesen, Timothy
item MCCLEAN, PHILLIP - North Dakota State University
item Faris, Justin

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 10/27/2022
Publication Date: 12/1/2022
Citation: Seneviratne, S., Shi, G., Szabo-Hever, A., Zhang, Z., Peters Haugrud, A., Running, K., Singh, G., Nandety, R., Fiedler, J.D., Xu, S.S., Friesen, T.L., Mcclean, P., Faris, J.D. 2022. Genetic diversity and marker-assisted elimination of the Snn1 gene in wheat. Meeting Abstract. Poster No. PO0487.

Interpretive Summary:

Technical Abstract: Septoria nodorum blotch (SNB) is a severe foliar and glume disease of durum and common wheat characterized by cell death that is initiated by interactions between necrotrophic effectors (NEs) produced by the fungus Parastagonospora nodorum and corresponding host sensitivity genes in wheat. The Snn1-SnTox1 interaction is one of multiple host sensitivity gene-NE interactions identified in the wheat-P. nodorum pathosystem, and it plays a significant role in SNB development. The host sensitivity gene Snn1 was previously cloned from wheat, but a diagnostic PCR marker has not been developed. In this study, the allelic diversity of Snn1 was studied to identify causal polymorphisms and to develop markers useful for marker-assisted elimination (MAE) of functional Snn1 alleles. The full length Snn1 gene was sequenced from 99 accessions including diploid, tetraploid, and hexaploid wheat species. Multiple sequence alignments revealed 27 haplotypes based on the coding sequence of the gene. Three mutations that possibly changed the primitive insensitive allele in wild emmer into the sensitive allele in domesticated wheat and four independent SNPs that subsequently changed the sensitive allele into insensitive alleles were identified. These SNPs are within each of the three exons of Snn1 affecting multiple domains. Kompetitive allele specific PCR (KASP) markers were developed for three of these mutations and the Snn1 null allele. These newly developed markers identify more than 95% of the durum and spring wheat accessions that are sensitive to SnTox1 and can be used for MAE. Results of this study also increase our understanding of the evolution of Snn1.