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Subject: wheat

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    Genomic Characterization of Necrotrophic Effector Sensitivity Genes in Wheat
    (North Dakota State University, 2022) Running, Katherine
    The necrotrophic fungal pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis cause the diseases septoria nodorum blotch (SNB) and tan spot, respectively, reducing yield by decreasing the photosynthetic area of the plant. The pathogens produce necrotrophic effectors (NEs) that target host genes to induce cell death. The Tsc1-Ptr ToxC and Tsn1-Ptr ToxA interactions contribute to plant susceptibility to tan spot, while the Tsn1-SnToxA and Snn5-B1-SnTox5 interactions contribute to SNB susceptibility. The three main goals of this dissertation were to clone susceptibility genes Tsc1 and Snn5 and develop robust genetic markers for use in marker-assisted elimination of Tsn1. A genetic linkage map was developed delineating the Tsc1 region to 184 kb. Structural and gene content comparisons of the identified Tsc1 and Tsn1 regions in using the sequenced wheat genomes revealed gene content variation correlating with host phenotypes, reducing the Tsc1 candidate gene list to just two genes. Comparative sequence analysis in two generated mutant populations revealed the identity of Tsc1, which has protein kinase and leucine-rich repeat domains. The structural and gene content comparison of the sequenced genomes in the Tsn1 region identified two conserved haplotypes in accessions with presence/absence variation corresponding with ToxA sensitivity. Genetic markers flanking Tsn1 were designed in segments syntenic between Tsn1+ and Tsn1- accessions, allowing the codominant detection of Tsn1. The Tsn1 markers were validated on over 1,500 wheat accessions, demonstrating a near perfect ability to determine if an accession would be insensitive to ToxA. The application of these markers in wheat breeding programs can effectively reduce susceptibility to ToxA-producing pathogens. Snn5-B1 candidates were identified in the Chinese Spring genome and validated using random mutagenesis, targeted mutagenesis, and the Cadenza TILLING mutants. Snn5-B1 contains protein kinase and major sperm protein domains. Furthermore, a second SnTox5 sensitivity locus, designated Snn5-B2, was mapped to the short arm of chromosome 2B in durum wheat. The cloning of susceptibility genes Tsc1 and Snn5-B1 allows for the development of molecular markers based on causal polymorphisms and for gene-disruption though gene-editing methods for the selection or creation of nonfunctional alleles that cannot be targeted by NE to induce cell death and disease.
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    Mapping and Characterization of Yield Component Traits and Septoria Nodorum Blotch Susceptibility in Wheat
    (North Dakota State University, 2021) Peters Haugrud, Amanda Rose
    Wheat, a major global economic crop and food source, is currently threatened by climate change and the cascading effects, including increased disease pressure. Additionally, wheat yields have not increased significantly for decades, which may impact future food supply. Compared to other crop species, relatively few genes related to wheat yield have been mapped and cloned, with the vast majority in bread, or hexaploid, wheat. In this dissertation, I used three tetraploid wheat populations, Ben × PI 41025 (BP025), Divide × PI 272527 (DP527), and Rusty × PI 193883 (RP883) which were derived from crossing durum cultivars with cultivated emmer accessions. These three populations were evaluated under field conditions in three seasons for 11 traits related to yield. Additionally, the DP527 population was evaluated under greenhouse conditions for these same 11 traits. The known genes ELF3, Ppd-B1, Vrn-A1, Q, Vrn-B1, WAPO-A1, FT-1, GNI-A1, GRF4 and Vrn2 were associated with numerous yield traits. For multiple QTL, the cultivated emmer parent contributed the increased effects. Findings from this study and the identified markers may be useful for breeders who are interested in introgressing the beneficial genes I identified into their germplasm. Here, I also report on the progress and markers developed for fine mapping of a kernels per spike gene that was first mapped in the BP025 population. The work I have done provides a foundation for the cloning of this kernels per spike gene. Lastly, in this dissertation, I screened a global winter wheat panel for genetic regions associated with susceptibility to the necrotrophic pathogen Parastagonospora nodorum, the causal agent of septoria nodorum blotch. I identified the previously cloned genes Tsn1 and Snn3-B1 to be associated with disease caused by the isolates Sn2000 and Sn4, respectively. I also report the first time a panel has been screened for sensitivity to the necrotrophic effectors SnTox267 and SnTox5, along with the prevalence of SnToxA, SnTox1, and SnTox3 sensitivity in this panel. In conclusion, results obtained from these studies provides knowledge of genes/markers which are available to breeders that may provide useful in breeding programs and the overall goal of increasing wheat yield.