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Title: Marker-assisted molecular profiling and RNA-Seq reveal a disease resistance cluster associated with Uromyces appendiculatus infection in common bean Phaseolus vulgaris L

item TODD, ANTONETTE - Delaware State University
item DONOFRIO, NICOLE - University Of Delaware
item SRIPATHI, VENKATESWARA - Delaware State University
item MCCLEAN, PHILIP - North Dakota State University
item LEE, RIAN - North Dakota State University
item Pastor Corrales, Marcial - Talo
item KALAVCHARLA, VENU - Delaware State University

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/13/2017
Publication Date: 5/23/2017
Citation: Todd, A., Donofrio, N., Sripathi, V., Mcclean, P., Lee, R., Pastor Corrales, M.A., Kalavcharla, V. 2017. Marker-assisted molecular profiling and RNA-Seq reveal a disease resistance cluster associated with Uromyces appendiculatus infection in common bean Phaseolus vulgaris L. International Journal of Molecular Sciences. 18(6)1109. doi: 10.3390/ijms18061109.

Interpretive Summary: The bean rust fungal disease reduces seed yield and pod quality in dry and snap beans. Genetic resistance is the most cost effective and environmentally friendly strategy to manage bean rust. The Ur-3 gene, present in pinto bean Sierra and many other dry bean varieties grown in the United States, confers resistance to many virulent strains (known as races) of the bean rust pathogen. However, Ur-3 requires the Cgr (complements resistance gene) gene to confer Ur-3-mediated rust resistance. Ur-3 is present in chromosome 10 of common bean; however, the location of Crg in the genome of common bean is unknown. In this study, Sierra, having the Ur-3 and Crg genes, and a mutant of Sierra missing Crg were inoculated with bean rust fungus race 53. Sierra was resistant and the mutant was susceptible. RNA was isolated from the plants and sequenced. The RNA sequences were mapped to DNA positions and the differences between the resistant and susceptible plants helped identify the potential location of Crg in the DNA chromosomes. These studies of plant-pathogen interactions are needed to understand the mechanisms that result in disease resistance in plants. The DNA information for Crg can be used by breeders and other scientists at universities, government agencies and private companies who are trying to develop beans more resistant to disease.

Technical Abstract: Common bean (Phaseolus vulgaris L.) is an important legume, useful for its high protein and dietary fiber. The fungal pathogen Uromyces appendiculatus (Pers.) Unger can cause major loss in susceptible varieties of common bean. The Ur-3 locus provides race specific resistance to fungal rust along with Crg, (Complements resistance gene), which is required for Ur-3-mediated rust resistance. In this study, we inoculated two common bean genotypes (resistant ‘Sierra’ and susceptible crg) with rust race 53, isolated leaf RNA at specific time points, and sequenced their transcriptomes. RNA-seq data and molecular markers were used to identify a deletion region in mutant crg (which carries a deletion at the Crg locus) using comparative differential expression. Subsequently, Mock Inoculated (MI) and Inoculated (I) samples of Sierra leaf RNA were compared for differential expression in a 250kb delineated region in the crg mutant. This research demonstrates the identification of a disease resistance cluster located on chromosome 10 in common bean. Both marker assisted molecular profiling paired with RNA-seq were used to identify possible transcriptomic locations of interest in regard to rust race 53 resistance in common bean. Identification of differential expression among samples in disease resistance clusters in the bean genome may elucidate significant genes underlying rust resistance. Along with preserving favorable traits in the crop, the current research may also aid in global sustainability of food stocks necessary for many populations.