Delineation and characterization of rust resistance regions in common bean Phaseolus vulgaris L.
Date
2015
Authors
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Journal ISSN
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Publisher
University of Delaware
Abstract
Common bean (Phaseolus vulgaris L.) is an important grain legume in many developing countries throughout the world. It is most useful for its high protein and dietary fiber content. The fungal rust pathogen Uromyces appendiculatus (Pers.) Unger can cause crop loss in susceptible cultivars of common bean. Of the 89 races of rust cultivated in the U.S., the Ur-3 locus provides resistance to 44 of those races along with at least one other gene, Crg (Complements resistance gene). Crg is required for Ur-3-mediated rust resistance. The release of the common bean genome enables the use of a whole transcriptome approach for an improved understanding of regions responsible for rust resistance. In order to better understand this interaction, several common bean genotypes were inoculated with bean rust race 53, leaf RNA isolated at numerous time points, and transcriptomes sequenced. Information generated from Illumina RNA-seq data was then used to analyze five genotypes, ‘Sierra’ (resistant) and ‘Olathe’ (susceptible), and three Sierra-derived susceptible mutants; crg, ur3-Δ2 and ur3-Δ3. RNA-seq data were used to identify and characterize the deletion region in crg (which carries a deletion of the Crg locus) using comparative gene expression analysis against Sierra. Genomic pcr and rt-pcr with candidate gene primers from this region indicates no amplification in crg, but indicates amplification in Sierra. Subsequently, Mock Inoculated (MI) and Inoculated (I) samples of Sierra leaf RNA were compared for differential expression among candidate genes in the deletion region, which is approximately 250 kb. A similar approach was used in an attempt to identify deletion regions in ur3-Δ2 and ur3-?3. However, differential genomic pcr amplifications of selected molecular markers between Sierra and ur3-Δ2/ur3-Δ3 did not yield an alignment to any gene. Since identity of a mutation in any particular gene(s) was unidentifiable, data were collected and compared expression across the transcriptomes of Sierra MI and I and ur3-Δ2 I. This research demonstrates the identification of a disease resistance cluster located on chromosome 10 in common bean. It also employs methods that use both genomic DNA amplification of deletion mutants, paired with RNA-seq to identify possible genomic locations of interest in regard to pathogen resistance in common bean. Identification of differential expression among resistant and susceptible genotypes in disease resistance clusters in the bean genome may elucidate important genes underlying resistance. Detecting candidate gene regions may help in yield loss of common bean due to virulent races of rust on susceptible genotypes. Besides preserving favorable traits in the crop, but can also help in global sustainability of food stocks necessary for many populations.