Agricultural products are becoming more homogenous in order to conform to consumer expectations. In doing so, they have become a high-risk target for widespread crop failure due to pathogens or other agricultural maladies. Presented here are a collection of tools and a work-flow for the wholesale detection and characterization of disease resistance-associated proteins from whole-genome sequences. These techniques were also adapted for identifying potential miRNA regulatory sequences. Putative R-gene sequences identified from the Malus x Domestica 'Golden Delicious' genome were acquired for verification against wild apple species. Resistance gene analogs were PCR amplified from R-gene associated domains (TIR, NBS, and LRR) in wild apple cultivars. Known R-gene sequences were clustered alongside the PCR analogs and putative R-genes from 'Golden Delicious'. A covariance model approach for the de novo detection of 3,187 putative pre-miRNA regulatory sequences is also explored. Vitis vinifera sequences used to build this model were retrieved with 38% efficiency. Computational clusters may be useful in the physical mapping of sequences to the chromosomally duplicated gene clusters characteristic of R-genes. Known R-genes included in computational clusters may also clarify the function of the unknown sequences. A possibility exists for the identification of resistance genes that have been lost in the selective breeding of commercial cultivars.
Library of Congress Subject Headings
Apples--Disease and pest resistance--Research; Grapes--Disease and pest resistance--Research; Genomics; Proteomics
Department, Program, or Center
Thomas H. Gosnell School of Life Sciences (COS)
Bailey, Aubrey, "Exploratory analysis of pathogen resistance responsible genetic elements in two eudicots from whole genome sequence" (2010). Thesis. Rochester Institute of Technology. Accessed from
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