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Document Type

Thesis - University Access Only

Award Date


Degree Name

Master of Science (MS)

Department / School

Biology and Microbiology

First Advisor

Madhav P. Nepal


Plants are constantly challenged by a diverse array of rapidly evolving pathogens that stimulate evolution of host defense molecules encoded by disease resistance genes (Rgenes). The main objectives of this research were to 1) identify CNL (Coiled coil Nucleotide binding site Leucine rich region) group of R-genes in soybean, 2) elucidate evolutionary divergence of Soybean CNL orthologs across the genomes of six plant species (Arabidopsis, Glycine, Medicago, Phaseolus, Poplar and rice), and 3) elucidate distribution and diversity of Cis-acting Regulatory Elements (CREs) across the six plant genomes. In order to achieve these objectives, approaches in bioinformatics and phylogenetics were used. The 188 soybean CNL genes, identified in this study, were nested into four clades consistent to their orthologs in Arabidopsis. The soybean CNL genes occurred in 42 CNL gene-clusters located on 13 different chromosomes. Analysis of selection pressure and chromosomal positioning suggested rapid evolution of the Rgenes through increased recombination rates. Analysis of six plant genomes yielded over 900 CNL R-genes which were also nested into four clades suggesting the presence of slowly evolving Type-I R genes. The crown groups contained abundant well-supported homogeneous subclades revealing the dominance of Type-II R-genes. Arabidopsis Orthologs of CNL-A and CNL-D were absent from rice genome suggesting a unique retention rate of the CNL genes in monocot. Analysis of Core regulatory elements (CREs) showed eight CREs were present in all genomes. The result that only monocot included had significantly lower CREs needs further analysis by including additional monocot genomes.

Library of Congress Subject Headings

Soybean -- Disease and pest resistance -- Genetic aspects
Plants -- Disease and pest resistance -- Genetic aspects


Includes bibliographical references (pages 114-115)



Number of Pages



South Dakota State University


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