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Title:Genic copy number variation associated with abiotic/biotic stress among a set of progenitors of contemporary maize germplasm
Author(s):Brohammer, Alex
Advisor(s):Mikel, Mark A.
Department / Program:Crop Sciences
Discipline:Crop Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:M.S.
Genre:Thesis
Subject(s):Maize
structural variation (SV)
Pan-Genome
Plant Breeding
Abstract:Maize (Zea mays L. ssp. mays) is a critically important food, fiber, and fuel crop that also serves as a model genetic organism. Although sequence variation is most commonly associated with single nucleotide polymorphisms, it is estimated that a greater portion of the genome is affected by structural variation (SV). This is a broad phenomenon that includes copy number variation (CNV), inversions, and translocations that affect an intermediate-scale of genomic sequence. Structural variation has the potential to influence phenotype and play a role in heterosis. My research objective is to identify regions of structural variation in the genomes of eight ex-PVP and two Dow AgroSciences proprietary maize inbreds, and specifically characterize variation occurring in genes associated with abiotic/biotic stress tolerance. To facilitate SV discovery those read sequences not aligning to B73 reference genome were first assembled and then bioinformatically characterized. This resulted in the discovery of 37 putative novel resistance genes (R-genes) not found in the B73 genome. The mapped reads were investigated and used to discover genic CNVs from read depth alignment to the B73 reference genome. These results indicate high levels of variation in defense-related genes that could impact the ability of a particular genotype to respond to a pathogen. Further, these CNV calls were validated with additional datasets including a high quality PH207 (also one of the eight ex-PVP inbreds in this study) de novo assembly. Visualization of these variable regions provided clear evidence that the criteria used for determination of CNV calls was accurate. The discovery of putative dispensable genes herein sets the stage for future investigation on their impact on phenotype and utility in breeding for stress resistance.
Issue Date:2014-05-30
URI:http://hdl.handle.net/2142/49803
Rights Information:Copyright 2014 Alex Brohammer
Date Available in IDEALS:2014-05-30
2016-09-22
Date Deposited:2014-05


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