Comparative genomics of repetitive elements between maize inbred lines B73 and Mo17

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dc.contributor.author Migeon, Pierre
dc.date.accessioned 2017-04-12T19:54:30Z
dc.date.available 2017-04-12T19:54:30Z
dc.date.issued 2017-05-01 en_US
dc.identifier.uri http://hdl.handle.net/2097/35377
dc.description.abstract The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, revealing differences in organization of highly repetitive sequences between the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement. en_US
dc.language.iso en_US en_US
dc.publisher Kansas State University en
dc.subject Noncoding DNA en_US
dc.subject Repetitive DNA en_US
dc.subject Maize en_US
dc.subject Bioinformatics en_US
dc.subject Genomic dark matter en_US
dc.subject Comparative genomics en_US
dc.title Comparative genomics of repetitive elements between maize inbred lines B73 and Mo17 en_US
dc.type Thesis en_US
dc.description.degree Master of Science en_US
dc.description.level Masters en_US
dc.description.department Genetics Interdepartmental Program en_US
dc.description.advisor Sanzhen Liu en_US
dc.date.published 2017 en_US
dc.date.graduationmonth May en_US


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