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Effects of Hybridization on Heterochromatic Small Interfering RNA and Gene Expression in Zea mays

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Title: Effects of Hybridization on Heterochromatic Small Interfering RNA and Gene Expression in Zea mays
Author: Coleman, Travis Korry
Department: Department of Plant Agriculture
Program: Plant Agriculture
Advisor: Lukens, Lewis
Abstract: Heterosis for quantitative traits in maize (Zea mays L.) is generally controlled by the cumulative effects of multiple genes and regulatory elements. In particular, 24-nt heterochromatic small interfering RNAs (hetsiRNAs) may affect heterosis of gene expression by mediating trans-genomic interactions when two genomes come into contact in an F1 nucleus. Previous research has suggested that hetsiRNAs exhibit non-additive expression upon hybridization, with the majority of hetsiRNAs being downregulated compared to parental levels. This could have implications for the regulation of nearby genes, thus influencing heterosis of gene expression in a non-Mendelian and epigenetic manner. This research sought to examine trends in hetsiRNA expression and hetsiRNA/gene co-expression resulting from hybridization of commercial maize germplasm. Small RNA and mRNA were isolated and deep sequenced from two inbred lines and their F1 hybrid. Results confirmed that mean hetsiRNA expression was significantly reduced in the F1 hybrid relative to its parents. The F1 hybrid also demonstrated a marked reduction in hetsiRNA diversity, with 41% of hetsiRNA clusters being expressed in one or both parents but not the hybrid. Similarly, classifying hetsiRNA expression in the hybrid relative to the expected midparent value demonstrated that the vast majority of hetsiRNA clusters were expressed below the midparent level, with many transgressive below the low parent. Localization of hetsiRNA clusters within the boundaries of a genic frame showed a strong enrichment of hetsiRNA clusters in the +/- 1 kb flanks of genic regions. Expression level analyses indicated a mean downregulation of both hetsiRNA and mRNA expression relative to expected midparent values for a small but significant number of genes with co-located hetsiRNA clusters. Furthermore, knockout of hetsiRNA production in the mediator of paramutation 1 mutant mop1-1 demonstrated a trend toward upregulation of genes relative to the wildtype. These results suggest that hetsiRNA may play a limited role in non-additive, epigenetic regulation of gene expression in hybrids. These findings have implications for the development of hybrid crop species and the notion of an epigenome that may not exhibit traditional patterns of Mendelian inheritance and may therefore affect phenotype in an unpredictable manner.
URI: http://hdl.handle.net/10214/10185
Date: 2017-01-06


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