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A bioinformatic analysis of genetic factors affecting primary root growth in Zea mays

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Title: A bioinformatic analysis of genetic factors affecting primary root growth in Zea mays
Author: Meyer, Ann
Department: Department of Plant Agriculture
Program: Plant Agriculture
Advisor: Lukens, Lewis
Abstract: Individuals in a population carry different alleles allowing them to respond uniquely to internal and external cues. Examining the effect of specific alleles and investigating genome-wide allelic expression in response to internal growth cues and external stress provides insights into agriculturally important phenomena such as heterosis. Zea mays (maize) primary roots are an ideal system for studying allelic effects as maize is genotypically diverse and the primary roots exhibit growth differences between inbreds early in development. I identified 12 QTL within the maize genome that each explained up to 22% of the variance in primary root growth between two inbreds in control, stress, and recovery conditions. Introgressing one of these loci from one inbred into the other increased root length, increased the proportion of explained variance to 66%, and changed the expression of genes associated with scavenging reactive oxygen species (ROS). I used RNA-Seq to evaluate differences in allele expression levels and the regulatory mechanisms contributing to the differences in allele expression levels in reciprocal hybrids. A major impediment to using RNA-Seq for allelic analyses is unequal mapping of allelic reads to a single reference genome. Very frequently more reads map from one allele than the other and all reads from both alleles map at only 18% of polymorphic loci. Masking polymorphic sites or replacing polymorphic sites reduces the frequency of unequal mapping genome-wide but introduces new sources of unequal mapping. To reduce unequal mapping of allelic reads, I assembled parent specific transcriptomes for two inbred lines and aligned reads to these transcriptomes. Genome-wide, more genes are trans-regulated than cis-regulated with alleles of the faster growing parent having greater abundances than alleles of the slower growing parent under cis-regulation and alleles of the slower growing parent having greater abundances than alleles of the faster growing parent under trans-regulation. Under stress conditions, the number of genes with differences in allelic expression abundances increases, the number of genes with trans-regulation increases, and the number of genes with maternal or paternal expression decreases. There are more enhancing cis- and trans-regulatory interactions than compensating interactions suggesting that breeding has increased the differences between inbreds.
URI: http://hdl.handle.net/10214/8779
Date: 2015-05


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