Agronomy and Crop Sciences Commons^™

Heritable Epigenetic Variation Among Maize Inbreds, Steve R. Eichten, Ruth A. Swanson, James C. Schnable, Amanda J. Waters, Peter J. Hermanson, Sanzhen Liu, Cheng-Ting Yeh, Yi Jia, Karla Gendler, Michael Freeling, Patrick S. Schnable, Matthew W. Vaughn, Nathan M. Springer

Department of Agronomy and Horticulture: Faculty Publications

Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of DNA methylation in two different genotypes of Zea mays (ssp. mays), an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation. The distribution of DNA methylation …

Gata-Family Transcription Factors In Magnaporthe Oryzae, Cristian F. Quispe

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The filamentous fungus, Magnaporthe oryzae, responsible for blast rice disease, destroys around 10-30% of the rice crop annually. Infection begins when the specialized infection structure, the appressorium, generates enormous internal turgor pressure through the accumulation of glycerol. This turgor acts on a penetration peg emerging at the base of the cell, causing it to breach the leaf surface allowing its infection.

The enzyme trehalose-6- phosphate synthase (Tps1) is a central regulator of the transition from appressorium development to infectious hyphal growth. In the first chapter we show that initiation of rice blast disease requires a regulatory mechanism involving an …

Herbicide-Resistant Risk Assessment: Response Of Common Nebraska Weeds To Dicamba Dose, Roberto J. Crespo

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Dicamba-resistant soybeans are being developed to provide an additional herbicide mechanism of action that can be used in soybean, and to provide a tool to help manage or mitigate the evolution of other herbicide-resistant weed populations. The objectives of this thesis were to assess the risk of common Nebraska weeds developing resistance to dicamba, quantify baseline dose-response to dicamba of high-risk weed species, and survey the variability in dicamba dose-response among populations of those species. Twenty-five weed scientists were asked to estimate the risk likelihood of ten weed species evolving resistance to dicamba following the commercialization of dicamba-resistant soybean. Palmer …

Genes Identified By Visible Mutant Phenotypes Show Increased Bias Toward One Of Two Subgenomes Of Maize, James C. Schnable, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (Zea mays L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these ‘‘classical’’ maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that …

Dose–Sensitivity, Conserved Non-Coding Sequences, And Duplicate Gene Retention Through Multiple Tetraploidies In The Grasses, James C. Schnable, Brent S. Pedersen, Sabarinath Subramaniam, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Whole genome duplications, or tetraploidies, are an important source of increased gene content. Following whole genome duplication, duplicate copies of many genes are lost from the genome. This loss of genes is biased both in the classes of genes deleted and the subgenome from which they are lost. Many or all classes are genes preferentially retained as duplicate copies are engaged in dose sensitive protein–protein interactions, such that deletion of any one duplicate upsets the status quo of subunit concentrations, and presumably lowers fitness as a result. Transcription factors are also preferentially retained following every whole genome duplications studied. This …