Document Type

Dissertation - University Access Only

Award Date

2012

Degree Name

Doctor of Philosophy (PhD)

Department / School

Mathematics and Statistics

First Advisor

Fedora Sutton

Abstract

The third largest wheat-producing country in the world is the United States and about half of the wheat crops are exported. Therefore, wheat is one of the most influential crops for human nutrition. Plants require a period of exposure to low non-freezing temperatures to withstand freezing, a phenomenon called "cold acclimation". Cold acclimation for wheat is 2-4 °C for 4-6 weeks, autumn conditions. I hypothesize that different cold acclimation responsive physiological processes and pathways are associated with differential freeze survival. Identification of differentially expressed functional categories and pathways from expression data are important tools because they allow insights into the functional working mechanisms of an organism. To test the hypothesis I made use of microarray data analysis methods. The observed dataset was analyzed with three different (Pathway Studio, PANTHER Classification System, and GOstat) programs to identify cold acclimated functional categories and pathways in Freeze Resistant (FR) and Freeze Susceptible (FS) winter wheat. Eight Affymetrix wheat chips were used in the analysis and each array was composed of 61,127 probe sets. Open source R-software was used to analyze data. The objectives to test the hypothesis were: (i) identification of genes that are differentially expressed in response to cold acclimation of FR and FS lines, (ii) identification and comparison of the highly enriched and unique Gene Ontology (GO) terms identified as cold acclimation responsive for the FR and FS lines using three different programs: Pathway studio, GO stat, and Panther classification system, (iii) identification and comparison of cold acclimation responsive highly enriched and unique pathways in FR and FS lines. The result of this dissertation is the novel identification of cold acclimation responsive functional categories and pathways associated with freeze survival of winter wheat. I successfully identified 17 unique cold acclimated GO terms ( 11 biological processes, 1 cellular component, and 5 molecular functions) in FR and 27 unique cold acclimated GO terms ( 13 biological processes, 5 cellular components, and 9 molecular functions) in FS. In addition, eight cold acclimated pathways were identified as unique in FR and one in FS.

Library of Congress Subject Headings

Winter wheat -- Frost resistance
Winter wheat -- Genetics
Winter wheat -- Effect of temperature on

Publisher

South Dakota State University

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Rights Statement

In Copyright