Doctor of Philosophy (PhD)



Document Type



Cotton (Gossypium hirsutum L) is an economically important crop that generates billions of dollars in annual revenue worldwide. However, contamination of cottonseed with a highly carcinogenic aflatoxin produced by Aspergillus flavus limits the use of cottonseed in the oil and animal feed industries. Much success has been achieved by the application of atoxigenic strains of A. flavus for controlling aflatoxin contamination in cotton, peanut, and maize. Understanding the gene (co)expression network in response to A. flavus infection with both toxigenic and atoxigenic strains of A. flavus pericarp and seed of cotton through genome-wide transcriptome profiling will not only unravel the complex interaction of the genes involved in the cotton-A. flavus interaction, but also will lead to the identification of key candidate genes for genetic manipulation to develop A. flavus-resistant germplasm. A comprehensive weighted gene (co)expression analysis identified nine modules in the network of cotton in response to Aspergillus flavus infection. The genes identified in a particular “hub” in the network provided clues to key candidate genes for further functional characterization. Some of these genes, such as 2-oxoglutarate (2OG), Fe (II)-dependent oxygenase superfamily proteins, alcohol dehydrogenase and UDP glycosyl transferase, were upregulated in response to both atoxigenic and toxigenic strains of A. flavus and gene encoed expansin A4 protein could be potential resistance-associated genes. Alternative splicing (AS) is an important biological process in transcriptional regulation, which contributes to transcriptome diversity and thus the plasticity of the genome. Among the four major AS events classified in plants, intron retention was the most frequent (36%), followed by alternative donor site (AD; 19%), alternative acceptor site (AA; 18%), and exon skipping (ES; 6%), in cotton in response to A. flavus infection. This is the first report of AS events in cotton (Gossypium hirsutum) in response to A. flavus infection. Two modules consisting of 75 genes and 34 genes each were regulated by alternative splicing and showed co-expression induced by A. flavus and represent candidate genes for further studies towards resistant cotton.



Committee Chair

Labonte, Don R.



Available for download on Tuesday, August 13, 2024