Molecular characterization of cotton: Genome size evolution and the genomics and metabolomics of osmotic stress in roots

The yield stability and fiber quality of cotton (Gossypium hirsutum L.) can be reduced as a result of drought stress. The objective of this research was to develop tools that plant breeders and molecular biologists can use to improve drought tolerance of cultivated cotton. Two approaches were pursued. The first approach focused on germplasm development. To develop hybrids compatible with cultivated cotton, the chromosomes of interspecific-hybrid plants comprising wild cotton relatives (G. davidsonii and G. anomalum) were doubled using colchicine. DNA contents of the synthetic lineage were assessed via flow cytometry. The mean DNA content of the F 1 hybrids was 1.93 pg, 11% lower than the expected value. Additionally, DNA content values for 37 Gossypium species were measured. The mean DNA content of the five natural tetraploid species was 6% lower than the expected value, similar to the DNA loss observed in the newly formed tetraploid hybrids. The second approach focused on the identification of genes and biochemical processes differentially regulated in response to polyethylene glycol-induced osmotic stress in roots as an initial step towards developing markers for drought-related QTLs in cotton. Time-course gene expression, ion, and metabolite profiles were measured in the roots of G. hirsutum 'Siokra L23' utilizing cotton-fiber based microarrays, HPLC, and atomic absorption spectroscopy. Four-hundred twenty two genes had statistically significant (FDR < 1%) expression changes. During the early phase of stress, the root organic acid:sugar ratio increased 65%. The regulation of several genes related to beta-oxidation and the glyoxylate pathway suggested these glyoxysomal reactions were involved in this shift. Osmotic adjustment occurred in the early phase of stress as K+ content increased 29% in stressed roots, consistent with the regulation of two genes involved in K+ transport. Potassium accumulation was coupled to simultaneous reductions in the expression levels of seven aquaporin genes. The association between K + and water transport was further explored using the yeast two-hybrid method. Regulation of membrane permeability to water, decreased cellular solute potential, and efficient production of carbon skeletons are the primary root-localized mechanisms by which Siokra L23 acclimated to osmotic shock.