Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)


Plant and Environmental Science

Committee Chair/Advisor

Sachin Rustgi

Committee Member

Michael A. Jones

Committee Member

B. Todd Campbell

Committee Member

Sruthi Narayanan


Cotton (Gossypium spp.) is a major export commodity for the U.S. Despite advances in plant breeding and management practices, the cotton yield gains in the U.S. have stagnated. Therefore, to increase cotton fiber yield, we undertook a novel approach by altering the growth habit of cotton from perennial to annual. In this effort, eight genotypes showing strong expression alleles for five floral induction and meristem identity genes were selected from 44 Upland cotton mini-core collection genotypes and genetically crossed in various combinations to stack the strong expression alleles in a genotype. These efforts have allowed us to develop high-yielding, high-fiber quality, and early-maturing cotton lines exhibiting reduced regrowth after defoliant. In addition, we identified 396 expression trait (e-trait) associated polymorphic SNPs through genome-wide association analysis. Among e-trait-associated markers, 159 were mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased distribution of the e-trait-associated markers was observed, where more markers mapped to D subgenome. Many e-trait-associated SNPs coincided to specific genomic regions. This finding has implications as these traits could be bred together. This analysis also allowed us to identify six candidate genes possibly involved in the regulation of flowering time and meristem identity-related traits. The functions of two candidate genes Gohir.D05G103700 encoding GATA transcription factor (TF) and Gohir.D12G153600 encoding SPL-TF, were characterized by virus-induced gene silencing. The downregulation of the Gohir.D05G103700 gene in two plants produced a unique phenotype where the fourth bract of the cotton square was missing, a trait indicative of indeterminate growth.

Author ORCID Identifier


Available for download on Saturday, August 31, 2024