Date of Award

12-2025

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Plant and Environmental Science

Committee Chair/Advisor

Dr. Christopher A. Saski

Committee Member

Dr. Churamani Khanal

Committee Member

Dr. Jeremy K. Greene

Committee Member

Dr. William C. Bridges

Abstract

Cotton has been central to human civilization and has contributed significantly to the economies of both developed and developing countries. Among the cultivated species, Upland cotton (Gossypium hirsutum) and Pima cotton (Gossypium barbadense) dominate global production, with G. hirsutum being the predominant species grown in the USA. The use of contemporary genomic tools is critical to improving cotton traits like plant architecture for increased productivity and robust biotic resilience, while improving fiber and seed quality traits. To achieve this, we utilized the CRISPR-Cas9 gene editing tool to engineer cotton plants with modified branch angles by knocking out the tiller angle control (TAC1) gene, which regulates branch angle in woody dicots. We conducted a gen analysis of the TAC1 gene in cotton, with our findings revealing that it is duplicated in cotton (3 copies) compared with 1 to 2 in other crops. We developed TAC1 lines (TAC1-73 and TAC1-74) exhibiting columnar branch angles, and we validated the low expression via gene profile analysis. Additionally, we utilized the CRISPR-Cas 9 gene editing mechanism to knock out the mildew resistance locus O (MLO), specifically the mlo3 gene, which is a negative regulator of plant immunity to the reniform nematode (Rotylenchulus reniformis). The knockout lines showed resistance to R. reniformis infection, as indicated by reduced reproductive capability. Furthermore, we developed a biparental mapping population to breed for oil content, lint percentage, and seed index. We evaluated these lines across six locations in the USA Cotton Belt and identified promising lines that exhibited consistent performance across the locations and years. Moreover, we detected stable quantitative trait loci (QTLs) across the tested environments. Some of these stable QTLs co-localize for lint and seed index, and we observed co-inherited QTLs for oil content and seed index. Candidate gene analysis also revealed several genes and regulatory proteins for oil, lint percentage, and seed index. This integrated strategy is elaborated upon in the following research, which combines genetic and molecular profiling with field studies. This facilitated the identification of plant architecture genes, unraveling novel alternative host-plant resistance mechanisms to plant-parasitic nematodes, and enhancing oil, fiber, and seed quality traits. Ultimately, my research aims to enhance upland cotton productivity, meeting stakeholder demands and providing valuable cotton germplasm for future breeding.

Author ORCID Identifier

0000-0001-5357-8621

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