China, particularly the cotton-growing province of Xinjiang, is experiencing acute agricultural water shortages, stifling the expansion of the cotton sector. Discovering drought resistance genes in cotton and generating high-quality, drought-resistant cotton varieties through molecular breeding procedures are therefore critical to the cotton industry’s success. The drought-resistant cotton variety Xinluzhong No. 82 and the drought-sensitive cotton variety Kexin No. 1 were utilised in this study to uncover a batch of drought-resistant candidate genes using whole transcriptome sequencing. The following are the key research findings: A competing endogenous RNA network (ceRNA) was built using complete transcriptional sequencing to screen the core genes in the core pathway, and two drought-related candidate genes were discovered. It was found that γ-aminobutyric acid aminotransferase (GhGABA-T, Gohir.A11G156000) was upregulated at 0 h vs. 12 h and downregulated at 12 h vs. 24 h. L-Aspartate oxidase (GhAO, Gohir.A07G220600) was downregulated at 0 h vs. 12 h and upregulated at 12 h vs. 24 h. GABA-T is analogous to a pyridoxal phosphate-dependent transferase superfamily protein (POP2) in Arabidopsis thaliana and influences plant drought resistance by controlling γ-aminobutyric acid (GABA) concentration. The analogue of GhAO in A. thaliana is involved in the early steps of nicotinamide adenine dinucleotide (NAD) production as well as in plant antioxidant responses. This study revealed that gene expression regulatory networks can be used for rapid screening of reliable drought resistance genes and then utilised to validate gene function.

Cotton mechanized harvesting is the development direction of cotton production. The rapid development of mechanized cotton harvesting in Xinjiang has significantly increased the efficiency of cotton harvesting and reduced the harvesting cost. However, in the rapid development of mechanized cotton harvesting, there are also the problems of net yield, recovery rate and poor harvesting quality, which lead to the poor quality competitiveness of mechanized cotton harvesting. In order to solve the problem of mechanized cotton loss, the key is to reduce the problem of cotton miscellaneous, and breed cotton varieties suitable for mechanized harvesting. The purpose of this study was to clarify the key trait correlation of defoliation through the establishment and association analysis of foliation and deciduous phenotype indicators in cotton. In this study, the phenotypic indexes of defoliation and deciduous traits were established through the comprehensive analysis of the defoliation rate of 273 cotton germplasm resources and other 11 related phenotypic traits in the field, in order to provide guidance for the breeding and production of cotton varieties collected by breeders. In addition to peeling rate, an analysis of the association between 11 agronomic parameters and peeling rate and hanging rate revealed that the number of effective branches, chlorophyll SPAD value, fruit branch angle, and hanging rate have substantial correlation in 3 years. Hence The hanging rate, fruit branch angle, effective branch number, and chlorophyll SPAD value can be used as the evaluation indicators of varieties for peeling ability trait index.