Transcriptome sequencing-based analysis on the formation mechanism of fiber micronaire differences between two sister lines derived from Gossypium hirsutum-G. barbadense hybrid

The fiber micronaire is a comprehensive index for characterizing the fineness and maturity of cotton fibers. However, high micronaire value hinders the production of high-count yarns in textiles. Reducing the micronaire remains a major challenge in breeding high-quality cotton cultivars. In this study, transcriptome sequencing was conducted on the fibers of sister lines derived from <italic>Gossypium hirsutum</italic>-<italic>G. barbadense</italic> hybrid, namely LM (line with low micronaire value) and HM (line with high micronaire value), at 15, 20, 25, and 30 days post anthesis (DPA), respectively. These two lines exhibited highly significant differences in micronaire values, while showing no significant differences in fiber length or strength. The mechanisms underlying the micronaire variation were investigated from multiple perspectives, including cellular structure, phytohormones, cellulose synthesis, and gene expression. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and hormone quantification suggested that auxin is likely the key plant hormone influencing secondary wall development in both LM and HM lines. Observations of fiber structure, measurements of cellulose content, and KEGG pathway analysis indicated that the orientation and arrangement of cellulose microfibrils may play a more critical role in determining micronaire than cellulose metabolism itself. This developmental process relies on coordinated biological events, including cellulose biosynthesis, cellulose synthase complex (CSC) formation, and the precise localization and dynamic adjustment of microtubules, actin filaments—all of which are modulated by auxin. Additionally, the differentially expressed genes related to cell content degradation may contribute to the differences in lumen size between mature LM and HM fibers. The identified metabolic pathways and differentially expressed genes provide a theoretical basis and genetic resources for breeding cotton varieties with optimized micronaire values suited for textile applications.