Fine-mapping of a major QTL controlling plant height by BSA-seq and transcriptome sequencing in cotton.

key messageGhSOT (GH_D05G3950) plays a negative role in regulating plant height development by modulating the GA signaling. Plant height is an important indicator affecting mechanical harvesting for cotton. Therefore, understanding the genes associated with the plant height is crucial for cotton breeding and production. In this study, we used bulk segregant analysis sequencing to identify a new quantitative trait locu (QTL) called qPH5.1, which is linked to plant height. Local QTL mapping using seven kompetitive allele-specific PCR (KASP) markers and linkage analysis successfully narrowed down qPH5.1 to ~ 0.34 Mb region harbored five candidate genes. Subsequently, RNA sequencing (RNA-seq) analysis and examination of expression patterns revealed that GhSOT exhibited the highest likelihood of being the candidate gene responsible for the plant height at this locus. Seven SNP site variations were identified in the GhSOT promoter between the two parents, and Luciferase experiments confirmed that the promoter of GhSOT from cz3 enhances downstream gene expression more effectively. Additionally, suppression of GhSOT in cz3 resulted in the restoration of plant height, further emphasizing the functional significance of this gene. Application of exogenous gibberellin acid (GA) significantly restored plant height in cz3, as demonstrated by RNA-seq analysis and exogenous hormone treatment, which revealed alterations in genes associated with GA signaling pathways. These results reveal GhSOT is a key gene controlling plant height, which may affect plant height by regulating GA signaling.