Genome-wide identification and analysis of paclobutrazol-resistance gene family in cotton and the positive role of GhPRE3 in salt stress and drought stress resistance

Compared with other transcription factors, much less studies have been performed on paclobutrazol-resistance (PRE), a subgroup of the extensive bHLH transcription factor gene family, and the research in cotton was also limited. By utilizing the PRE genes and their conserved domains identified in Arabidopsis, a total of 23, 22, 11, and 12 PRE genes were identified from two major cultivated cotton species and their two ancestors, respectively. The cotton PRE gene family was categorized into three subgroups based on evolutionary tree analysis. Motif and intron analyses indicated that the PRE gene has remained highly conserved throughout evolution. Collinearity analysis indicated that gene duplication, particularly through fragment replication, has significantly contributed to the expansion of the cotton PRE family. An exploration of the conserved elements within the PRE gene family uncovered numerous elements associated with plant stress resistance. Additionally, cotton transcriptome and qRT-PCR analysis showed that PRE genes were associated with a variety of abiotic stresses, including salt, drought, and cold treatments. Subcellular localization experiments indicated that the GhPRE3 gene is associated with membrane proteins. Finally, we selected the GhPRE3 gene for a VIGS experiment, which revealed that under salt stress and drought stress conditions, the wilting of leaves in the GhPRE3-silenced plants was significantly more severe than that observed in the control group, with T-AOC levels notably lower and MDA levels significantly higher. Overexpression of GhPRE3 enhanced seed germination and root development in transgenic Arabidopsis thaliana under salt stress and drought stresses. This suggests that GhPRE3 plays a positive regulatory role in cotton tolerance to salt and drought stressed, providing a reference for molecular genetic breeding of cotton with salt and drought tolerance.