Abstract

The chromosomes of allotetraploid cotton underwent extensive structural variations (SVs), which is one of the critical features for gaining the polyploid vigor and the success of cotton domestication. The molecular mechanisms underlying beneficial SVs in polyploid genomes are still not well understood, which hinders the efficient application of SV in breeding. This study identifies a novel lncRNA, NEXUS (Non-coding RNAEXpands theUniverse ofStructural-variations), activated by the absence of about 6.3 kilobases (presence-absence variation, PAV-) on chromosome A06 in tetraploid cotton. Additionally, evolution trajectory unveiled that NEXUS arose during allotetraploid cotton diversification and commonly expressed in most cultivated cotton strains. Knocking down NEXUS through VIGS or knocking out NEXUS via CRISPR-Cas9 impairs the drought tolerance in upland cotton. Physiological studies indicated that NEXUS positively regulates tolerance to drought stress by maintaining ROS homeostasis, protecting chloroplast structure, and sustaining photosynthetic activity. Furthermore, NEXUS interacts with the promoter of stress-responsive gene GhRDUF1. Under drought stress, NEXUS recruits GhWDRL (WDR5a-like) to facilitate Histone 3 lysine 4 trimethylation (H3K4me3). This trans-effect enhances the expression of numerous target genes to increase stress resilience. Intriguingly, PAV- is highly correlated with increased drought tolerance, without affecting fiber yield and quality. Population analysis revealed that the PAV- variant has been positively selected in cultivated upland cotton. Therefore, these findings shed light on a new epigenetic marker fine-tuning complex traits in cotton, and provide potential insights into molecular breeding for maintaining stable and high yield under environmental stress.