The long non-coding RNA NEXUS arose from a chromosomal structural variation and enhances drought tolerance through...

The chromosomes of allotetraploid cotton have accumulated numerous structural variations (SVs), which are critical features underlying the acquisition of polyploid vigor and the success of cotton domestication. The molecular mechanisms that underlie beneficial SVs in polyploid genomes are still not well understood, hindering their efficient use in cotton breeding. Here, we identify a novel long non-coding RNA, NEXUS (Non-coding RNA Expands the Universe of Structuralvariations), that is activated by the absence of a ∼6.3-kb presence-absence variation (PAV^-) on chromosome A06 of tetraploid cotton. Analysis of its evolutionary trajectory revealed that NEXUS arose during the diversification of allotetraploid cotton and is expressed in most cultivated cotton accessions. Knockdown of NEXUS by virus-induced gene silencing or knockout by CRISPR-Cas9 genome editing impaired the drought tolerance of upland cotton. Physiological studies indicated that NEXUS positively regulates drought tolerance by maintaining reactive oxygen species homeostasis, chloroplast structure, and photosynthetic activity. Furthermore, NEXUS interacts with the promoter of the stress-responsive gene GhRDUF1. Under drought stress, NEXUS recruits GhWDRL (WDR5a-like) to facilitate histone H3 lysine 4 trimethylation (H3K4me3). This trans-effect enhances the expression of numerous target genes to increase stress resilience. Intriguingly, PAV^- is strongly correlated with increased drought tolerance but does not affect fiber yield or quality. Population analysis revealed that the PAV^- variant has been positively selected in cultivated upland cotton. These findings identify a new epigenetic marker for fine-tuning complex traits in cotton and provide insights to support molecular breeding for maintaining high and stable yields under environmental stress.