Watermelon (Citrullus lanatus) is a globally important Cucurbitaceae crop in which grafting is commonly used to improve stress tolerance and enhance nutrient utilization. However, the mechanism underlying grafting-enhanced nutrient assimilation remains unclear. Here, we demonstrate the possible involvement of a novel Cucurbitaceae miRNA, ClmiR86, in grafting-enhanced phosphate-starvation tolerance via CALCINEURIN B-LIKE INTERACTING PROTEIN KINASE 5 (ClCIPK5) suppression in watermelon. Transcript analyses revealed that the induction of ClmiR86 expression was correlated with the downregulation of ClCIPK5 in squash-grafted watermelon under phosphate starvation. In addition, the differential expression of ClmiR86 in various watermelon genotypes was consistent with their phosphate utilization efficiency. Furthermore, ClmiR86 overexpression in Arabidopsis enhanced root growth and phosphate uptake under phosphate starvation and promoted inflorescence elongation under normal conditions. These results suggest that the ClmiR86–ClCIPK5 axis is involved in phosphate starvation response as well as grafting-enhanced growth vigor and phosphate assimilation. The present study provides valuable insights for investigating long-distance signaling and nutrient utilization in plants.

Waterlogging, like other abiotic stresses, severely inhibits the growth and development of watermelon. However, few genes conferring waterlogging escape response have been identified in this crop to date. In this study, we performed bulked segregant analysis on a F₂ population exhibiting significant variation in waterlogging-induced shoot elongation. A 6.59 Mb candidate region on chromosome 7 was identified to be associated with waterlogging-induced shoot elongation. Integrated resequencing, fine-mapping and transcriptome analyses indicated that Cla97C07G134400 (ClSCPL50) candidate gene associated with waterlogging-induced shoot elongation. These findings provide novel insights into the genetic basis of the waterlogging escape response in watermelon and identify a potential target gene for improving waterlogging escape response in other dryland crops.