Clade specific divergence, cumulative haplo-pheno analysis, and genomic prediction of cytokinin oxidase (CKX) gene family under drought stress in rice.

Cytokinin oxidases (CKXs) function in regulating yield and abiotic stress tolerance. In rice, though CKXs phylogeny is well understood, clade specific divergence in motifs, expression, and genetic associations for drought stress tolerance are not comprehensively studied. The clade specific motifs analysis identified a motif, UvrA_inter domain of OsCKX10 is present in five species (O. barthii, O. glaberrima, O. meridionalis, and both O. sativa subspecies indica and japonica) of rice. Specifically, major Clade II CKXs (CKX6, CKX7, and CKX10) expression is less prominent in developmental tissues. Further, fourteen genetic variants (three in exons and eleven in regulatory regions) of seven CKXs (OsCKX1, OsCKX2, OsCKX4, OsCKX5, OsCKX8, OsCKX9 and OsCKX10) were associated with different root related traits under drought stress contributing to phenotypic variance of 10–57%. Cumulative haplo-pheno analysis of all seven associated CKXs identified significant differences for plant height (p = 0.03*) and convex hull width (p = 0.04*) under stress. Further, correlation coefficient was in the range of 0.32–0.73 for different drought stress related traits between the genomic predicted values and actual phenotypic values. Thus, uniqueness of clade II, seven CKXs associated with drought stress, high genomic prediction of phenotypes using fourteen CKXs genetic variants are the major findings of this study. These findings underscore the critical roles of OsCKX genes in drought responses and offer valuable insights for developing drought-resilient rice varieties.