Phosphoproteomic and physiological analysis revealed 6-benzyladenine improved the operation of photosynthetic apparatus in waterlogged summer maize

•Waterlogging-induced damages on summer maize were related with phosphorus signals.•Application of 6-BA effectively improved the operation of photosynthetic apparatus in waterlogged summer maize by affecting the cytokinin-induced phosphorus signals.•Application of 6-BA in agricultural practices provides new insights into curbing adverse climate change-related effects on crop production.