The rye transcription factor ScSTOP1 regulates the tolerance to aluminum by activating the ALMT1 transporter

•The transcription factor ScSTOP1 of rye has been identified and located on rye chromosome arm 3RS.•Several TF binding sites for STOP1 were detected in the promoter regions of the ScALMT1, TaALMT1 and TaMATE1 genes.•The transcription factor ScSTOP1 is involved in the regulation of the expression of the aluminum tolerance gene ScALMT1.•The Arabidopsis AtSTOP1 is more important for the stress caused by root illumination than by Pi deficiency. Plants have evolved different mechanisms to increase their tolerance to aluminum (Al) toxicity and low pH in the soil. The Zn finger transcription factor SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) plays an essential role in the adaptation of plants to Al and low pH stresses. In this work, we isolated the ScSTOP1 gene from rye (Secale cereale L.), which is located on chromosome 3RS. The ectopic expression of ScSTOP1 complements the Arabidopsis stop1 mutation in terms of root growth inhibition due to Al and pH stress, as well as phosphate starvation tolerance, suggesting that rye ScSTOP1 is a functional ortholog of AtSTOP1. A putative STOP1 binding motif was identified in the promoter of a well-known STOP1 target from rye and Arabidopsis and was later corroborated by genomic DAP-seq analyses. Coexpression analyses verified that ScSTOP1 activated the promoter of ScALMT1. We have also identified a putative phosphorylatable serine in STOP1 that is phylogenetically conserved and critical for such activation. Our data indicated that ScSTOP1 also regulated Al and pH tolerance in rye.