Repeat variants for the SbMATE transporter protect sorghum roots from aluminum toxicity by transcriptional interplay in and .

Acidic soils, where aluminum (Al) toxicity is a major agricultural constraint, are globally widespread and are prevalent in developing countries. In sorghum, the root citrate transporter SbMATE confers Al tolerance by protecting root apices from toxic Al, but can exhibit reduced expression when introgressed into different lines. We show that allele-specific transactivation occurs and is caused by factors located away from Using expression-QTL mapping and expression genome-wide association mapping, we establish that transcription is controlled in a bipartite fashion, primarily in but also in Multiallelic promoter transactivation and ChIP analyses demonstrated that intermolecular effects on expression arise from a WRKY and a zinc finger-DHHC transcription factor (TF) that bind to and -activate the promoter. A haplotype analysis in sorghum RILs indicates that the TFs influence expression and Al tolerance. Variation in expression likely results from changes in tandemly repeated sequences flanking a transposable element (a miniature inverted repeat transposable element) insertion in the promoter, which are recognized by the Al-responsive TFs. According to our model, repeat expansion in Al-tolerant genotypes increases TF recruitment and, hence, expression, which is, in turn, lower in Al-sensitive genetic backgrounds as a result of lower TF expression and fewer binding sites. We thus show that even dominant regulation of an agronomically important gene can be subjected to precise intermolecular fine-tuning. These concerted c/ interactions, which allow the plant to sense and respond to environmental cues, such as Al toxicity, can now be used to increase yields and food security on acidic soils.