Aluminum (Al) toxicity restricts root growth and agricultural yield in acid soils, which constitute approximately 40% of the potentially arable lands worldwide. The two main mechanisms of Al tolerance in plants are internal detoxification of Al and its exclusion from root cells. Genes encoding membrane transporters and accessory transcription factors, as well as cis-elements that enhance gene expression, are involved in Al tolerance in plants; thus studies of these genes and accessory factors should be the focus of molecular breeding efforts aimed at improving Al tolerance in crops. In this review, we describe the main genetic and molecular studies that led to the identification and cloning of genes associated with Al tolerance in plants. We include recent findings on the regulation of genes associated with Al tolerance. Understanding the genetic, molecular, and physiological aspects of Al tolerance in plants is important for generating cultivars adapted to acid soils, thereby contributing to food security worldwide.

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 Al³⁺, but can exhibit reduced expression when introgressed into different lines. We show that allele-specificSbMATEtransactivation occurs and is caused by factors located away fromSbMATE. Using expression-QTL mapping and expression genome-wide association mapping, we establish thatSbMATEtranscription is controlled in a bipartite fashion, primarily incisbut also intrans. Multiallelic promoter transactivation and ChIP analyses demonstrated that intermolecular effects onSbMATEexpression arise from a WRKY and a zinc finger-DHHC transcription factor (TF) that bind to andtrans-activate theSbMATEpromoter. A haplotype analysis in sorghum RILs indicates that the TFs influenceSbMATEexpression and Al tolerance. Variation inSbMATEexpression likely results from changes in tandemly repeatedcissequences flanking a transposable element (a miniature inverted repeat transposable element) insertion in theSbMATEpromoter, which are recognized by the Al³⁺-responsive TFs. According to our model, repeat expansion in Al-tolerant genotypes increases TF recruitment and, hence,SbMATEexpression, 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 dominantcisregulation of an agronomically important gene can be subjected to precise intermolecular fine-tuning. These concerted cis/transinteractions, which allow the plant to sense and respond to environmental cues, such as Al³⁺toxicity, can now be used to increase yields and food security on acidic soils.

Summary: Impaired root development caused by aluminum (Al) toxicity is a major cause of grain yield reduction in crops cultivated on acid soils, which are widespread worldwide. In sorghum, the major Al‐tolerance locus, Alt_SB, is due to the function of SbMATE, which is an Al‐activated root citrate transporter. Here we performed a molecular and physiological characterization of various Alt_SB donors and near‐isogenic lines harboring various Alt_SB alleles. We observed a partial transfer of Al tolerance from the parents to the near‐isogenic lines that was consistent across donor alleles, emphasizing the occurrence of strong genetic background effects related to Alt_SB. This reduction in tolerance was variable, with a 20% reduction being observed when highly Al‐tolerant lines were the Alt_SB donors, and a reduction as great as 70% when other Alt_SB alleles were introgressed. This reduction in Al tolerance was closely correlated with a reduction in SbMATE expression in near‐isogenic lines, suggesting incomplete transfer of loci acting in trans on SbMATE. Nevertheless, Alt_SB alleles from the highly Al‐tolerant sources SC283 and SC566 were found to retain high SbMATE expression, presumably via elements present within or near the Alt_SB locus, resulting in significant transfer of the Al‐tolerance phenotype to the derived near‐isogenic lines. Allelic effects could not be explained by coding region polymorphisms, although occasional mutations may affect Al tolerance. Finally, we report on the extensive occurrence of alternative splicing for SbMATE, which may be an important component regulating SbMATE expression in sorghum by means of the nonsense‐mediated RNA decay pathway.

Controlled germination has emerged as an effective and sustainable bioprocess to enhance the nutritional and functional quality of cereal grains, including sorghum, a climate-resilient crop widely cultivated in tropical and semi-arid regions. Germination triggers coordinated physiological and molecular responses that activate secondary metabolism, particularly the phenylpropanoid pathway, resulting in qualitative and quantitative changes in phenolic compounds. This review summarizes current evidence on germination-driven modulation of sorghum phenolics, with emphasis on bioactivity and genetic regulation. Germination promotes the transcriptional activation of key biosynthetic genes, including those encoding phenylalanine ammonia-lyase and flavonoid pathway enzymes, while regulatory genes associated with condensed tannin biosynthesis, such as Tannin1 (Tan1) and Tannin2 (Tan2), may undergo functional modulation during sprouting, contributing to reduced antinutritional tannin levels. Gene expression and metabolic outcomes are strongly influenced by environmental factors such as soaking duration, temperature, oxygen availability, and elicitation conditions. The resulting phenolic profile exhibits enhanced antioxidant capacity and health-promoting potential. In sorghum-based systems, germination represents a promising strategy to increase bioactive density, reduce antinutritional constraints, and add value to grains. Improved understanding of gene–metabolite interactions during germination may support targeted breeding and the development of functional foods with improved nutritional performance.