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Aluminum (Al) toxicity is the major constraint for crop productivity in acid soils. Wild rye species (Secale spp.) exhibited high Al-tolerance being a good source of genes related to this trait. The Alt1 locus located on 6RS chromosome arm is one of the four main loci controlling Al tolerance in rye and is known to harbor major genes but, so far, none has been found. Through the synteny among the short arm of the rye chromosome 6R and the main grass species, we found a candidate MATE gene for the Atl1 locus, posteriorly named ScMATE3,