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Background  Aluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition to naturally occurring acid soils, agricultural practices may decrease soil pH, leading to yield losses due to Al toxicity. Elucidating the genetic and molecular mechanisms underlying maize Al tolerance is expected to accelerate the development of Al-tolerant cultivars.    Results  Five genomic regions were significantly associated with Al tolerance, using 54,455 SNP markers in a recombinant inbred line population derived from Cateto Al237. Candidate genes co-localized with Al tolerance QTLs were further investigated. Near-isogenic lines (NILs) developed for  ZmMATE2  were as Al-sensitive as the recurrent line, indicating that this candidate gene was not responsible for the Al tolerance QTL on chromosome 5,  qALT5 . However,  ZmNrat1 , a maize homolog to  OsNrat1 , which encodes an Al 3+  specific transporter previously implicated in rice Al tolerance, was mapped at ~40 Mbp from  qALT5 . We demonstrate for the first time that  ZmNrat1  is preferentially expressed in maize root tips and is up-regulated by Al, similarly to  OsNrat1  in rice, suggesting a role of this gene in maize Al tolerance. The strongest-effect QTL was mapped on chromosome 6 ( qALT6 ), within a 0.5 Mbp region where three copies of the Al tolerance gene,  ZmMATE1,  were found in tandem configuration.  qALT6  was shown to increase Al tolerance in maize; the  qALT6- NILs carrying three copies of  ZmMATE1  exhibited a two-fold increase in Al tolerance, and higher expression of  ZmMATE1  compared to the Al sensitive recurrent parent. Interestingly, a new source of Al tolerance via  ZmMATE1  was identified in a Brazilian elite line that showed high expression of  ZmMATE1  but carries a single copy of  ZmMATE1 .    Conclusions  High  ZmMATE1  expression, controlled either by three copies of the target gene or by an unknown molecular mechanism, is responsible for Al tolerance mediated by  qALT6 . As Al tolerant alleles at  qALT6  are rare in maize, marker-assisted introgression of this QTL is an important strategy to improve maize adaptation to acid soils worldwide.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-153) contains supplementary material, which is available to authorized users.

Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan