Open Access Open Badges Research article

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

Claudia T Guimaraes1*, Christiano C Simoes2, Maria Marta Pastina1, Lyza G Maron3, Jurandir V Magalhaes1, Renato CC Vasconcellos2, Lauro JM Guimaraes1, Ubiraci GP Lana1, Carlos FS Tinoco4, Roberto W Noda1, Silvia N Jardim-Belicuas2, Leon V Kochian5, Vera MC Alves1 and Sidney N Parentoni1

Author Affiliations

1 Nucleus of Applied Biology, Embrapa Maize and Sorghum, Road MG424, km 65, Sete Lagoas, MG 35701-970, Brazil

2 Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil

3 Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA

4 Departamento de Biologia, Centro Universitário de Sete Lagoas, Sete Lagoas, MG, Brazil

5 Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture – Agriculture Research Service, Cornell University, Ithaca, NY, USA

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BMC Genomics 2014, 15:153  doi:10.1186/1471-2164-15-153

Published: 24 February 2014



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.


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 Al3+ 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.


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.

Genotyping-by-sequencing; MATE; Marker-assisted selection; Copy number variation