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Genetics, Vol. 179, 669-682, May 2008, Copyright © 2008
doi:10.1534/genetics.107.083451
An ALMT1 Gene Cluster Controlling Aluminum Tolerance at the Alt4 Locus of Rye (Secale cereale L.)
N. C. Collins*,2,
N. J. Shirley*,
M. Saeed*,1,
M. Pallotta* and
J. P. Gustafson
* Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA 5064, Australia and United States Department of Agriculture–Agricultural Research Service, Plant Genetic Research Unit, University of Missouri, Columbia, Missouri 65211
2 Corresponding author: Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA 5064, Australia.
E-mail: nick.collins{at}acpfg.com.au
Aluminum toxicity is a major problem in agriculture worldwide. Among the cultivated Triticeae, rye (Secale cereale L.) is one of the most Al tolerant and represents an important potential source of Al tolerance for improvement of wheat. The Alt4 Al-tolerance locus of rye contains a cluster of genes homologous to the single-copy Al-activated malate transporter (TaALMT1) Al-tolerance gene of wheat. Tolerant (M39A-1-6) and intolerant (M77A-1) rye haplotypes contain five and two genes, respectively, of which two (ScALMT1-M39.1 and ScALMT1-M39.2) and one (ScALMT1-M77.1) are highly expressed in the root tip, typically the main site of plant Al tolerance/susceptibility. All three transcripts are upregulated by exposure to Al. High-resolution genetic mapping identified two resistant lines resulting from recombination within the gene cluster. These recombinants exclude all genes flanking the gene cluster as candidates for controlling Alt4 tolerance, including a homolog of the barley HvMATE Al-tolerance gene. In the recombinants, one hybrid gene containing a chimeric open reading frame and the ScALMT1-M39.1 gene each appeared to be sufficient to provide full tolerance. mRNA splice variation was observed for two of the rye ALMT1 genes and in one case, was correlated with a 
400-bp insertion in an intron.