Molecular markers linked to the aluminium tolerance gene Alt1 in rye (Secale cereale L.)

 Rye has one of the most efficient group of genes for aluminium (Al) tolerance among cultivated species of Triticeae. This tolerance is controlled by at least two independent and dominant loci (Alt1 and Alt3) located on chromosomes 6RS and 4R. We used two pooled DNA samples, one of Al-tolerant individuals and another of Al-sensitive plants from one F2 that segregated for the Alt1 locus. We also used two pooled DNA samples, one with genotypes 11 and another with genotypes 22 for the Lap1 locus (leucin aminopeptidase) from another F2 progeny that segregated for this locus, located on the 6RS chromosome arm. We identified several RAPD markers associated with the pooled Al-tolerant plants and also with one of the bulks for the Lap1 locus. The RAPD fragments linked to Alt1 and Lap1 genes were transformed into SCAR markers to confirm their chromosomal location and linkage data. Two SCARs (ScR01600 and ScB157900) were closely linked to the Alt1 locus, ScR01600 located 2.1 cM from Alt1 and ScB15790 located 5.5 cM from Alt1, on the 6RS chromosome arm. These SCAR markers can aid in the transfer of Al tolerance genes into Al-sensitive germplasms.