ORIGINAL PAPER V.T. Nguyen ® B.D. Nguyen ® S. Sarkarung ® C. Martinez A.H. Paterson ® H.T. Nguyen Mapping of genes controlling aluminum tolerance in rice: comparison of different genetic backgrounds Received: 11 September 2001 /Accepted: 25 April 2002 / Published online: 7 June 2002 Ó Springer-Verlag 2002 Abstract Aluminum toxicity is the main factor limiting the productivity of crop plants in acid soils, particularly in the tropics and subtropics. In this study, a doubled- haploid population derived from the rice (Oryza sativa L.) breeding lines CT9993 and IR62266 was used to map genes controlling Al tolerance. A genetic linkage map consisting of 280 DNA markers (RFLP, AFLP and SSR) was constructed to determine the position and nature of quantitative trait loci (QTLs) affecting Al tolerance. Three characters – control root length (CRL), Al-stressed root length (SRL) and root length ratio (RR) – were evaluated for the DH lines and the parents at the seedling stage in nutrient solution. A total of 20 QTLs controlling root growth under Al stress and control conditions were detected and distributed over 10 of the 12 rice chromosomes, reflecting multigenic control of these traits. The two QTLs of largest effect, qALRR-1-1 and qALRR-8 for root length ratio (a measurement of Al tolerance) were localized on chromosomes 1 and 8, respectively. Three other QTLs in addition to qALRR-8 were apparently unique in the CT9993 · IR62266 mapping population, which may explain the high level of Al tolerance in CT9993. Comparative mapping identi- fied a conserved genomic region on chromosome 1 as- sociated with Al tolerance across three rice genetic backgrounds. This region provides an important starting point for isolating genes responsible for different mech- anisms of aluminum tolerance and understanding the genetic nature of this trait in rice and other cereals. Keywords QTL mapping ® Aluminum toxicity ® Rice genetics ® Oryza sativa L. ® Abiotic stress Introduction Soilsalinity,acidityandmineraldeficiencieswillcontinue tobeoneofthemajorproblemslimitingcropproductivity throughouttheworld.SanintandWood(1998)estimated thatmorethan45.5%ofriceproducedinLatinAmericais grown under upland conditions. The upland soils are in- fertile and mostly acidic in nature. Crops grown in such soils suffer from aluminum toxicity and calcium and phosphate deficiencies (Howeler and Cadavid 1976). Aluminum (Al) toxicity is the most important factor limitingcropproductivityintheacidsoilswhichcomprise large areas of the world (Kochian 1995), particularly in the tropics and subtropics (Foy et al. 1978; Foy 1984). The major symptom of aluminum toxicity is rapid in- hibition of root growth (Lu¨ttge and Clarkson 1992; Rengel 1992; Delhaize and Ryan 1995). The effect of aluminum toxicity is to arrest or slow down root growth. Asaresult,stuntedorshortenedrootsaretheprimaryand earliest symptom of aluminum toxicity. Bennett et al. (1987)suggestedthattherootcapisasiteofperceptionof Al-mediated injury. Roots injured by high Al are usually stubby and thick, and become dark-colored, brittle, Mol Genet Genomics (2002) 267: 772–780 DOI 10.1007/s00438-002-0686-1 Communicated by R. Hagemann The first two authors contributed equally to this study V.T. Nguyen College of Natural Sciences, Vietnam National University, Hanoi, Vietnam B.D. Nguyen ® H.T. Nguyen (&) Molecular Genetics and Plant Genomics Laboratory, Texas Tech University, Lubbock, TX 79409, USA E-mail: nguyenhenry@missouri.edu Tel.: +1-573-8825494 Fax: +1-573-8821469 S. Sarkarung International Rice Research Institute (IRRI), MCPO Box 3127, Mataki City, Philippines C. Martinez International Center for Tropical Agriculture (CIAT), Apartado Aereo 6713, Cali, Colombia A.H. Paterson Plant Genome Mapping Laboratory, Texas A and M University, College Station, Texas, TX 77843, USA Present address: A. H. Paterson Applied Genetic Technology Center (AGTEC), University of Georgia, Athens, GA 30602, USA