QTLs and epistasis for aluminum tolerance in rice (Oryza sativa L.) at different seedling stages

To investigate the genetic background for aluminum (Al) tolerance in rice, a recombinant inbred (RI) population, derived from a cross between an Al-se nsitive lowland indica rice variety IR1552 and an Al-tolerant upland japoni ca rice variety Azucena, was used in culture solution. A molecular linkage map, together with 104 amplified fragment length polymorphism (AFLP) marker s and 103 restriction fragment length polymorphism (RFLP) markers, was cons tructed to map quantitative trait loci (QTLs) and epistatic loci for Al tol erance based on the segregation for relative root length (RRL) in the popul ation. RRL was measured after stress for 2 and 4 weeks at a concentration o f 1mM of Al3+ and a control with a pH 4.0, respectively. Two QTLs were dete cted at both the 2nd and the 4th weeks on chromosomes 1 and 12 from uncondi tional mapping, while the QTL on chromosome 1 was only detected at the 2nd stress week from conditional mapping. The effect of the QTL on chromosome 1 2 was increased with an increase of the stress period from 2 to 4 weeks. Th e QTL on chromosome 1 was expressed only at the earlier stress, but its con tribution to tolerance was prolonged during growth. At least one different QTL was detected at the different stress periods. Mean comparisons between marker genotypic classes indicated that the positive alleles at the QTLs we re from the Al-tolerant upland rice Azucena. An important heterozygous non- allelic interaction on Al tolerance was found. The results indicated that t olerance in the younger seedlings was predominantly controlled by an additi ve effect, while an epistatic effect was more important to the tolerance in older seedlings; additionally the detected QTLs may be multiple allelic lo ci for Al tolerance and phosphorus-uptake efficiency, or for Al and Fe2+ to lerance.