Two mechanisms are believed to contribute to drought tolerance (DT) in rice. A deep and thick root system in the upland rice lines (japonicas)is largely responsible for their tolerance to drought. Alternatively, a better developed osmotic adjustment (OA) capacity in indica cultivars is considered to be a reliable mechanism to maintain the cell turgor under diminishing leaf water potential, potentially contributing to DT. To test the hypothesis of whether the two different DT mechanisms can be combined through QTL pyramiding four QTLs (Located on chromosomes 1, 2, 7, and 9) identified in a rice DH population were transferred into an indica variety, IR64, using a marker-assisted back cross program. Thirty BC_3F_3 near isogenic lines with 1-2 introgressed QTLs were obtained and evaluated in a replicated greenhouse experiment for the target root traits and two nontarget traits-number of tillers per plant and plant height. Three of the 4 introgressed QTLs (targets 1, 7, and 9), which were detected with greater LOD previously, were associated with the expected root phenotype, while the other (target 2) was not. The introgressed root QTLs were associated with either reduced tiller number or increased height, but this association was inconsistent, indicating that the observed genetic drag was more likely due to linkage rather than to pleiotropy. The concept and procedure of a new approach-the molecular backcross breeding strategy - were propose that allow simultaneous identification, transfer, and allelic diversity discovery of desirable QTLs. This approach should be able to overcome all the limitations of MAS for QTLs and has all the advantages of the AB-QTL analysis. However, the effectiveness of phenotypic selection for DT in the BC progenies remains the key to success for this approach
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