Identification of quantitative trait loci (QTL) and genetic networks underlying drought tolerance using introgression and pyramiding lines of rice (Oryza sativa L.)

A new strategy was tried to genetically characterize drought tolerance (DT) in rice (Oryza sativa L.). A large backcross (BC) breeding program involving two recipients, IR64 (an elite indica line developed by IRRI) and Tequing (a high yielding and widely adaptable indica line from China), and eight donors from seven countries (including seven indica and one japonica lines). The recipients were crossed with the donors and backcrossed with the recipients twice to create 14 second generation of second backcross (BC2F2) bulk populations, from which a total of 373 DT introgression lines (ILS) were selected under severe terminal drought stress. The DT ILs were genotyped with simple sequence repeat (SSR) markers. Results of X square tests and linkage disequilibrium (LD) analyses revealed the identification of 78 putative DT QTLs as loci of significant excess of introgression and 20 association loops (ALs) as the multilocus structure of DT QTLs from both upland and lowland stresses. Two F2 populations were created from crosses between four promising DT ILs which were harboring QTLs based on the first experiment. The F2 populations were subjected to severe drought and survival DT plants were selected. The selected DT F2 plant were genotyped with differentiating SSR markers and progeny tested for yield and yield related traits under both stress and non-stress conditions. X square tests on the genotypic data at single locus and LD analyses on pairwise loci in the F2 populations verified most (greater than 85 percent) putative DT QTLs and QTL networks identified in the parental ILs. Graphic presentation of the genotypic data revealed a few predominant QTL group or genotype groups (multi-locus) in the selected DT lines from each F2 populations. Rhenotypic characterization of the selected F2 progeny in replicated experiments under stress and non-stress conditions revealed mechanism underlying DT in different group genotypes. Results suggest that the genetic basis of DT in rice and the breeding strategies for its improvements are as follows: (1) A large number of loci are involved in DT in rice and most of them are acting in groups, (2) High yielding rice cultivars with DT could be developed more efficiently by pyramiding of suitable QTL groups; and (3) Early flowering probably is the important mechanism for DT of the selected lines.