Accurate mapping of the target traits is prerequisite for effectiveness of marker-assisted selection (MAS). Two previously identified quantitative trait loci (QTLs) conferring thicker basal root thickness (BRT) and higher index of drought resistance (IDR), located on chromosomes 4 and 6, designated brt4.1 and idr6.1 respectively, were chosen as target QTLs to study the MAS effects for traits related to rice drought resistance. Four segregating populations derived from crosses between a drought resistance upland rice cultivar and two lowland rice cultivars with high yield potential and better grain quality were used in this study. The results showed that flanking markers of brt4.1 and idr6.1 were genetically stable in different populations, with different genetic backgrounds. In populations YIBC1, JIBC1 and JIF2 under upland condition, the differences between the means of the basal root thickness (BRT) of individuals carrying and not carrying favorable alleles of brt4.1 flanking markers were 0.05–0.06 mm, significant at 5% or 1% probability levels. MAS effects were 5.05%–6.12%. When selection with flanking markers of idr6.1, the differences between the means of the upland grain yield per plant (YP) were 5.04–8.18 g, significant at 5% or 1% probability levels. MAS effects were 34.89%–58.88%. For the flanking markers of both of these QTLs were selected simultaneously, the corresponding differences were 0.06–0.08 mm and 4.88–11.15 g. MAS effects were 6.06%–8.16% and 39.91%–70.48% respectively. The results also revealed that selection with flanking markers of brt4.1or idr6.1 or both of them could not obtain the expected drought resistance in population YIBC1 under lowland conditions. MAS effects based on selection for one or both of the flanking markers of the target QTLs were also studied. A working procedure for rice drought resistance breeding was suggested.
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