Genetic analysis of rooting ability of transplanted rice (Oryza sativa L.) under different water conditions

In order to assess the benefits of superior rooting ability of rice (Oryza sativa L.) for growth after transplanting under water-limiting conditions, genetic differences in the rooting ability of rice seedlings 30 d after sowing, with their visible roots either pruned or not pruned, were quantified by several root parameters 4 d after transplanting (DAT), under flooded or non-flooded paddy fields (four treatments in total), together with production traits at maturity. Ninety-eight recombinant inbred lines from the two japonica ecotypes, a lowland variety Otomemochi, and an upland variety Yumenohatamochi, were genotyped with 107 simple sequence repeat (SSR) markers. Otomemochi in general produced more adventitious roots, partitioned a greater proportion of biomass to roots, and had a greater increment of root dry weight (DeltaRW) at 4 DAT than Yumenohatamochi, but these variety differences were less clear under non-flooded conditions without root pruning. Several quantitative trait loci (QTLs) associated with rooting ability were identified mainly in chromosomes 1, 4, and 6 across the four treatments or in combined analysis. On the other hand, QTLs for DeltaRW around RM2357 in chromosome 5 and for maximum new root length in RM215-RM205 in chromosome 9 were found only under root pruning treatments and under non-flooded conditions without root pruning, respectively. Greater DeltaRW was associated with higher head dry weight per hill at maturity only in the non-flooded and root-pruning treatments. This study suggests the importance of rooting ability after transplanting and, possibly, other mechanisms for adaptation to non-flooded conditions.