Mapping QTLs for morphological traits under two water supply conditions at the young seedling stage in rice

Plant seedling morphological characteristics are known to be important in drought resistance of rice (Oryza sativa L.) varieties. Ninety six recombinant inbred-line (RIL) rice lines of an indica and japonica cross were grown in both flooding condition and upland condition and QTLs for seedling morphology traits were examined using 256 markers. A total of 33 putative QTLs were associated with the four seedling traits: shoot height (SH), root biomass (RW), shoot biomass (SW) and root to shoot dry weight ratio (RSR). Four QTLs detected were the same under control and upland conditions. The ratio between the mean value of the seedling trait under upland and flooding conditions was used for assessing drought tolerance. A total of 7 QTLs for drought tolerance were detected with contribution rates varying from 10.0 to 27.0%. Comparative analysis was performed for the QTLs detected in this case and those reported from two other populations with the same upland rice variety Azucena as parent. Several identical QTLs for plant mass and seedling length across the three populations with the positive alleles from the upland rice Azucena were found, which suggests that these alleles of Azucena may be involved in water stress-accelerated plant mass and elongation of rice under different genetic backgrounds. Four cell wall-related candidate genes for OsEXP2, OsEXP4, EXT and XET were mapped on the intervals carrying the QTLs for seedling traits. These identified QTLs for seedling traits might be useful for improving drought resistance of rice by MAS.