| Water deficiency has become the bottleneck of agriculture and economy in China. In order to improve the drought resistance of rice variety, it is important to dissect QTLs of traits related to drought resistance and to perform molecular marker assisted selection in rice drought resistance breeding. A Doubled Haploid (DH) population and a Recombinant Inbred Line (RIL) population including 116 and 120 plants respectively, derived from the same cross between Japonica upland rice IRAT109 and paddy rice Yuefu, were used in this study. Two molecular linkage maps with 165 and 201 markers covering 1535.1 cM and 1833.8 cM respectively were produced. The average genetic distance between adjacent markers was 9.3 cM and 9.0 cM respectively. Phenotypic values of root traits, culm traits, yield and its components, index of drought resistance, osmotic potential, water potential and stomatal resistance of DH, RIL population and the parents were obtained under upland, lowland and PVP pipe cultivated conditions. Using index of drought resistance (IDR), the ratio of yield under upland condition to yield under lowland condition, as the criteria of drought resistance, correlation analysis between root traits, physiological traits, yield and its components traits and IDR were conducted. QTLs associated with these traits were located on the two molecular linkage maps. The result showed that basal root thickness and maximum root length were significantly positively correlated with IDR, while root number was negatively correlated with IDR. High IDR lines had thicker BRT, longer MRL and less RN than low IDR lines.Osmotic potential, osmotic adjustment and water potential under lowland condition were significantly correlated with IDR, while no significant correlations were observed of these traits under upland condition. This result indicated the complexity of physiological traits (OP, OA and WP) to drought resistance under upland condition. Correlation and path analysis of yield components to plant yield under upland and lowland conditions showed that seed set ratio and 1000-grain weight were more easily affected by water stress than grains per tiller and tillers per plant did. Path analysis showed that root traits (BRT, MRL and RDW), physiological traits (OP, OA and WP) were directly contributed to IDR.QTLs and Q*E interactions for root traits at tillering stage in DH population and dynamic QTLs for root traits during the whole growth period of RIL population were obtained. The results demonstrated that QTLs for root traits expressed differently at different stages. Some pleiotropic or tightly linked QTL regions such as RM529-RM1068 on chromosome 1, RM521-RM438 on chromosome 12, controlling both root traits and IDR (yield components) were found. QTL mapping for osmotic potential, osmotic adjustment, water potential and stomatal resistance were also practiced. It was found that QTLs for osmotic potential and osmotic adjustment were expressed by environmental inducement. Compared the QTL regions for different traits, it was found that there were some pleiotropic or tightly linked QTLs such as R2558-G1458 on chromosome 5, RM270-RM235 on chromosome 12, for physiological traits. QTLs of yield and its components for DH and RIL populations under upland and lowland conditions were obtained. Some QTLs expressed only underupland condition. QTL analysis on lodging resistance (including culm length, basal culm thickness and culm strength) under upland and lowland conditions were also conducted using DH population and the constructed molecular linkage map. Some QTLs with high general contributions to phenotypic variation were detected.Some common QTL regions between DH and R1L populations, such as nine QTL regions for root traits, four QTL regions for physiological traits and five QTL regions for yield and its components traits were found. Based on the common QTL regions, pleiotropic or tightly linked QTLs, and QTLs with high general contributions under upland condition, molecular markers for MAS i.e., RM529-RM1068 on chromosome 1 a...
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