| Increasing yield potential in rice depends largely on plant type improvement and heterosis utilization. Rates of rice yield advances through rice breeding programs have apparently declined in recent years, which may be related to limited understanding of genetic basis for rice growth and yield development. Rice agronomic traits are quantitative traits, consequently controlled by multiple genes. Moreover, the main effects, epistatic effects and their environmental interactions of QTLs are all important genetic components of quantitative traits In this study, we analyzed the main effects,epistatic effects of the QTLs, and QTL by environment interactions (QEs) underlying six agronomic traits under two phosphorus supply conditions in 2008 and 2009 at WuXue, using a recombinant inbred population from Zhenshan 97 and Minghui 63 cross (F11, F12). The main results are as follows:1. We mapped QTLs for tiller number at different stages under two phosphorus conditions in the two years using conditional and unconditional QTL mapping. A total of 97 QTLs associated with tiller number were detected, which distributed in 12 chromosomes. QTL analysis reveals that the intervals of R1128b-RM81A on chromosome 1, RG360-R3166 on chromosome 5 and RG667-RG570 on chromosomes 9 are the three chromosomal regions which can simultaneously detected in different developmental stages under different environments. Results suggested that above regions maybe include alleles for controlling tiller development, which were worth further genetic identification and fine mapping.2. We mapped QTLs for plant height at different stages under two phosphorus conditions in the two years using conditional and unconditional QTL mapping. A total of 49 QTLs associated with plant height were detected, which distributed in 9 chromosomes except for chromosome 2, chromosome 5 and chromosome 12. QTL analysis reveals that the intervals of RZ471-RG678 on chromosome 7 and RM201-R1687 on chromosome 9 are the two chromosomal regions which can simultaneously detected in different developmental stages under different environments.They should be the important regions of fine mapping for plant height. 3. We mapped QTLs for plant height at maturity under two phosphorus conditions in the two years. A total of 4 QTLs were detected, which were all located on chromosome 7. The interval of RG128-RG528 was simultaneously detected in both two phosphorus levels in 2008. The interval of R1440-C1023 was simultaneously detected in both two phosphorus levels in 2009. The additive effects of four QTLs detected were all from MH63, which were in the direction of increasing plant height.4. We mapped QTLs for leaf area index at heading stage under two phosphorus supply conditions in the two years. A total of 8 QTLs were detected, which distributed in chromosome 1,4,6,7 and 11, respectively. The interval of RZ471-RG678 on chromosome 7 was simultaneously detected under both phosphorus-supply and no phosphorus-supply condition in 2008, which accounting for 26.85%and 9.16%of phenotypic variation, respectively. Two QTLs were detected under no phosphorus-supply conditions in 2009, which collectively explained 31.95%of phenotypic variation. The additive effects of four QTLs detected were all from MH63, which were in the direction of increasing plant height. The other two QTLs were detected under both phosphorus-supply and no phosphorus-supply conditions in 2008, which were located on chromosome 6 and chromosome 11. Alleles from Minghui 63 at six of the QTLs were in the direction of increasing leaf area index.5. We mapped QTLs for biomass at heading stage under two phosphorus conditions in the two years. A total of 6 QTLs were detected, which distributed in chromosome 7,10 and 11, respectively. The interval of R1440-C1023 on chromosome 7 was simultaneously detected under phosphorus-supply and no phosphorus-supply conditions in 2009 and phosphorus-supply condition in 2008, accounting for 32.64%,24.33%and 13.52%of phenotypic variation, respectively. The additive effects of four QTLs detected were all from MH63, which were in the direction of increasing biomass.6. We mapped QTLs for biomass at maturity under two phosphorus supply conditions in the two years. A total of 9 QTLs were detected, which distributed in chromosome 6,7,10 and 11, respectively. The interval of R2918-CDO127 on chromosome 11 was simultaneously detected under phosphorus-supply and no phosphorus-supply condition in 2008 and no phosphorus-supply condition in 2009, accounting for 10.62%,14.41%and 13.34%of phenotypic variation, respectively. This QTL was detected under three different environments. Results suggested that it might be the major gene controlling biomass at maturity. The interval of R1245-RZ471 on chromosome 7 was simultaneously detected under both phosphorus conditions in 2008. Alleles from Minghui 63 at eight of the QTLs were in the direction of increasing biomass.7. Interval of R1440-C1023 on chromosome 7 and R2918-CDO127 on chromosome 11 showed pleiotropic effects. QTLs distributed in same or similar regions, while significantly correlation among traits.8. Eleven QTLs with main effects showed QEs, but no Q×E was detected for the QTLs involved in epistatic interactions.
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