In this study,a RIL population(Recombination Inbreeding Lines)derived from a cross between 9311(Indica)and Nipponbare(Japonica),containing 173 lines,was employed to construct molecular genetic linkage map and carry out the genetic analysis of hybrid breakdown by mapping of QTL related to spikelet and pollen fertilities The main results were described as follows: Construction of genetic linkage map of rice A total of 635 SSR(Simple Sequence Repeat)markers,34 STS(Sequence Tagged Site)and CAPS markers were used to screen the polymorphism between two parents,201 markers were finally used to construct a genetic linkage map in population of 173 lines.