The panicle apical abortion (PAAB) of rice is a typical quantitative trait determined by both genotypes that interact with growth environments (i.e. the ambient temperature). A chromosome segment substitution line Ats1 (aborted top spikelet mutant 1), which was originated from the cross-combination of Qiuguang ? Qishanzhan, was used for map-based cloning of the PAAB gene ATS1. Previous linkage analysis suggested that the candidate gene of AST1 was localized on chromosome 8, sharing a long fragment of positioning interval with that of the unidentified gene qPAA8. We compared the climate differences between 2018 and other years in Beijing and the phenotype of Ats1 under different growth environment conditions. The PAAB severity of Ats1 under the high environmental temperature in 2018 was significantly alleviated compared with ordinary years, indicating that high temperature might reduce the incidence of PAAB in Ats1. In addition, through the genetic analysis to the F2 population of newly created cross-combination IRAT129?Ats1, we further found that the genetic separation of PAAB obviously deviated from ratio of the single gene dominant inheritance, i.e. 3 PAAB to 1 normal, indicating that there are additional PAAB genes involved. Here we provided a convenient strategy on developing a single gene segregating population (SGSP), based on the phenotypic analysis in combination with marker-associated selection to individuals of F2:3 lines. Finally, we finally delimited the candidate gene of ATS1 to a 57 Kb interval including four potential candidate genes, settling a foundation for the final cloning of the target gene. This method could be helpful using in fine mapping on other complex traits easily affected by environmental conditions.