Through a map-based cloning approach, a long-RNA -encoding gene for photoperiod-sensitive genie male sterility, pms3, which can regulate the pollen fertility in rice, is isolated. The nucleotide acid sequence of pms3 is a shown in SEQ ID NO: 2. The nucleotide acid sequence of its allele is shown in SEQ ID NO: 3, which contains an allelic mutation of C to G at position 790bp. A molecular marker for selectively breeding the genes for rice photoperiod-sensitive genie male sterility is also identified. SEQ ID NO: 1 represents the nucleotide acid sequence of this molecular marker, which contains a point mutation at position 4730bp. Uses of the said pms3 gene, its allele and molecular marker in breeding and genetic improvement of rice, especially in the production of new rice male sterile lines and the selective breeding of rice photoperiod-sensitive male sterile lines are provided.
