Male sterility in a near-isogenic line S45 AB with 25 generations of sub-crossing, is controlled by two pairs of duplicate genes.The genotype of S45A is Bnms1Bnms1Bnms2Bnms2, and that of S45B is BnMs1Bnms1Bnms2Bnms2.The histological observations revealed that the abnormality of anther development appeared in tapetum and pollen exine during tetrad stage.This male sterility was characterized by the hypertrophy of tapetal cells at tetrad stage and a complete lack of microspore exine after the release of microspores from the tetrads.To elucidate the mechanism of this recessive genic male sterility (RGMS), the flower bud expression profiles of S45A and S45B lines were analyzed using an Arabidopsis thaliana ATH1 oligonucleotide array.Compared with that in S45B line, a total of 69 down regulated and 46 up regulated genes whose expression changed in S45A line at a significant level were identified.The real-time PCR was then used to verify the result of microarray analysis and the majority of down regulated genes in S45A line were expressed abundantly and specifically in anther.The results of real-time PCR suggested that the BnMs1 might be involved in metabolism of lipid/fatty acids, and the homologous mutation of BnMs1 might block the biosynthesis of sporopollenin or the deposition of it on the microspore surface which lead to failure of the pollen exine formation.The role of BnMs1 in the regulation network of exine formation is discussed as well.