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Background  In flowering plants, the development of male reproductive organs is controlled precisely to achieve successful fertilization and reproduction. Despite the increasing knowledge of genes that contribute to anther development, the regulatory mechanisms controlling this process are still unclear.    Results  In this study, we analyzed the transcriptome profiles of early anthers of sterile mutants  aborted microspores  ( ams ) and found that 1,368 genes were differentially expressed in  ams  compared to wild type anthers, affecting metabolism, transportation, ubiquitination and stress response. Moreover, the lack of significant enrichment of potential AMS binding sites (E-box) in the promoters of differentially expressed genes suggests both direct and indirect regulation for AMS-dependent regulation of anther transcriptome involving other transcription factors. Combining  ams  transcriptome profiles with those of two other sterile mutants,  spl/nzz  and  ems1/exs , expression of 3,058 genes were altered in at least one mutant. Our investigation of expression patterns of major transcription factor families, such as  bHLH, MYB  and  MADS , suggested that some closely related homologs of known anther developmental genes might also have similar functions. Additionally, comparison of expression levels of genes in different organs suggested that anther-preferential genes could play important roles in anther development.    Conclusion  Analysis of  ams  anther transcriptome and its comparison with those of  spl/nzz  and  ems1/exs  anthers uncovered overlapping and distinct sets of regulated genes, including those encoding transcription factors and other proteins. These results support an expanded regulatory network for early anther development, providing a series of hypotheses for future experimentation.

AMS-dependent and independent regulation of anther transcriptome and comparison with those affected by other Arabidopsis anther genes