<p>B chromosomes are nonessential chromosomes and are considered genetically inert. However, the maize B chromosome possesses several genetic properties during male gamete development in anthers. To determine whether the transcriptome of maize anthers is influenced by the B chromosome, we established the correlation between anther length and developmental stage in the maize B73 inbred line and applied complementary DNA-amplified fragment length polymorphism (cDNA-AFLP) analysis to microsporogenetic (MS) anthers, microgametogenetic (MG) anthers and mature pollen (MP) of B73 plants carrying zero (0B) and two B chromosomes (2B). The results revealed that 6.4%, 7.4% and 25.1% of 0B-extra or 2B-extra cDNA-AFLP fragments from MS anthers, MG anthers and MP, respectively, are present between B73 + 0B and B73 + 2B. Twelve out of the 13 2B-extra cDNA-AFLP fragments from MS anthers and MP are A chromosome-located sequences and are transcribed in the presence of the B chromosome. Some of these sequences are functional genes. The remaining 2B-extra cDNA-AFLP fragment isolated from MS anthers is a novel B chromosome-specific repeat, pMS4. On the basis of three B-10L translocations and fluorescence in situ hybridization, pMS4 was mapped to the short arm and the junction between the centromeric knob and the proximal euchromatin of the B chromosome. Reverse transcriptase PCR revealed that pMS4 is transcribed in a B chromosome dosage-dependent and tissue-specific manner. Taken together, our data suggest that the maize B chromosome can transcribe and influence the transcription of A chromosome-located genes in anthers at different developmental stages.</p>