Barley (Hordeum vulgare L.) carrying recessive mutations at the Low number of tillers1 (Lnt1) gene does not develop secondary tillers and only develops one to four tillers by maturity. Double mutant analysis determined that the lnt1 mutant was epistatic to five of the six low and high tillering mutants tested. Double mutants of lnt1 and the low tillering mutant intermedium-b (int-b) resulted in a uniculm plant, indicating a synergistic interaction and that Lnt and Int-b function in separate tillering pathways. RNA profiling identified 70 transcripts with either increased or decreased abundance in the lnt1 mutant compared to wild-type. One gene with reduced transcript levels in the lnt1 mutant was the BELL-like homeodomain transcription factor JuBel2. The JuBel2 allele in the lnt1. a mutant contained a frameshift mutation that eliminated most of the predicted polypeptide, indicating that the Lnt1 gene encodes JuBel2. Previous studies with the low-tillering mutant absent lower laterals (als) showed that the tillering phenotypes and genetic interactions of als and lnt1 with other tillering mutants were very similar. However, the transcriptomes were very different; many transcripts annotated as stress and defense response exhibited increased abundance in the als mutant. This difference suggests a functional separation between Als and Lnt1 in the genetic control of tillering.