Axillary meristem growth and development help define plant architecture in barley (Hordeum vulgare L). Plants carrying the recessive uniculm2 (cul2) mutation initiate vegetative axillary meristem development but fail to develop tillers. In addition, inflorescence axillary meristems develop into spikelets, but the spikelets at the distal end of the inflorescence have an altered phyllotaxy and are sometimes absent. Double mutant combinations of cul2 and nine other recessive mutations that exhibit low to high tiller number phenotypes resulted in a uniculm vegetative phenotype. One exception was the occasional multiple shoots produced in combination with granum-a; a high tillering mutant that occasionally produces two shoot apical meristems. These results show that the CUL2 gene product plays a role in the development of axillary meristems into tillers but does not regulate the development of vegetative apical meristems. Moreover, novel double-mutant inflorescence phenotypes were observed with cul2 in combination with the other mutants. These data show that the wild-type CUL2 gene product is involved in controlling proper inflorescence development and that it functions in combination with some of the other genes that affect branching. Our genetic analysis indicates that there are genetically separate but not distinct regulatory controls on vegetative and inflorescence axillary development. Finally, to facilitate future positionally cloning of cul2, we positioned cul2 on chromosome 6(6H) of the barley RFLP map.

Circular RNAs (circRNAs) are covalently closed, single-stranded RNA molecules. Recent studies in human showed that circRNAs can arise via transcription of reverse complementary pairs of transposons. Given the prevalence of transposons in the maize genome and dramatic genomic variation driven by transposons, we hypothesize that transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. To test our hypothesis, we performed circRNA-Seq on B73 seedling leaves and integrate these data with 977 publicly available mRNA-Seq datasets. We uncovered 1,551 high-confidence maize circRNAs, which show distinct genomic features as compared to linear transcripts. Comprehensive analyses demonstrated that LINE1-like elements (LLE) and their Reverse Complementary Pairs (LLERCPs) are significantly enriched in the flanking regions of circRNAs. Interestingly, the accumulation of circRNA transcripts increases, while the accumulation of linear transcripts decreases as the number of LLERCPs increases. Furthermore, genes with LLERCP-mediated circRNAs are enriched among loci that are associated with phenotypic variation. These results suggest that LLERCPs can modulate phenotypic variation by the formation of circRNAs. As a proof of concept, we showed that the presence/absence variation of LLERCPs could result in expression variation of one cicrRNA, circ352, and further related to plant height through the interaction between circRNA and functional linear transcript. Our first glimpse of circRNAs uncovers a new role for transposons in the modulation of transcriptomic and phenotypic variation via the formation of circRNAs.