Genome-wide profiling of circular RNAs in the hybridization of two elite inbred lines of Gossypium hirsutum.

• Around 340 circRNAs were identified from leaf, fiber and ovule in upland cotton. • Single parent expressed circRNAs played an essential role in heterosis. • Thirty-two key circRNAs related to formation of heterosis were identified. • A cotton fiber development related potential ceRNA-PPI network were established. Circular RNA (CircRNA) is a type of single-stranded RNA that plays a vital role in gene regulation during and after transcription. However, the functional role of circRNA in polyploid crop hybridization has not yet been reported. In this study, a high-yield elite upland cotton (Gossypium hirsutum) inbred line, 4133Bt, crossed with a high-quality elite inbred line, J02–247, produced a high -yield and high-quality F 1 hybrid. An RNA-sequence library was constructed from three biological replicates of the parents and F 1 hybrids in the vegetative and reproductive growth periods. A total of 340 high-confidence circRNAs were identified. Our results showed that the circRNAs were more active in ovules than in fiber and leaves and that the host genes of ovule-specific circRNAs were involved in nucleoside metabolic processes. In addition, single parent expressed (SPE) circRNAs and extremely nonadditively expressed (ENAE) circRNAs had different expression patterns in the F 1 hybrid. Moreover, 32 out of the 340 circRNAs were found to be dominant (expression level dominance, ELD) or overdominant (transgressive) at the expression level. These circRNAs might regulate the expression of their host genes through competitive inhibition. Eight of these 32 circRNAs might regulate gene expression through a putative ceRNA network. At 0 days post-anthesis (0 DPA) ovule, five circRNAs were found to interact with six miRNAs that are associated with the regulation of cytoskeleton- and plant cell wall-related genes during the initiation stage of cotton fiber development. Two circRNAs that interacted with two miRNAs to regulate vesicle transport and signal transduction pathways during the fiber elongation stage were identified at 10 DPA (fiber). These results indicate that circRNA may regulate the initiation and elongation stages of cotton fiber via a sponge model during the hybridization process. This study provides a deeper understanding of the molecular mechanism of hybrid breeding from a new perspective. [ABSTRACT FROM AUTHOR]