Integrating Tobacco Whole-Transcriptome and Competitive Endogenous RNA Network Reveal the Potential Cytoplasmic Male Sterility Mechanism

Cytoplasmic male sterility (CMS) is significant in crop breeding, but a few studies have addressed the whole-transcriptomes and competitive endogenous RNA (ceRNA) network. Our study conducted a comparative analysis between CMS lines and maintainer lines of tobacco cultivars Zhongyan 90 using a combination of phenotypic observation and whole-transcriptome sequencing. The morphological and cytological observation showed that the CMS lines exhibited stamen developmental anomalies, and no pollen formation was observed in the anther; the whole-transcriptome analysis identified 2247 differentially expressed messenger RNAs (DEmRNAs), 529 DElncRNAs, 59 DEmiRNAs, and 16 DEcircRNAs, which are involved in anther and pollen development; the ceRNA network analysis revealed that several non-coding RNAs (miR156 and miR172, etc.) and genes (AP2 and bZIP, etc.) might affect tobacco fertility through the regulation of anther development, pollen wall formation, and tapetum PCD. In particular, candidate factors related to fertility such as OPT, MSTRG.72279.1, MSTRG.15634.1, miR6164 and NW_015800836.1:90|2321 have received insufficient attention in previous CMS studies. This study not only enriches the non-coding RNA candidate factors and their regulatory networks in tobacco CMS research, but also provide novel ideas for genetic improvement and hybrid vigor utilization in related crops.