Comparative transcriptome analysis provides insights into the gene regulation network of cytoplasmic male sterility in chilli pepper

Abstract Cytoplasmic male sterility (CMS) is a common biological phenomenon in chilli pepper hybrid production. Although several restorer-of-fertility (Rf) genes have been identified in pepper CMS lines, a regulatory network has yet to be constructed. Morphological characteristics of the sterile, maintainer, and restorer flower buds were studied at three different developmental stages. We conducted transcriptome analysis of the CMS/Rf system in pepper plants. Pentose and glucuronate interconversion pathways were particularly enriched in most comparison groups. In addition, differentially expressed genes among the different lines at flower bud stages 2 and 3 were generally enriched in amino sugar and nucleotide sugar metabolism pathways. In our study, the small auxin upregulated RNA (SAUR), A-ARR and GH3 genes in the plant hormone signal transduction pathway, Capana12g000348, CKX7 and cis-zeatin O-glucosyltransferase (CISZOG) genes in the zeatin biosynthesis pathway, and receptor-like protein kinase 2 (RLK2) in the germplasm development signal pathway showed gradual upregulation across developmental stages in the restorer line. However, expression of these genes was stable in the sterile and maintainer lines. qRT-PCR analysis showed that SAUR, A-ARR, GH3, Capana12g000348, CKX7, CISZOG, CRE1, AHP and TIR1 participate in CMS fertility regulation in chilli pepper. We constructed a regulatory network based on critical genes. Overall, our research provides a solid theoretical foundation for the development of CMS fertility studies on chilli pepper.