Integrative transcriptome and long non-coding RNA analysis to decipher the molecular basis of cleistogamy in...

This study uncovered potential regulatory networks associated with cleistogamy in pigeonpea by analyzing interactions between lncRNAs, mRNAs, and miRNAs. Cleistogamy, a unique floral adaptation, is a valuable trait offering a unique reproductive advantage in self-pollinated species. In crops like pigeonpea, outcrossing significantly contributes to the deterioration of varietal purity, impacting the overall seed purity. Thus, as a primary effort to get molecular insights governing cleistogamy in pigeonpea, we performed RNA-seq analysis of unopened flower buds from three pigeonpea genotypes having different flower morphologies i.e., ICPL87154 (cleistogamous), ICPL87119 (chasmogamous), and UP26 (partially wrapped petals). Comparative analysis revealed differential gene expression patterns in the cleistogamous vs. chasmogamous combination. Comparative transcriptome profiling identified differential enrichment of biological pathways between the genotypes. Relative to the non-cleistogamous genotype, the cleistogamous genotype exhibited increased expression of genes involved in carbohydrate metabolism and ubiquitin-mediated proteolysis, whereas genes associated with hormone signaling and endocytosis showed reduced expression. To further delineate the regulation, LncRNAs were predicted from the assembled transcriptome, and a total of 25,307 transcripts were identified as lncRNAs based on length, exon number, and coding potential. Further interaction analysis revealed regulatory lncRNA-miRNA-mRNA networks, and expression validation of key networks uncovered some candidate genes, such as FT-interacting protein 1 (FTIP1) and auxin response factor 2A, that can be potentially involved in this trait. Upregulation of miRNAs miR156b, miR169g, and miR171g in the cleistogamous genotype suggests the post-transcriptional regulation of cleistogamy. Additionally, simple sequence repeats (SSRs) identified in differentially expressed genes and lncRNAs offer additional genomic resources pertaining to this trait. This study provides the first comprehensive identification of DEGs and DE-lncRNAs associated with cleistogamy in pigeonpea, laying the groundwork for further molecular dissection.