Genome-wide identification of long non-coding RNAs revealing their regulatory roles under seed development in ricebean (Vigna umbellata)

Long non-coding RNAs (lncRNAs) are crucial components of regulatory networks that govern plant growth, development, and various stress responses. Vigna umbellata (ricebean) is a nutritious and underutilized legume with significant potential to enhance sustainable food security. However, the lack of characterization of lncRNAs and gene expression patterns in ricebean limits understanding of its regulatory mechanisms. High-throughput RNA-seq was used to identify high-confidence lncRNAs in contrasting genotypes of ricebean at 5 and 10 days post-anthesis (DPA). A total of 3,369 potential lncRNAs were identified. Among these, 955 were differentially expressed lncRNAs (DE-lncRNAs), which either cis-regulate or trans-regulate the expression of adjacent or distant genes. Further, 151 lncRNAs were acting as putative precursors of 228 known miRNAs, targeting 475 protein-coding genes. The competing endogenous RNA network analysis revealed that 8 lncRNAs interacted with 19 miRNAs and competed for 446 mRNAs. We also identified endogenous target mimics (eTMs) and found that 78 lncRNAs interacted with 59 miRNAs, forming a total of 151 lncRNA–miRNA mimicry interactions. Functional enrichment analysis confirmed the involvement of these lncRNAs in seed development, having functions like DAR-1 protein, ubiquitin-conjugating enzymes, LEUNIG_HOMOLOG (LUH), Auxin-responsive protein IAA8, Expansin-like B1 (EXLB1), and Nuclear Transcription Factor Y. The target genes enrichment analysis showed that these genes were involved in epigenetic regulation and the control of gene expression. Notably, several targets belonged to key transcription factor families, including SQUAMOSA PROMOTER-BINDING-LIKE (SPL), ethylene-responsive (RAP2), and MYB. In addition, they were enriched in signalling pathways including jasmonate, brassinosteroid, Gibberellin (GA), abscisic acid (ABA), Auxin, and MAPK, which play a crucial role in seed development, germination, and stress response. This study reports the first identification of long non-coding RNAs in ricebean. It provides new insights into their possible regulatory roles during seed development. The findings improve our understanding of the molecular processes involved in seed development in ricebean. They also lay the groundwork for future studies on function and comparison in legume crop improvement.