Transcriptome Analysis of lncRNA and mRNA Expression Profiles During Safflower (Carthamus tinctorius) Seed Germination and Seedling Establishment

Background: Safflower (Carthamus tinctorius L.) is a high-value economic crop with broad applications in agriculture, industry, and traditional medicine. Seed germination and seedling establishment are critical stages in the safflower life cycle, as they directly influence subsequent seedling establishment, survival, and plant growth. However, the transcriptomic dynamics and regulatory mechanisms underlying these processes remain largely unexplored, and the functional roles of long non-coding RNAs (lncRNAs) in this context are also poorly understood. Methods: In this study, transcriptome sequencing was performed across five developmental stages from seed germination to seedling establishment in safflower, followed by a comprehensive transcriptomic analysis and lncRNA identification. Results: Transcriptome sequencing identified a total of 3027 lncRNAs, including 940 natural antisense transcript (NAT)-pair-associated lncRNAs, which were classified into the divergent, convergent, and chimeric categories. Among these, 767 lncNATs were differentially expressed. Further analysis identified 542 NAT pairs in which both the protein-coding gene and its corresponding lncNAT exhibited a differential expression across the five developmental stages. A functional enrichment analysis of the predicted target genes of these lncRNAs suggested their involvement in photosynthesis and hormone-related responses. An enrichment analysis of differentially expressed genes (DEGs) across developmental stages further revealed the significant enrichment of photosynthesis and plant hormone signal transduction-related pathways, suggesting that these pathways are closely associated with safflower seed germination and seedling establishment. A further analysis of photosynthesis-related genes, particularly the expression patterns of LHC family members, suggested that Stage 3 may represent an important developmental transition associated with the optimization of the light-harvesting capacity during early seedling establishment, whereas plant-hormone-related genes are involved in regulating seed germination and subsequent leaf growth during seedling establishment. In addition, a weighted gene co-expression network analysis (WGCNA) identified candidate transcription factors associated with photomorphogenesis and plant hormone responses in safflower. Conclusions: This study advances our understanding of the regulatory mechanisms underlying safflower seed germination and subsequent growth and provides valuable molecular resources for future safflower breeding programs.