High-throughput transcriptomic analysis of circadian rhythm under different photoperiods in carrot

Carrot (<italic>Daucus carota</italic> L.) is an important root vegetable crop belonging to the Apiaceae family. The biological clock, or circadian rhythm, is typically a 24 h endogenous cycle that plays a crucial role in how higher plants perceive environmental changes through its function as an internal timing molecular network. Photoperiod regulates growth and development processes, and also affects the chlorophyll synthesis of carrot plants. This study employed high-throughput transcriptome analysis technology to investigate changes in gene expression within chlorophyll metabolism-related genes of carrots under different treatments in a single photoperiod (24 h). Three distinct environments were used: photoperiodic lighting (16 h of light : 8 h of dark, 16L/8D), photoperiodic lighting (12 h of light : 12 h of dark, 12L/12D), and photoperiodic lighting (8 h of light : 16 h of dark, 8L/16D) conditions. Time-series sampling was conducted at 3 h intervals (24 h), during which chlorophyll values were measured. Subsequently, transcriptome sequencing was performed at four time points, and bioinformatics analysis was used to identify and annotate differentially expressed genes involved in chlorophyll metabolism. The present results demonstrate that long-day conditions (16L/8D) significantly promote the accumulation of chlorophyll <italic>a</italic>, chlorophyll <italic>b</italic>, and total chlorophyll in carrot leaves, with peak values reaching 1.160 and 0.486 mg·g⁻¹ at 15 h, respectively. Transcriptome analysis revealed numerous differentially expressed genes (DEGs) associated with the circadian rhythm and chlorophyll metabolism across the different photoperiods. Key chlorophyll biosynthetic genes, such as <italic>Hem</italic> and <italic>POR</italic>, were upregulated under long-day conditions, whereas genes like <italic>CAO</italic> and <italic>CHL</italic> showed differential expression patterns indicative of photoperiodic regulation. The present findings provide a potential molecular basis for understanding how photoperiods regulate chlorophyll metabolism in carrots, revealing the intrinsic mechanisms of circadian rhythm regulation in carrots.