A Comparative Analysis of cDNA-AFLP and Transcriptome Sequencing Data Identifies Uncharacterized Gene(s) Potentially Involved in Artificial Flower Induction Following Potassium Chlorate Treatment in the Thai Dimocarpus Longan Cultivar E-Daw

Abstract

Artificial induction of flowering in longan (Dimocarpus longan) is typically achieved through the application of potassium chlorate (KClO<inf>3</inf>), a chemically unstable and environmentally toxic compound. Given the associated risks, the development of alternative flowering induction methods is urgently required. To investigate the early molecular responses to KClO<inf>3</inf> treatment, cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis was employed to identify differentially expressed transcripts between treated and control samples. Seven differentially expressed fragments were successfully cloned, sequenced and utilized for primer design. Alignment analysis revealed that LcAF9, LcAF14 and LcAF18 sequences share similarity with transcriptomic data from previous studies in Thai and Chinese longan cultivars, particularly those associated with KClO₃-induced flowering experiments and various longan tissues. The remaining four fragments showed no similarity to existing sequences, suggesting they may represent novel genes involved in flowering regulation. Semi-quantitative RT-PCR and real-time PCR confirmed the differential expression of specific genes at particular time points especially in KClO<inf>3</inf>-treated samples (LcAF7, LcAF10, LcAF14, and LcAF17), while LcAF9 and LcAF18 exhibited dynamic patterns of upregulation and downregulation in a time-dependent manner. These findings demonstrate the utility of cDNA-AFLP in detecting differentially expressed genes that may not be captured by RNA sequencing due to detection thresholds. Furthermore, all seven LcAF primers successfully amplified genomic DNA from longan. Notably, LcAF8, LcAF9 and LcAF17 primers displayed polymorphic PCR patterns among 32 Thai longan samples, indicating their potential as molecular markers. These markers may serve as valuable tools for various applications, particularly in longan breeding programs aimed at genetic improvement and cultivar selection.