Comparative Transcriptomic Analysis of the Weeping Branch Phenotype in Cunninghamia lanceolata var. Luotian

Cunninghamia lanceolata var. Luotian is a valuable variant of Chinese fir characterized by a weeping branch architecture, a narrow crown, and excellent natural pruning compared with Cunninghamia lanceolata. The weeping branch phenotype is a typical characteristic of Cunninghamia lanceolata var. Luotian; however, the molecular mechanisms potentially associated with this phenotype remain unclear. To investigate the gene expression characteristics associated with this phenotype, terminal buds and basal parts of one-, three-, and six-year-old lateral branches from C. lanceolata var. Luotian and C. lanceolata with comparable growth status were sampled for de novo transcriptome sequencing using the Illumina high-throughput platform. A total of 59,109 unigenes were obtained from transcriptome sequencing. The Q30 values of all samples were above 93.76%, with an average unigene length of 1175 bp and an N50 of 2293 bp. The mapping rates ranged from 68.11% to 79.25%, with an average of 75.65%. Comparative transcriptomic analysis revealed substantial differences in gene expression between C. lanceolata var. Luotian and C. lanceolata, with the largest number of DEGs detected in the terminal buds of three-year-old lateral branches. Differences in DEG numbers were also observed among comparisons involving different branch ages and tissue positions. KEGG enrichment analysis identified phenylpropanoid biosynthesis, plant hormone signal transduction, and MAPK signaling pathway–plant among the top-ranked pathways. Based on the analysis of the top 50 DEGs, several candidate genes, including TRINITY_DN19150_c0_g1, TRINITY_DN27401_c0_g1, and TRINITY_DN14240_c0_g1, were identified as potentially associated with lateral branch development. These findings suggest that signal transduction and secondary metabolism may be associated with the weeping branch phenotype of C. lanceolata var. Luotian. This study provides preliminary transcriptomic evidence and candidate gene resources for further investigation of the weeping branch phenotype, although the specific regulatory roles of these pathways and genes remain to be experimentally validated.