Global transcriptome analysis reveals genes associated with seedling advance growth traits in a selfed family of Chinese fir (Cunninghamia lanceolata)

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is a major timber conifer species in southern China. In this study, we aimed to capture the rarely advanced phenomenon for selfing in this species and illustrated the underlying molecular mechanism, especially the hub gene-regulated networks and pathways, by global transcriptome analysis assays (RNA-Seq). Self-pollination trials revealed a wide variation of selfing effects among parents. Parent cx569 produced a selfed family with the best growth performance at the seedling stage. The growth-based extremely advanced (AD) (n=3) and depressed (DE) variants (n=3; different types) were then subjected to comparative RNA-Seq. The transcriptome data revealed more than 5000 differentially expressed genes (DEGs) for each comparison group (AD versus DE). Weighted gene co-expression network analysis (WGCNA) further identified more than 80 important DEGs that were significantly associated with growth traits in each comparison group. A subsequent enrichment analysis showed that the identified DEGs belonged to six main types, including xylem metabolism-related, sugar and energy metabolism-related, plant hormone signal transduction-related, stress response-related, cytochrome-related, and transcription factor genes. Ten hub genes represented by the ERF071, MYB-relate 305, WRKY6, WRKY31, PER3, LAC4, CESA8, CESA9, GID1, and PR1 genes were co-identified between AD and DE variants. These genes exhibited rather different expression patterns between AD and DE variants, especially of the transcription factor ERF071 gene that presented a low transcript level in the AD seedlings with only 4.45% activity compared to DE's. While, the plant hormone signal transduction GID1 gene was significantly upregulated in AD by about 20-fold when compared to DE's, and fold change of the lignin biosynthesis-related PER3, CESA9 and LAC4 gene expression parallel reached to 10–15 times in an upregulation pattern in AD seedlings. The set of hub gene-linked interaction networks and pathways revealed in this study may be responsible for the rarely advanced phenomenon for selfing at the seedling stage in Chinese fir.