Transcriptome-wide analysis to dissect the transcription factors orchestrating the phase change from vegetative to reproductive development in Larix kaempferi

Abstract

The timing of phase change from vegetative to reproductive development during aging of forest trees is important for wood and seed production. In a previous study, we investigated the effects of aging on wood formation by measuring the transcriptomic changes in the uppermost main stems of 1-, 2-, 5-, 10-, 25-, and 50-year-old Larix kaempferi. Based on the published transcriptome data, here we investigated the transcriptomic differences between the juvenile vegetative (1-and 2-year-old) and adult reproductive (25-and 50year-old) phases to determine the molecular mechanisms underlying the phase change. In total, 12,789 transcripts were identified as differentially expressed genes, including 573 transcription factors. Further analysis showed that 27 transcription factors belonging to 8 families were common to all four comparisons between old and young life stage categories: (I) 25 vs 1 year old; (II) 50 vs 1 year old; (III) 25 vs 2 years old; and (IV) 50 vs 2 years old. The analysis of their expression patterns in six age categories showed that members of the AP2 and Dof families were expressed highly in 1-and 2-year-old trees, weakly in 25-and 50-year-old trees, while members of the C3H, G2-like, GRAS, MYB-related, and MADS families had the opposite patterns. Notably, one member of the MADS family was only detected in 25-and 50-year-old trees. These results suggest that the phase change might (1) occur in the early stage of the L. kaempferi lifetime and (2) be controlled by a complex regulatory network of different transcription factors, some of which are known to play roles in the phase change in model plants. These findings not only provide molecular markers to distinguish different stages of tree growth and development and potential targets for genetic manipulation to improve the reproductive traits of trees, but also improve our understanding of the phase change with aging in trees.

Effects of Cutting, Pruning, and Grafting on the Expression of Age-Related Genes in Larix kaempferi

“…Many genes have been found to function in plant aging, some of which promote maturation, such as Suppressor of Overexpression of Constans 1 (SOC1) [8], APETALA1 (AP1) [9], Squamosa-Promoter Binding Protein-Like (SPL) [10], and DAL1 (a MADS-box gene) [11], and some delay maturation or maintain the juvenile state, such as microRNA miR156 [12], miR171 [13], Tempranillo (TEM) [14], Terminal Flower 1 (TFL1) [15], MdTFL1 and MdTFL1a [16], Juvenile-to-Adult transition (JAT) [17], LaAP2L1 (a heterosis-associated AP2/EREBP transcription factor from Larix) [18], and Picea abies APETALA2-like genes [19]. In our previous study, 27 age-related transcripts were found to be expressed differentially in stems between the juvenile vegetative (1-and 2-year-old) and adult reproductive (25-and 50-year-old) phases of L. kaempferi, and some of them are homologous to the genes noted above (Figure 1), indicating that they might have similar functions in aging; meanwhile, they may be useful as molecular markers to determine the state of plants [20]. Together, these findings not only aid studies of the molecular mechanisms of aging and rejuvenation, but also provide candidate genes as molecular markers to assess the state of plants.…”

“…The open reading frame (ORF) finder (https://www.ncbi.nlm.nih.gov/orffinder/) was used to identify the ORFs of the 27 transcription factors reported in our previous work [20] (Table 2). Based on the results, primers (Table S1) were designed to clone their full-length cDNA sequences (https://www.ncbi.nlm.nih.gov/tools/primer-blast/) with Platinum ® Taq DNA polymerase (Invitrogen, Carlsbad, CA, USA).…”

“…Based on the results of blast analysis with Arabidopsis thaliana homologs, we assigned the Gene Ontology (GO) terms associated with the A. thaliana homologs to larch transcription factors. [20].…”

“…Analytical flowchart. Twenty-seven transcripts differentially expressed between the juvenile vegetative (1-and 2-year-old) and adult reproductive (25-and 50-year-old) phases of Larix kaempferi, identified in a previous study [20] were analyzed again and used to identify molecular markers and assess the effects of cutting, grafting, and pruning on gene expression.…”

Over-Expression of Larch DAL1 Accelerates Life-Cycle Progression in Arabidopsis

“…& Zucc. to reveal the molecular basis of the conifer reproductive phase change [1][2][3]. Differentially expressed genes have been identified, and a regulatory network model has been proposed for L. kaempferi based on these genes [3].…”