Transcriptome dynamics of rooting zone and aboveground parts of cuttings during adventitious root formation in Cryptomeria japonica D. Don

Abstract

Background: Adventitious root formation is an essential physiological process for successful propagation of cuttings in various plant species. Because coniferous species are highly heterozygous, propagation of cuttings is of great practical use in breeding. Although various factors influence adventitious root formation, little is known of the associated regulatory mechanisms. Whereas adventitious roots generally form from the base of cuttings, this process is accompanied by physiological changes in leaves, which supply assimilates and metabolites. Herein, we present microarray analyses of transcriptome dynamics during adventitious root formation in whole cuttings in the coniferous species, Cryptomeria japonica.

Results: Temporal patterns of gene expression were determined in the base, the middle, and needles of cuttings at eight time points during adventitious root formation. Global gene expression at the base had diverged from that in the middle by 3-h post-insertion, and changed little in the subsequent 3-days post-insertion, and global gene expression in needles altered characteristically at 3- and 6-weeks post-insertion. In Gene Ontology enrichment analysis of major gene clusters based on hierarchical clustering, the expression profiles of genes related to carbohydrates, plant hormones, and other categories indicated multiple biological changes that were involved in adventitious root formation.

Conclusions: The present comprehensive transcriptome analyses indicate major transcriptional turning and contribute to the understanding of the biological processes and molecular factors that influence adventitious root formation in C. japonica.

Keywords: Adventitious root formation; Conifer; Cryptomeria japonica; Microarray; Needles; Transcriptome.

Fig. 1

Three parts of C. japonica cutting collected for microarray analyses

Fig. 2

Data processing

Fig. 3

Principal component analysis of microarray data. The plot illustrates the principal components of (a) all 24 sample groups for 10,327 genes in “all”, (b) all 16 sample groups for 9,633 genes in “base and middle” and (c) all 8 sample groups for 6,555 genes in “needles” that were differentially expressed among time points. Abbreviations for time points are as described in the Methods

Fig. 4

Hierarchical clustering analyses of differentially expressed genes among time points. Heatmaps include (a) all 24 sample groups for 10,327 genes in “all”, (b) all 16 sample groups for 9,633 genes in “base and middle” and (c) all 8 sample groups for 6,555 genes in “needles”, respectively. Labeled bars indicate distinct clusters that were used in further analyses. Color strengths of red and green indicate up- and down-regulation of gene expression level, respectively. Abbreviations for time points are described in the methods; B, base of cuttings; M, middle of cuttings; N, needles

Fig. 5

Expression profiles of major clusters. Expression levels of transcripts that varied for at least one sample group were categorized into (a) 13 groups in “all”, (b) 12 groups in “base and middle” and (c) 8 groups in “needles” based on Pearson’s correlations. Red lines indicate the average expression profiles of each cluster. Abbreviations for time points are as described in the Methods

Fig. 6

Expression profiles of specific terms in major clusters. Line graphs show expression levels of specific terms in major clusters for (a) “all”, (b) “base and middle” and (c) “needles”. Abbreviations for time points are as described in the Methods

Fig. 7

Heatmap of expression of the top 100 genes with the largest PC1. Abbreviations for time points are as described in the Methods

Fig. 8

Expression patterns of candidate genes related to adventitious root formation. Abbreviations for time points are as described in the Methods

Fig. 9

Major trends of gene expression during adventitious root formation in C. japonica. Color strengths of red and green indicates up- and down-regulation of gene expression level, respectively