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Gene expression profiles in different stem internodes reveal the genetic regulation of primary and secondary stem development in Betula platyphylla

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Abstract

Secondary growth of stems is an important process for the radial increase of trees. To gain an insight into the molecular mechanisms underlying stem development from primary to secondary growth and to provide information for molecular research and breeding in Betula platyphylla (birch), the gene expression profiles of material from the first, third, and fifth internodes (IN) of 3-month-old seedlings were analyzed. Compared with the first IN, 177 genes were up-regulated and 157 genes down-regulated in the third IN; in the fifth IN, 180 genes were up-regulated and 275 genes were down-regulated. The expressions of 24 genes were up-regulated and 6 genes were down-regulated in the fifth IN relative to the third IN. The differentially expressed genes were annotated as having roles in cambium, xylem, and phloem development and formation; including cell wall expansion, cellulose biosynthesis, lignin biosynthesis and deposition, xylem extension, cell wall modification, and growth hormone responses. The expressions of genes related to cell wall expansion and cellulose biosynthesis in the primary cell wall were down-regulated in the third and fifth IN relative to the first IN. Genes involved in lignin biosynthesis, xylem extension, and cellulose synthesis in the secondary cell wall were up-regulated in the third and fifth IN relative to the first IN. These results described the patterns of gene expression during stem development in birch and provided candidate genes for further functional characterization.

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Acknowledgments

This work was supported by the National High Technology Research and Development Program (“863” program) of China (2013AA102704) and the National Natural Science Foundation of China (31470671).

Author contributions

HG, YW, CY, and CW conceived and designed the experiments. HG, PH, and YJ participated in the experiments. HG, YW, and CW performed the data analysis. HG, YW, CY, and CW drafted the manuscript. HG and CW provided reagents and analysis tools. All authors read and approved the final version of the manuscript.

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Authors and Affiliations

  1. State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China

    Huiyan Guo, Yucheng Wang, Ping Hu, Chuanping Yang & Chao Wang

  2. Forestry Science Research Institute of Heilongjiang Province, Harbin, 150081, China

    Yanmin Wang

  3. Forestry College of Beihua University, Jilin, 132013, China

    Ying Jiang

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  1. Huiyan Guo
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  2. Yucheng Wang
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Correspondence to Chuanping Yang or Chao Wang.

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Communicated by P. Ingvarsson

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Table S1

Primer sequences and amplicon sizes used for real-time RT-PCR assays. (DOC 62 kb)

Table S2

Differentially expressed genes identified by digital gene expression (DGE) analysis (FDR ≤0.001, |log2 ratio| ≥1). (XLSX 139 kb)

Fig. S1

Sections analyzed by scanning electron microscopy (×500) in the first, third, and fifth stem internodes. co cortex, xy xylem, sx secondary xylem, pi pith. Bars = 25 μm. (GIF 118 kb)

High-resolution image (TIFF 3008 kb)

Fig. S2

Tag expression distribution. The column indicates the distribution of total tags of the studied stem internodes. (GIF 45 kb)

High-resolution Image (TIFF 563 kb)

Fig. S3

Saturation evaluation of the different gene expression levels. The solid line indicates genes that were mapped by all clean tags, and the dotted line indicates genes (GIF 321 kb)

High-resolution image (TIFF 3149 kb)

Fig. S4

Statistics of the clean tags alignment. The column indicates mapping of the tags from the studied stem internodes. PM (Sense) perfect match to gene (Sense), 1 tag- >1 gene match to one gene; 1 tag- >n gene match to more than one gene, 1 MM (Sense) match to gene (Sense) with 1-bp mismatch, PM (Antisense) perfect match to an antisense gene sequence, 1 MM (Antisense) match to antisense gene with 1-bp mismatch, PM Genome 1 tag- >1 position perfect match to genome sequence with one best hit, PM Genome 1 tag- >n position perfect match to genome sequence with multiple best hits, 1 MM Genome match to genome sequence with 1 bp mismatch, Unknown Tag not matched to a gene (Sense and Antisense) or genome sequence. (GIF 58 kb)

High-resolution image (TIFF 610 kb)

Fig. S5

Gene ontology (GO) categories assigned to differentially expressed genes in the first, third, and fifth stem internodes. The x-axis represents the number of unigenes, and the y-axis indicates the GO subcategories. (GIF 51 kb)

High-resolution image (TIFF 550 kb)

Fig. S6

Hierarchical cluster analysis of differentially expressed genes in the studied stem internodes. All ratios are log2 transformed. Log ratios of 0 (ratios of 1) are indicated in black, and increasingly positive (induction) or negative (repression) log ratios are indicated in red or green, respectively, with increasing intensities. Red indicates induction, and green indicates repression in the arrays. (PNG 43 kb)

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Guo, H., Wang, Y., Hu, P. et al. Gene expression profiles in different stem internodes reveal the genetic regulation of primary and secondary stem development in Betula platyphylla . Tree Genetics & Genomes 12, 113 (2016). https://doi.org/10.1007/s11295-016-1068-x

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