Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation

Abstract

Background: Cold tolerance is a key determinant of the geographical distribution range of a plant species and crop production. Cold acclimation can enhance freezing-tolerance of plant species through a period of exposure to low nonfreezing temperatures. As a subtropical evergreen broadleaf plant, oil-tea camellia demonstrates a relatively strong tolerance to freezing temperatures. Moreover, wild oil-tea camellia is an essential genetic resource for the breeding of cultivated oil-tea camellia, one of the four major woody oil crops in the world. The aims of our study are to identify variations in transcriptomes of wild oil-tea camellia from different latitudes and elevations, and discover candidate genes for cold acclimation.

Results: Leaf transcriptomes were obtained of wild oil-tea camellia from different elevations in Lu and Jinggang Mountains, China. Huge amounts of simple sequence repeats (SSRs), single-nucleotide polymorphisms (SNPs) and insertion/deletions (InDels) were identified. Based on SNPs, phylogenetic analysis was performed to detect genetic structure. Wild oil-tea camellia samples were genetically differentiated mainly between latitudes (between Lu and Jinggang Mountains) and then among elevations (within Lu or Jinggang Mountain). Gene expression patterns of wild oil-tea camellia samples were compared among different air temperatures, and differentially expressed genes (DEGs) were discovered. When air temperatures were below 10 °C, gene expression patterns changed dramatically and majority of the DEGs were up-regulated at low temperatures. More DEGs concerned with cold acclimation were detected at 2 °C than at 5 °C, and a putative C-repeat binding factor (CBF) gene was significantly up-regulated only at 2 °C, suggesting a stronger cold stress at 2 °C. We developed a new method for identifying significant functional groups of DEGs. Among the DEGs, transmembrane transporter genes were found to be predominant and many of them encoded transmembrane sugar transporters.

Conclusions: Our study provides one of the largest transcriptome dataset in the genus Camellia. Wild oil-tea camellia populations were genetically differentiated between latitudes. It may undergo cold acclimation when air temperatures are below 10 °C. Candidate genes for cold acclimation may be predominantly involved in transmembrane transporter activities.

Keywords: Camellia oleifera; Cold acclimation; Differential gene expression; Genetic structure; Molecular marker; Transcriptome; Wild oil-tea camellia.

Fig. 1

KEGG pathway classification of unigenes. A Cellular Processes, B Environmental Information Processing, C Genetic Information Processing, D Metabolism, and E Organismal Systems

Fig. 2

Distribution of SSR motifs. The x-axis indicates number of bases in SSR motif unit. The different color bars represent different repeat types (repeat number ranges of SSR motif unit)

Fig. 3

Phylogenetic tree of wild oil-tea camellia from different elevations in Lu and Jinggang Mountains. Tip labels indicate sample names and elevations. Those begin with “LS” are from Lu Mountain and “JG” from Jinggang Mountain. Node numbers indicate posterior probabilities (%)

Fig. 4

Density distribution of gene expression in different temperature groups. Gene expression levels are represented as log₁₀(FPKM). See Table 1 for details of temperature groups

Fig. 5

Hierarchical clustering heat map of differentially expressed genes. T2, T5, T10, T14 and T18 represent different temperature groups (different columns). A horizontal line shows the expression of a gene in different temperature groups. The expression of such a gene is significantly different in at least one of the pairwise comparisons between different temperature groups. Different colors indicate different levels of gene expression: from red to blue, the log₁₀(FPKM + 1) value ranges from large to small

Fig. 6

Venn diagrams of differentially expressed genes. a Number of differentially expressed genes in pairwise comparisons of gene expression between T5 and T10/T14/T18. b Number of differentially expressed genes in pairwise comparisons of gene expression between T2 and T10/T14/T18. Numbers in the overlapping regions refer to those genes differentially expressed in more than one pairwise comparison

Fig. 7

GO classification of genes. a GO classification of all expressed genes detected in our study including all temperature groups (T2, T5, T10, T14 and T18). b GO classification of differentially expressed genes (DEGs) at T5 versus T10/T14/T18. c GO classification of DEGs at T2 versus T10/T14/T18. Stars above bars indicate the amounts of differentially expressed genes are significantly higher or lower than the amounts of genes in random samples from the GO classification of all genes

Fig. 8

Gene expression levels of differentially expressed genes (DEGs) through RNA-seq and qRT-PCR analyses. All the genes are sugar transporter genes