Uncovering the molecular mechanisms of Acer fabri in adjusting to low-temperature stress through integrated physiological and transcriptomic analysis

Abstract

Acer fabri is an excellent color-leaf tree species, with high ornamental value. Low temperatures are known to limit the growth and geographical distribution of A. fabri. The molecular mechanism of A. fabri in response to low-temperature stress was rarely reported. To understand the molecular mechanism of A. fabri in response to low-temperature stress, relevant physiological changes were identified and the transcriptome sequencing was conducted under different stress durations. The results showed that the proline, the soluble sugar (SS) and the soluble protein (SP) content increased in A. fabri leaves under low-temperature stress, while the peroxidase (POD) and activating superoxide dismutase (SOD) activity increased first and then decreased. It was also found by the OPLS-DA analysis that SOD is the most important physiological indicator of A. fabri in response to low-temperature stress. By transcriptome sequencing, a total of 56,732 genes were identified, including 832 transcription factors (TFs). Differentially expressed genes (DEGs) were significantly enriched in metabolic pathways, phytohormone signaling, and plant mitogen-activated protein kinase (MAPK) signaling pathways. Moreover, the analysis of gene co-expression networks, specifically weighted gene co-expression network analysis (WGCNA), indicates that Af0048792 and Af0026061 could be significant in the response to stress from low temperatures. Furthermore, it was observed that NAC (Af0033429) and MIKC (Af0004917) might have interactions with Af0048792, and MIKC (Af0004917) may additionally interact with Af0026061. These findings could enhance our understanding of the molecular mechanisms of A. fabri in response to low-temperature stress.

Keywords: Acer Fabri; Low-temperature stress; Transcriptome analysis; WGCNA.

Fig. 1

Effect of low-temperature treatment on the physiological indexes of A. fabri and PCA analysis. (A) is the content of proline, (B) is soluble protein (SP), (C) is soluble sugar (SS), (D) is peroxidase (POD) activity, (E) is superoxide dismutase (SOD) activity. (F) is principal component analysis of the physiological indicators of A. fabri under low- temperature treatment.

Fig. 2

PCA of samples, correlation coefficient analysis and quantitative analysis of TF families. (A) The principal component analysis (PCA) of the samples under low-temperature stress in A. fabri. (B) The analysis of sample correlation under low-temperature stress in A. fabri. (C) The analysis of the member numbers of TF families in A. fabri.

Fig. 3

Statistics of differentially expressed genes (DEGs) in A. fabri. (A) is the number of DEGs under different stress durations compared with the CK. (B) is the DEGs at different time points compared with the CK are shown in a V enn diagram.

Fig. 4

Heatmap of differential genes in plant MAPK signaling and phytohormone signaling. (A) is the plant MAPK signaling pathway. (B) is the plant hormone signaling pathway.

Fig. 5

Physiological index-module association analysis and hub gene network. (A) Pro is for proline, SS is soluble sugar, SP is soluble protein, SOD is superoxide dismutase activity, and POD is peroxidase activity, (B) shows the top 15 central hub genes of light green module, (C) shows the top 15 central hub genes of skyblue module.

Fig. 6

qRT-PCR results for nine randomly selected genes and correlation analysis. (A) illustrates the relative expression levels of nine genes under conditions of low temperature stress, with the black columns representing qRT-PCR results and the red line indicating FPKM values. (B) depicts the correlation analysis between FPKM values and qRT-PCR results, where the black line signifies the corresponding trend line.

Fig. 7

qRT-PCR results and correlation analysis of the three candidate key genes. (A) illustrates the relative expression levels of the three candidate key genes under low temperature stress conditions. The black column represents the qRT-PCR data, while the red line indicates the FPKM values, (B) illustrates the correlation analysis between FPKM values and qRT-PCR results, with the black line depicting the corresponding trend.

Fig. 8

qRT-PCR results and interaction gene analysis of two TF genes. (A) illustrates the relative expression levels of the two TF genes under low-temperature stress conditions, with the black column representing qRT-PCR data and the red line indicating FPKM values. (B) depicts the correlation analysis between the FPKM values of interacting genes and qRT-PCR outcomes, where the black line signifies the corresponding trend line. (C) presents the regulatory network diagram of candidate key genes and TF genes.