Integrative Omics Analysis of Three Oil Palm Varieties Reveals (Tanzania × Ekona) TE as a Cold-Resistant Variety in Response to Low-Temperature Stress

Abstract

Oil palm (Elaeis guineensis Jacq.) is an economically important tropical oil crop widely cultivated in tropical zones worldwide. Being a tropical crop, low-temperature stress adversely affects the oil palm. However, integrative leaf transcriptomic and proteomic analyses have not yet been conducted on an oil palm crop under cold stress. In this study, integrative omics transcriptomic and iTRAQ-based proteomic approaches were employed for three oil palm varieties, i.e., B × E (Bamenda × Ekona), O × G (E. oleifera × Elaeis guineensis), and T × E (Tanzania × Ekona), in response to low-temperature stress. In response to low-temperature stress at (8 °C) for 5 days, a total of 5175 up- and 2941 downregulated DEGs in BE-0_VS_BE-5, and a total of 3468 up- and 2443 downregulated DEGs for OG-0_VS_OG-5, and 3667 up- and 2151 downregulated DEGs for TE-0_VS_TE-5 were identified. iTRAQ-based proteomic analysis showed 349 up- and 657 downregulated DEPs for BE-0_VS_BE-5, 372 up- and 264 downregulated DEPs for OG-0_VS_OG-5, and 500 up- and 321 downregulated DEPs for TE-0_VS_TE-5 compared to control samples treated at 28 °C and 8 °C, respectively. The KEGG pathway correlation of oil palm has shown that the metabolic synthesis and biosynthesis of secondary metabolites pathways were significantly enriched in the transcriptome and proteome of the oil palm varieties. The correlation expression pattern revealed that TE-0_VS_TE-5 is highly expressed and BE-0_VS_BE-5 is suppressed in both the transcriptome and proteome in response to low temperature. Furthermore, numerous transcription factors (TFs) were found that may regulate cold acclimation in three oil palm varieties at low temperatures. Moreover, this study identified proteins involved in stresses (abiotic, biotic, oxidative, and heat shock), photosynthesis, and respiration in iTRAQ-based proteomic analysis of three oil palm varieties. The increased abundance of stress-responsive proteins and decreased abundance of photosynthesis-related proteins suggest that the TE variety may become cold-resistant in response to low-temperature stress. This study may provide a basis for understanding the molecular mechanism for the adaptation of oil palm varieties in response to low-temperature stress in China.

Keywords: TE; cold tolerance; low-temperature stress; oil palm; proteome; transcriptome.

Figure 1

General information of oil palm iTRAQ-based proteomic data output. (A) Basic information statistics. (B) Peptide number distribution.

Figure 2

Differentially expressed genes and proteins (DEGs and DEPs) identified in oil palms under cold stress. (A) Up- and downregulated genes in three oil palm varieties treated at 8 °C cold stress vs. control at 28 °C for 5 days in leaves. (B) DEPs for three oil palm varieties under cold treatment at 8 °C vs. control for five days post-treatment at 28 °C.

Figure 3

Cluster analysis of DEGs and DEPs for correlation expression of the oil palm transcriptome and proteome under cold stress. Heat map represents the DEGs and DEPs based on the log₂ relative abundance of the transcriptome and proteome for up- and downregulated (red and green color) genes and proteins of three oil palm varieties.

Figure 4

GO analysis for DEPs in oil palm leaves under cold stress. GO categories for identified DEPs based on iTRAQ proteomics in the oil palm proteome are demarcated in three different colors at the bottom of the graph.

Figure 5

COG functional classification of DEPs identified in oil palm varieties under cold stress. The various colors illustrate each category of functional class.

Figure 6

KEGG pathway enrichment analysis of DEPs of oil palm varieties. (A–C) Top 16/17 in KEGG pathways enrichment of DEPs for three oil palm varieties. RichFactor and P/Q values for each pathway are demarcated at the bottom and right of the graphs, respectively.

Figure 7

KEGG pathway correlation enrichment analysis of oil palm in response to low-temperature stress. Top 20 in KEGG pathways enrichment involved in DEGs and DEPs of the transcriptome and proteome correlations in oil palm varieties.

Figure 8

Transcription factors (TFs) identified in oil palm under cold stress. The top 20 TFs involved in the transcriptomes of three oil palm varieties, i.e., BE, OG, and TE.

Figure 9

Stress-responsive, photosynthesis, and respiration-related DEPs identified in oil palm proteomes under cold stress. (A) Total number of DEPs involved in stress responses, photosynthesis, and respiration in three oil palm varieties. (B) Different categories of DEPs for stress responses, photosynthesis, and respiration in the proteomes of three oil palm varieties.

Figure 10

Heatmap illustration for stress response, photosynthesis, and respiration DEPs in oil palm. (A) Stress-response DEPs categorized into oxidative, abiotic, biotic, and heat stresses. (B) Showing DEPs involved in photosynthesis. (C) Displays the DEPs related to respiration for three oil palm varieties. Alphabetical symbols X, Y, and Z denote the BE-0_VS_BE-5, OG-0_VS_OG-5, and TE-0_VS_TE-5 oil palm varieties respectively.