Peanut leaf transcriptomic dynamics reveals insights into the acclimation response to elevated carbon dioxide under semiarid conditions

Abstract

Introduction: Elevated atmospheric carbon dioxide [CO₂] increases peanut carbon assimilation and productivity. However, the molecular basis of such responses is not well understood. We tested the hypothesis that maintaining high photosynthesis under long-term elevated [CO₂] is associated with the shift in C metabolism gene expression regulation.

Methods: We used a field CO₂ enrichment system to examine the effects of elevated [CO₂] (ambient + 250 ppm) across different soil water availability and plant developmental stages on the molecular responses in a peanut runner-type genotype. Plants under both [CO₂] treatments were grown in semiarid conditions. We evaluated a comparative leaf transcriptomic profile across three periodic water deficit/re-hydration (well-watered/recovery) cycles throughout the growing season using RNAseq analysis.

Results: Our results showed that the transcriptome responses were influenced by [CO₂], water availability, and developmental stages. The traditional Mercator annotation analysis based on percentage total revealed that lipid metabolism, hormone biosynthesis, secondary metabolism, amino acid biosynthesis, and transport were the most regulated biological processes. However, our new approach based on the comparative relative percentage change per individual category across stages revealed new insights into the gene expression patterns of biological functional groups, highlighting the relevance of the C-related pathways regulated by elevated [CO₂].

Discussion: The photosynthesis analysis showed that 1) The light reaction was the most upregulated pathway by elevated [CO₂] during water stress, 2) Photorespiration was downregulated across all stages, 3) Sucrose synthesis genes were upregulated by elevated [CO₂] before stress, 4) Starch synthesis genes were upregulated by elevated [CO₂] under drought periods, and 5) CO₂ regulation of sucrose and starch degradation was critical under drought periods. Our findings provide valuable insights into the molecular basis underlying the photosynthetic acclimation response to elevated [CO₂] in peanuts.

Keywords: acclimation; drought; gene expression; photorespiration; water stress.

Figure 1

Effect of elevated CO₂ on the percentage of total (%) differentially expressed genes (DEGs) per functional group resulted from the peanut leaf transcriptomic. Differential gene expressions as a percentage of the total DGEs in six selected data points, representing different plant growth stages with different soil water availability: pre-water deficit (R2), first water deficit (R3), first recovery (R4), third water deficit (R7), third recovery (R7), and physiological maturity-harvest (R8). Carbohydrate-CHO.

Figure 2

Effect of elevated CO₂ on the percentage of total differentially expressed genes (DEGs) for different functional groups. Leaf transcriptomic profile from pair vertical comparisons between the two CO₂ treatments (control, ambient 400 ppm and elevated 60 ppm) at selected growth stages with different soil water availability: (A) pre-water deficit (R2), (B) first water deficit (R3), and (C) well-watered/first recovery (R4)], using the “percentage of total” approach (% indicates the effect of elevated CO₂ over ambient treatment). Carbohydrate-CHO, the oxidative pentose phosphate-OPP. Stats criteria for differentially expressed genes. Genes with |log2 fold-change|>1and adjusted P-value uc1≤ .05 (FDR (false discovery rate).

Figure 3

Effect of elevated CO₂ on the percentage change of differentially expressed genes (DEGs) per functional group and between stages (first stage as a baseline) in field-grown peanuts. The gene expression regulation exhibited conserved and altered patterns represented by three colors. Black indicates similar pattern (“no change pattern”) for the three comparisons between stages (A) R2/R3, (B) R3/R4 and (C) R2/R4). for the three comparisons), green color indicates an increase (“up pattern”) in the percentage change. Orange indicates a decrease in the percentage change. The % change mean across all the functional groups for each comparison between stages showed distinct expression patterns.

Figure 4

Photosynthetic (PS)-related pathways modulation by elevated [CO₂]. (A) the number (No) of differentially expressed genes (DEGs) per pathway during pre-water deficit (at the R2 developmental stage), first water deficit (R3), and first recovery (R4); (B) the percentage of total for each pathway, averaging across stages; and (C) the summary of total and unique DEGs per stage and pathway. Stats criteria for determining the DEGs was P-value uc1≤ .05 and |log2 fold-change|>1. The * indicates significant difference at P<0.05, T test (pwd as control).

Figure 5

Major carbohydrate (CHO) metabolism-related pathways modulation by elevated [CO₂]. (A) the number of differentially expressed genes (DEGs) per pathway during pre-water deficit (at the R2 developmental stage), first water deficit (R3), and the first recovery (R4); (B) the percentage of total for each pathway, averaging across stages; and (C) summary of total and unique DEGs per stage and pathway. Stats criteria for determining the DEGs was P-value uc1≤ .05 and |log2 fold-change|>1. The * indicates significant difference at P<0.05, T test (pwd as control).