The Regulatory Network of Sweet Corn (Zea mays L.) Seedlings under Heat Stress Revealed by Transcriptome and Metabolome Analysis

Abstract

Heat stress is an increasingly significant abiotic stress factor affecting crop yield and quality. This study aims to uncover the regulatory mechanism of sweet corn response to heat stress by integrating transcriptome and metabolome analyses of seedlings exposed to normal (25 °C) or high temperature (42 °C). The transcriptome results revealed numerous pathways affected by heat stress, especially those related to phenylpropanoid processes and photosynthesis, with 102 and 107 differentially expressed genes (DEGs) identified, respectively, and mostly down-regulated in expression. The metabolome results showed that 12 or 24 h of heat stress significantly affected the abundance of metabolites, with 61 metabolites detected after 12 h and 111 after 24 h, of which 42 metabolites were detected at both time points, including various alkaloids and flavonoids. Scopoletin-7-o-glucoside (scopolin), 3-indolepropionic acid, acetryptine, 5,7-dihydroxy-3',4',5'-trimethoxyflavone, and 5,6,7,4'-tetramethoxyflavanone expression levels were mostly up-regulated. A regulatory network was built by analyzing the correlations between gene modules and metabolites, and four hub genes in sweet corn seedlings under heat stress were identified: RNA-dependent RNA polymerase 2 (RDR2), UDP-glucosyltransferase 73C5 (UGT73C5), LOC103633555, and CTC-interacting domain 7 (CID7). These results provide a foundation for improving sweet corn development through biological intervention or genome-level modulation.

Keywords: heat stress; metabolites; metabolomics; sweet corn; transcriptomics.

Figure 1

Transcriptome analysis for sweet corn in response to heat stress. PCA analysis among different time points under heat stress (A). Veen diagram between two groups at 12 h and 24 h under heat stress (B). Volcano plot shows DEGs with the conditions |Log₂FC| ≥ 1 and FDR < 0.05 under heat stress at 12 h (C) and 24 h (D) under heat stress. KEGG enrichment analysis for sweet corn after 12 h (E) and 24 h (F) under heat stress.

Figure 2

DEGs involved in phenylpropanoid biosynthesis and the phenylpropanoid metabolic process in response to heat stress. A graph of DEGs in phenylpropanoid biosynthesis and phenylpropanoid metabolic process under heat stress (A). Compare gene expression patterns between RNA-seq files (FRKM) and RT-qPCR data (B). The colors of ovals and letters in (A,B) are green and blue, respectively, indicating down-regulation of gene expression and simultaneous up- and down-regulation.

Figure 3

DEGs involved in the photosynthesis process in response to heat stress. Diagram of DEGs in photosynthesis–antenna proteins and photosynthesis process under heat stress. Red, green, and blue boxes represent up-, down-, and both up- and down-regulated gene expression, respectively (A,B). Index values after 24 h recovery for 12 and 24 h heat treatment seedlings (C). Heatmap of genes related to chlorophyll biosynthetic and catabolic (D), photosystem II assembly and repair (E), regulation of photosynthesis (F), and photosynthetic carbon fixation (G). ETRmax, maximum electron transport rate; E_K, saturating irradiance; F_v/F_m, maximum photosynthetic rate; Y(II), actual photosynthetic rate; qP, photochemical quenching coefficient; and Y(NPQ), quantum yield of regulatory energy dissipation.

Figure 4

Metabolomic profiles of sweet corn seedlings under heat stress. Top 20 metabolites detected under heat stress after 12 h (A) and 24 h (B). Orange bars stand for up-regulated compounds, and cyan bars stand for down-regulated compounds. Select conditions were VIP ≥ 1 and |Log₂FC| ≥ 1. Cluster results of 130 metabolites into five groups at different time points (C). A heatmap for 42 metabolites detected in the groups CK12h vs. HT12h and CK24h vs. HT24h (D). Spearman correlation results among 14 metabolites (E). The serial number in D (red color) and E (dark color) means corresponding metabolites in Table S8. According to the principle of mass spectrometry detection, the metabolites with isomers cannot be distinguished should marked with “*”, as shown in (A,B,D,E).

Figure 5

Correlation analysis to mine key pathways and hub genes involved in heat response in sweet corn. Spearman correlation analysis between metabolites and DEGs. The squares with different colors in the first column presented different modules (A). KEGG enrichment analysis of brown (B), dark green (C), magenta (D), and tan (E) modules. Hub genes identified in the brown (F), dark green (G), magenta (H), and tan (I) modules. Log₂FC of each connected gene is shown by the thickness of lines and the size of circles; the degree between the hub gene and connected genes is indicated by the color intensity of the circle color. The most connected genes are marked. Abbreviations for genes: RDR2: RNA-dependent RNA polymerase 2; UGT73C5: UDP-glycosyltransferase 73C5; CID7: CTC-interacting domain 7; ACOX2: acyl-coenzyme A oxidase 2; TBL29: trichome birefringence-like 29; RLT3: ringlet 3; SCKL2: fructokinase-like 2; PP297: pentatricopeptide repeat-containing protein; GXM3: glucuronoxylan 4-O-methyltransferase 3; MANA2: probable alpha-mannosidase; C92C5: cytochrome P450 92C5; PIP13: plasma membrane intrinsic protein 1-3; PIP22: plasma membrane intrinsic protein 2-2; AATPD: AAA-ATPase; HS24M: 24.1 kDa heat shock protein; CLPB1: casein lytic proteinase B1; GSTU1: glutathione S-transferase 1; GLNA2: glutamine synthetase root isozyme 2; HSP21: heat shock protein 21; HSP7C: heat shock cognate 70 kDa protein; LPCT2: lysophospholipid acyltransferase 2; EDR2L: enhanced disease resistance 2-like; KEA2: K(+) efflux antiporter 2.