Transcriptome Analysis Reveals Candidate Pathways and Genes Involved in Wheat (Triticum aestivum L.) Response to Zinc Deficiency

Abstract

Zinc (Zn) deficiency poses a major global health challenge, and wheat grains generally contain low Zn concentrations. In this study, the wheat cultivar 'Zhongmai 175' was identified as zinc-efficient. Hydroponic experiments demonstrated that Zn deficiency induced the secretion of oxalic acid and malic acid in root exudates and significantly increased total root length in 'Zhongmai 175'. To elucidate the underlying regulatory mechanisms, transcriptome profiling via RNA sequencing was conducted under Zn-deficient conditions. A total of 2287 and 1935 differentially expressed genes (DEGs) were identified in roots and shoots, respectively. Gene Ontology enrichment analysis revealed that these DEGs were primarily associated with Zn ion transport, homeostasis, transmembrane transport, and hormone signaling. Key DEGs belonged to gene families including VIT, NAS, DMAS, ZIP, tDT, HMA, and NAAT. KEGG pathway analysis indicated that phenylpropanoid biosynthesis, particularly lignin synthesis genes, was significantly downregulated in Zn-deficient roots. In shoots, cysteine and methionine metabolism, along with plant hormone signal transduction, were the most enriched pathways. Notably, most DEGs in shoots were associated with the biosynthesis of phytosiderophores (MAs, NA) and ethylene. Overall, genes involved in Zn ion transport, phytosiderophore biosynthesis, dicarboxylate transport, and ethylene biosynthesis appear to play central roles in wheat's adaptive response to Zn deficiency. These findings provide a valuable foundation for understanding the molecular basis of Zn efficiency in wheat and for breeding Zn-enriched varieties.

Keywords: Triticum aestivum L.; ethylene biosynthesis; nicotianamine; phenylpropanoid biosynthesis pathway; transcriptome; zinc deficiency; zinc ion transport.

Figure 1

Grain zinc concentrations of 42 wheat cultivars.

Figure 2

Root morphology of Zhongmai 175 under Zn-sufficient (CK, 2 µM) and Zn-deficient (-Zn, 0 µM) conditions.

Figure 3

Organic acid content in root exudates of Zhongmai 175 under Zn-sufficient (CK) and Zn-deficient (-Zn) conditions. Different letters indicate significant differences (p < 0.05). Asterisks (*) denote significant changes compared to CK (p < 0.05). Data are means of three replicates.

Figure 4

Pearson correlation heatmaps among biological replicates. (A) Root samples (CKR vs. -ZnR). (B) Aboveground samples (CKA vs. -ZnA). CKR: roots under Zn-sufficient conditions; -ZnR: roots under Zn-deficient conditions; CKA: aboveground parts under Zn-sufficient conditions; -ZnA: aboveground parts under Zn-deficient conditions.

Figure 5

Volcano plots of DEGs under Zn deficiency. (A) Roots: zinc deficiency (-ZnR) versus those grown under normal conditions (CKR). (B) Aboveground: zinc deficiency (-ZnA) versus those grown under normal conditions (CKA).

Figure 6

GO classification of DEGs. (A) DEGs from root tissues (-ZnR vs. CKR). (B) DEGs from aboveground tissues (-ZnA vs. CKA). CKR: roots under Zn-sufficient conditions; -ZnR: roots under Zn-deficient conditions; CKA: aboveground parts under Zn-sufficient conditions; -ZnA: aboveground parts under Zn-deficient conditions.

Figure 7

KEGG pathway enrichment of DEGs under Zn deficiency. (A) Upregulated DEGs in roots. (B) Upregulated DEGs in aboveground tissues. (C) Downregulated DEGs in roots. (D) Downregulated DEGs in aboveground tissues.

Figure 8

Expression profiles of DEGs involved in lignin biosynthesis within the phenylpropanoid pathway in wheat roots under zinc deficiency. Red and blue represent up- and downregulated genes, respectively. PAL: phenylalanine ammonia lyase; C4H: cinnamate 4-hydroxylase; C3H: p-coumarate 3-hydroxylase; COMT: caffeic acid O-methyltransferase; F5H: ferulate 5-hydroxylase; 4CL: 4-coumarate: CoA ligase; HCT: hydroxycinnamoyl transferase; CCoAOMT: caffeoyl-CoA O-methyltransferase; CCR: cinnamoyl-CoA reductase; CAD: cinnamyl alcohol dehydrogenase; LAC: laccases; POD: peroxidase; FC: fold change.

Figure 9

Expression profiles of DEGs involved in S-adenosylmethionine and ethylene biosynthesis in the cysteine and methionine metabolism pathway in the aboveground parts of wheat under zinc deficiency stress.

Figure 10

qPCR validation of 16 DEGs in the roots and aboveground parts of wheat seedlings under zinc deficiency. Error bars represent the SD of three biological replicates. FC: fold change. ZIP: ZRT- and IRT-like proteins; VIT: vacuolar iron transporter; HMA: heavy metal ATPase; NAS: nicotianamine synthase; SAUR: auxin response protein; CCR: cinnamoyl-CoA reductase; CAD: cinnamyl alcohol dehydrogenase; SAMS: S-adenosylmethionine synthase; ACO: ACC oxidase; NAAT: nicotianamine aminotransferase; tDT: tonoplast dicarboxylate transporter.