Dynamic Changes in Ion Accumulation and Gene Expression Reveal Root-Specific Iron Uptake Strategies in Iron-Deficient Rice after Iron Supplementation

doi:10.1016/j.rsci.2026.02.002

摘要/Abstract

. [J]. Rice Science, 2026, 33(2): 260-276.

Fig. 1. Performance of shoot and root of three-week-old rice seedlings under iron (Fe) deficiency (0 μmol/L), control (40 μmol/L), and excess (1 000 μmol/L) conditions. A and B, Shoot (A) and root (B) phenotype of rice seedlings after three weeks under three different Fe conditions. Scale bars in A and B are 4 cm and 2 cm, respectively. C, Fresh weight, dry weight, and shoot length, as well as leaf number, chlorophyll content of the first leaf. D, Fresh weight of root, dry weight of root, total root length, number of crown roots, and lengths of seminal and crown roots. In C and D, data are mean ± SD (n = 3). Different lowercase letters above bars indicate significant differences at the 0.05 level according to Student’s t-test.

Fig. 2. Effects of iron (Fe) stress and Fe supplementation on metal ion concentrations in rice roots and shoots. A and B, Concentrations of Fe, zinc (Zn), manganese (Mn), copper (Cu), and cadmium (Cd) in shoots and roots of three-week-old rice seedlings under Fe deficiency (0 μmol/L), control (40 μmol/L), and excess (1 000 μmol/L) conditions. C, Dynamic changes in shoot and root ion concentrations in Fe-deficient rice after supplementing with 40 μmol/L Fe. Data are mean ± SD (n = 3). Different lowercase letters above bars indicate significant differences at the 0.05 level according to Student’s t-test (A and B) and one-way ANOVA (C), respectively.

Fig. 3. RNA sequencing analysis of steady-state response of rice to iron (Fe) deficiency and excess, and dynamic response of Fe-supplemented rice under Fe deficiency. A and B, Principal component analysis (PCA) of RNA sequencing data from root (A) and shoot (B) samples under eight growth conditions: static treatment groups [control (40 μmol/L), deficiency (0 μmol/L), excess (1 000 μmol/L)] and dynamic Fe supplementation time points (10 min, 30 min, 2 h, 5 h, 8 h) in Fe-deficient plants. C, Venn diagram showing total number of unique differentially expressed genes (DEGs) identified in both roots and shoots across all comparisons. Each treatment includes three biological replicates (15 plants per replicate).

Table 1. Metal homeostasis-related genes involved in all differentially expressed genes (DEGs) in roots and shoots

NCBI_Locus	Gene	Tissue	Cluster^a
LOC4342862	Nramp1	Root, shoot	8, 6
LOC4330161	YSL2	Root, shoot	8, 6
LOC4336546	YSL16	Root	4
LOC9268232	YSL15	Root	5
LOC4346978	VIT2	Root, shoot	8, 6
LOC4336074	VIT1	Root	4
LOC4342431	EIN2	Root	4
LOC4324610	COPT1	Root	5
LOC4332069	FRDL1	Root, shoot	7, 6
LOC4326394	ZIP1	Root	8
LOC4333667	IRT2	Root	4
LOC4333669	IRT1	Root, shoot	4, 6
LOC4343412	ABCG43	Root	4
LOC4332125	MTP4	Shoot	6

Fig. 4. Cluster analysis of gene expression and expression of iron transport genes in rice following iron deficiency and supplementation. A and B, Relative expression of cluster #8 in roots (A) and cluster #6 in shoots (B). Pearson correlation is used as the distance metric in k-means clustering. The number of differentially expressed genes (DEGs) included in each cluster is noted in the upper left corner of the graph. Complete clustering data for DEGs in roots and shoots are shown in Fig. S1, respectively. Each grey line represents the expression of one gene across three biological replicates, with the red line indicating the average expression of all genes within the cluster. C-F, Transcript levels of RNA sequencing (RNA-seq, left) and qRT-PCR (right) of OsIRT1, OsNramp1, OsYSL2, and OsIRO2 in roots and shoots of iron-deficient rice seedlings after iron supplementation, respectively. The internal gene is the house-keeping gene EP. Samples collected at specified time points (0 min, 10 min, 30 min, 2 h, 5 h, 8 h after iron supplementation). Expression levels in qRT-PCR are normalized, setting the condition with 0 μmol/L Fe at 0 min as 1. Different lowercase letters above bars indicate significant differences at the 0.05 level between root and shoot samples by Student’s t-test.

Fig. 5. Patterns of regulation of short-term iron (Fe) uptake by rice roots and shoots after Fe supplementation in Fe-deficient rice. ‘-’ indicates downregulation, ‘+’ indicates upregulation, and the higher number of ‘+’ indicates higher expression. ‘0 Fe’ indicates Fe deficiency treatment (0 μmol/L). FRDL, Ferric reductase defective like; IRT, Iron-regulated transporter; Nramp, Natural resistance-associated macrophage protein; TF, Transcription factors; VIT, Vacuolar iron transporter; YSL, Yellow stripe-like transporter.

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