Comparative Transcriptome Analysis of Iron and Zinc Deficiency in Maize (Zea mays L.)

Abstract

Globally, one-third of the population is affected by iron (Fe) and zinc (Zn) deficiency, which is severe in developing and underdeveloped countries where cereal-based diets predominate. The genetic biofortification approach is the most sustainable and one of the cost-effective ways to address Fe and Zn malnutrition. Maize is a major source of nutrition in sub-Saharan Africa, South Asia and Latin America. Understanding systems' biology and the identification of genes involved in Fe and Zn homeostasis facilitate the development of Fe- and Zn-enriched maize. We conducted a genome-wide transcriptome assay in maize inbred SKV616, under -Zn, -Fe and -Fe-Zn stresses. The results revealed the differential expression of several genes related to the mugineic acid pathway, metal transporters, photosynthesis, phytohormone and carbohydrate metabolism. We report here Fe and Zn deficiency-mediated changes in the transcriptome, root length, stomatal conductance, transpiration rate and reduced rate of photosynthesis. Furthermore, the presence of multiple regulatory elements and/or the co-factor nature of Fe and Zn in enzymes indicate their association with the differential expression and opposite regulation of several key gene(s). The differentially expressed candidate genes in the present investigation would help in breeding for Fe and Zn efficient and kernel Fe- and Zn-rich maize cultivars through gene editing, transgenics and molecular breeding.

Keywords: functional genomics; homeostasis; hormonal regulation; iron; maize; malnutrition; photosynthesis; zinc.

Figure 1

Phenotypic expression of 19 days-old maize SKV616 seedlings in response to 12 days exposure to Zn and Fe deficiencies (–Zn, –Fe and –Fe–Zn): (A) whole plant; (B) leaves; and (C) roots.

Figure 2

The morpho-physiological response of maize seedlings to –Zn, –Fe and –Fe–Zn deficiencies at 12 days after transplanting (DAT): (A) change in the chlorophyll content (soil plant analysis development (SPAD) value) of the leaves in response to the (B) transpiration rate; (C) stomatal conductance; (D) photosynthesis rate; (E) quantum efficiency of PS II photochemistry (Fv/Fm); and (F) root length (*, **, *** significant at p < 0.05, p < 0.01 and p < 0.001, respectively; NS: non-significant).

Figure 3

The overview of the spatial transcriptome responses to Fe and Zn stresses in the maize inbred line of SKV616 seedlings. The genes showing > 2-fold expression under stress treatments and p < 0.05 are considered as differentially expressed genes (DEGs) in stress treatments as compared to the control: (A) total number of upregulated and downregulated genes in response to –Zn, –Fe and –Fe–Zn stresses in the root and shoot; and (B) the Venn diagram depicting the stress-specific and common DEGs in response to –Zn, –Fe and –Zn–Fe stresses in the root and shoot tissues.

Figure 4

Functional gene ontology annotations of differentially expressed genes (DEGs) under Fe and Zn stresses in the root: (A) –Zn; (B) –Fe; and (C) –Fe–Zn. For graphical representation, we have the top 15 significant terms under each category viz., biological process (blue), cellular component (orange), and molecular function (green). The complete list of terms along with significance of false discovery rate (FDR) < 0.05 are mentioned in Table S1.

Figure 5

Functional gene ontology annotations of differentially expressed genes (DEGs) under Fe and Zn stresses in the shoot: (A)–Zn; (B)–Fe; and (C)–Fe–Zn. For graphical representation, we have the top 15 significant terms under each category viz., biological process (blue), cellular component (orange), and molecular function (green). The complete list of terms along with the significance of FDR < 0.05 are mentioned in the Table S1.

Figure 6

The clustering of KEGG-enriched functional categories of DEGs in the root and shoot under Fe and Zn stresses: (A) –Zn in root; (B) –Fe in root; (C) –Fe–Zn in the root; (D). –Zn in the shoot; (E) –Fe in shoot; and (F) –Fe–Zn in shoot.

Figure 7

The transcription factors (TFs) and miRNAs mediated the regulation of differentially expressed transporters under Fe and Zn deficiency in maize: the regulatory network is characterized by 148 miRNA–target gene and 306 TF–target genes interactions. The green triangles represent the TFs, the red ovals represent the target transporters and mugineic acid pathway genes, and the blue diamonds represent miRNAs.