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. 2017 May 15:8:775.
doi: 10.3389/fpls.2017.00775. eCollection 2017.

Genome Wide Identification of Orthologous ZIP Genes Associated with Zinc and Iron Translocation in Setaria italica

Ganesh Alagarasan  1 , Mahima Dubey  1 , Kumar S Aswathy  2 , Girish Chandel  1
Affiliations

Genome Wide Identification of Orthologous ZIP Genes Associated with Zinc and Iron Translocation in Setaria italica

Ganesh Alagarasan et al. Front Plant Sci. .

Abstract

Genes in the ZIP family encode transcripts to store and transport bivalent metal micronutrient, particularly iron (Fe) and or zinc (Zn). These transcripts are important for a variety of functions involved in the developmental and physiological processes in many plant species, including most, if not all, Poaceae plant species and the model species Arabidopsis. Here, we present the report of a genome wide investigation of orthologous ZIP genes in Setaria italica and the identification of 7 single copy genes. RT-PCR shows 4 of them could be used to increase the bio-availability of zinc and iron content in grains. Of 36 ZIP members, 25 genes have traces of signal peptide based sub-cellular localization, as compared to those of plant species studied previously, yet translocation of ions remains unclear. In silico analysis of gene structure and protein nature suggests that these two were preeminent in shaping the functional diversity of the ZIP gene family in S. italica. NAC, bZIP and bHLH are the predominant Fe and Zn responsive transcription factors present in SiZIP genes. Together, our results provide new insights into the signal peptide based/independent iron and zinc translocation in the plant system and allowed identification of ZIP genes that may be involved in the zinc and iron absorption from the soil, and thus transporting it to the cereal grain underlying high micronutrient accumulation.

Keywords: Setaria italica; expression profiling; gene characterization; signal peptide; zinc and iron regulated transporters.

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Figures

FIGURE 1
FIGURE 1
Ortholgous genes for the ZIP family have been identified among three species viz. Arabidopsis, rice and foxtail millet. Seven orthologous clusters along with its Phylogenetic tree have been presented.
FIGURE 2
FIGURE 2
The distribution of ZIPs across the length of the chromosome, along with its name is mentioned on the right side of every chromosomal segment. There were a total of 36 genes, 16 from Arabidopsis, 13 from rice and 7 from foxtail millet. Gray color chromosomes indicates rice, whereas pink and green for Arabidopsis and foxtail millet, respectively.
FIGURE 3
FIGURE 3
Molecular Phylogenetic analysis by Maximum Likelihood method. The evolutionary history was inferred by using the Maximum Likelihood method based on W-IQ-TREE. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed (Felsenstein, 1985). The analysis involved 36 amino acid sequences.
FIGURE 4
FIGURE 4
The distribution of zinc and iron responsive (TF) transcription factors across ZIP in S. italica.
FIGURE 5
FIGURE 5
Heatmap showing the expression pattern of SiZIP genes in four tissues, namely root, leaf, spica and stem along with control and drought stress library of Setaria italica. The colored bar at top left represents relative expression value, where 0.0, 2.0, and 4.0 denotes low, medium, and high expression, respectively.
FIGURE 6
FIGURE 6
(A) RT-PCR expression analysis of seven ZIP genes from S. italica in shoot tissues. (B) Differential expression analysis of ZIP family gene in little millet. Le, leaf; St, stem and Sp, spica. (C) Standing crop view of little millet genotypes.
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