Comparative Transcriptional Profiling of Two Wheat Genotypes, with Contrasting Levels of Minerals in Grains, Shows Expression Differences during Grain Filling

<div><p>Wheat is one of the most important cereal crops in the world. To identify the candidate genes for mineral accumulation, it is important to examine differential transcriptome between wheat genotypes, with contrasting levels of minerals in grains. A transcriptional comparison of developing grains was carried out between two wheat genotypes- <i>Triticum aestivum</i> Cv. WL711 (low grain mineral), and <i>T. aestivum</i> L. IITR26 (high grain mineral), using Affymetrix GeneChip Wheat Genome Array. The study identified a total of 580 probe sets as differentially expressed (with <i>log2</i> fold change of ≥2 at p≤0.01) between the two genotypes, during grain filling. Transcripts with significant differences in induction or repression between the two genotypes included genes related to metal homeostasis, metal tolerance, lignin and flavonoid biosynthesis, amino acid and protein transport, vacuolar-sorting receptor, aquaporins, and stress responses. Meta-analysis revealed spatial and temporal signatures of a majority of the differentially regulated transcripts.</p></div

Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination

<div><p>The recruitment of RNA polymerase II on a promoter is assisted by the assembly of basal transcriptional machinery in eukaryotes. The Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex plays an important role in transcription regulation in eukaryotes. However, even in the advent of genome sequencing of various plants, SAGA complex has been poorly defined for their components and roles in plant development and physiological functions. Computational analysis of <i>Arabidopsis thaliana</i> and <i>Oryza sativa</i> genomes for SAGA complex resulted in the identification of 17 to 18 potential candidates for SAGA subunits. We have further classified the SAGA complex based on the conserved domains. Phylogenetic analysis revealed that the SAGA complex proteins are evolutionary conserved between plants, yeast and mammals. Functional annotation showed that they participate not only in chromatin remodeling and gene regulation, but also in different biological processes, which could be indirect and possibly mediated <i>via</i> the regulation of gene expression. The <i>in silico</i> expression analysis of the SAGA components in <i>Arabidopsis</i> and <i>O</i>. <i>sativa</i> clearly indicates that its components have a distinct expression profile at different developmental stages. The co-expression analysis of the SAGA components suggests that many of these subunits co-express at different developmental stages, during hormonal interaction and in response to stress conditions. Quantitative real-time PCR analysis of SAGA component genes further confirmed their expression in different plant tissues and stresses. The expression of representative salt, heat and light inducible genes were affected in mutant lines of SAGA subunits in <i>Arabidopsis</i>. Altogether, the present study reveals expedient evidences of involvement of the SAGA complex in plant gene regulation and stress responses.</p></div

Differentially expressed transcripts with ≥2 <i>log2</i> fold change expression difference at p≤0.01, between IITR26 <i>vs.</i> WL711.

<p>(a) Venn diagram shows the total number of the differentially expressed transcripts and overlap at 14 and 28 DAA (b) Differentially regulated transcripts in biological and functional MapMan BINs.</p

Real time PCR for <i>Arabidopsis</i> SAGA complex subunits in different development tissues and stress conditions.

<p><b>(A)</b> The expression pattern of the SAGA complex subunits in different tissues. Relative expression analysis of each was plotted with reference to the expression of ubiquitin (either 6-day-old light-grown seedlings 16 / 8hr, mature leaves, stems, flowers, siliques and roots). <b>(B)</b> The expression pattern of <i>Arabidopsis</i> SAGA complex subunits in response to abiotic salt stress conditions. <i>Arabidopsis</i> Col-0 leaves treated with MS liquid medium (as a control) and NaCl (150 mM in MS media). <b>(C)</b> The expression pattern of <i>Arabidopsis</i> SAGA complex subunits in response to high temperature conditions. <i>Arabidopsis</i> Col-0 leaves kept in MS liquid medium at 22°C (as a control) and 37°C (2 hr in MS media). The asterisks (*) denote <i>P ≤</i> 0.01.</p

Differentially expressed transcripts representing metal tolerance and stress responses.

<p>Differentially expressed transcripts representing metal tolerance and stress responses.</p

Concentration of micronutrients (Fe, Zn and Mn) in developing grains of IITR26 and WL711 of (a) 14 DAA and (b) 28 DAA.

<p>Concentration of micronutrients (Fe, Zn and Mn) in developing grains of IITR26 and WL711 of (a) 14 DAA and (b) 28 DAA.</p

<i>In silico</i> expression patterns of the SAGA complex genes in developmental tissues.

<p>The expression patterns in different developmental tissues for SAGA genes were obtained from the Genevestigator microarray database tool. <b>(A)</b><i>Arabidopsis</i> developmental tissues; <b>(B)</b><i>O</i>. <i>sativa</i> developmental tissues.</p

Enrichment of GO terms in 466 genes up-regulated (≥2 <i>log2</i> fold) in developing grains of WL711 during 14 and/or 28 DAA.

<p>Contingency and key as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111718#pone-0111718-t001" target="_blank">Table 1</a>.</p><p>Enrichment of GO terms in 466 genes up-regulated (≥2 <i>log2</i> fold) in developing grains of WL711 during 14 and/or 28 DAA.</p

Differentially expressed transcripts at 14 and 28 DAA.

<p>(a) Correlation plot represents the pairwise correlation between biological replicates of the samples (b) Volcano plots represents the differentially expressed transcripts, satisfying the criteria of p≤0.01.</p

Quantitative RT-PCR analyses of a few candidate genes: Metallothionein, NAM-1, LEA-12, and Sec-E. Each bar indicates standard error in three biological replicates.

<p>Quantitative RT-PCR analyses of a few candidate genes: Metallothionein, NAM-1, LEA-12, and Sec-E. Each bar indicates standard error in three biological replicates.</p