Root transcriptome of two contrasting indica rice cultivars uncovers regulators of root development and physiological responses.

The huge variation in root system architecture (RSA) among different rice (Oryza sativa) cultivars is conferred by their genetic makeup and different growth or climatic conditions. Unlike model plant Arabidopsis, the molecular basis of such variation in RSA is very poorly understood in rice. Cultivars with stable variation are valuable resources for identification of genes involved in RSA and related physiological traits. We have screened for RSA and identified two such indica rice cultivars, IR-64 (OsAS83) and IET-16348 (OsAS84), with stable contrasting RSA. OsAS84 produces robust RSA with more crown roots, lateral roots and root hairs than OsAS83. Using comparative root transcriptome analysis of these cultivars, we identified genes related to root development and different physiological responses like abiotic stress responses, hormone signaling, and nutrient acquisition or transport. The two cultivars differ in their response to salinity/dehydration stresses, phosphate/nitrogen deficiency, and different phytohormones. Differential expression of genes involved in salinity or dehydration response, nitrogen (N) transport, phosphate (Pi) starvation signaling, hormone signaling and root development underlies more resistance of OsAS84 towards abiotic stresses, Pi or N deficiency and its robust RSA. Thus our study uncovers gene-network involved in root development and abiotic stress responses in rice.

Sulfur alleviates arsenic toxicity by reducing its accumulation and modulating proteome, amino acids and thiol metabolism in rice leaves.

Arsenic (As) contamination of water is a global concern and rice consumption is the biggest dietary exposure to human posing carcinogenic risks, predominantly in Asia. Sulfur (S) is involved in di-sulfide linkage in many proteins and plays crucial role in As detoxification. Present study explores role of variable S supply on rice leaf proteome, its inclination towards amino acids (AA) profile and non protein thiols under arsenite exposure. Analysis of 282 detected proteins on 2-DE gel revealed 113 differentially expressed proteins, out of which 80 were identified by MALDI-TOF-TOF. The identified proteins were mostly involved in glycolysis, TCA cycle, AA biosynthesis, photosynthesis, protein metabolism, stress and energy metabolism. Among these, glycolytic enzymes play a major role in AA biosynthesis that leads to change in AAs profiling. Proteins of glycolytic pathway, photosynthesis and energy metabolism were also validated by western blot analysis. Conclusively S supplementation reduced the As accumulation in shoot positively skewed thiol metabolism and glycolysis towards AA accumulation under AsIII stress.

Comparative Transcriptional Profiling of Contrasting Rice Genotypes Shows Expression Differences during Arsenic Stress.

Accumulation of arsenic (As) in rice (Oryza sativa L.) grain is a serious concern worldwide. Long-term exposure to As affects nutritional status in rice grain and is associated with higher rates of skin, bladder, and lung cancers, and heart disease. Genotypic variations in rice for As accumulation or tolerance are prevalent and are regulated by genetic and environmental factors. To understand molecular networks involved in As accumulation, genome-wide expression analysis was performed in roots of low- and high-As accumulating rice genotypes (LARGs and HARGs). Six rice genotypes with contrasting As accumulation potential and tolerance were used in this study. Genome-wide expression analysis suggested their differential response against As stress. This study suggests up- and downregulation of a number of unique genes involved in various pathways and biological processes in response to As stress in rice genotypes. A comparison of gene expression profiles, principal component analysis, and K-means clustering suggests that an independent pathway is operating during As stress tolerance or accumulation in contrasting genotypes. It was also observed that the differential behavior of aus genotype, Nayanmoni, from other LARGs might be due to its different genetic background. Cis-motif profiling of As-induced coexpressed genes in diverse rice genotypes led to the identification of unique cis-motifs present in differentially expressed genes. This study suggests that the genetic mechanism regulating the differential As accumulation in different genotypes may not be dependent on gene expression at the transcriptional level. However, many genes identified in this study can be analyzed and used for marker-trait associations related to As accumulation in diverse genotypes around the world.

Arsenic accumulation and tolerance in rootless macrophyte Najas indica are mediated through antioxidants, amino acids and phytochelatins.

Arsenic (As) accumulation and tolerance response of a submerged rootless macrophyte Najas indica were evaluated during arsenate (As(V); 10-250 µM) and arsenite (As(III); 1-50 µM) exposure. Higher As accumulation at As(III) exposure and more tolerance upon As(V) exposure resulted in more toxicity during As(III) stress than As(V), which was evident through measurement of growth parameters and oxidative stress related parameters viz., lipid peroxidation (MDA content), electrical conductivity (EC) and hydrogen peroxide (H2O2) levels. Antioxidant enzymes and various amino acids were more prominent during moderate exposure of As(V), suggesting their possible role in As tolerance and detoxification. Various non-enzymatic antioxidant metabolites viz., ascorbic acid (ASC), glutathione (GSH), non-protein thiols (NPTs) and phytochelatins (PCs) biosynthesis involving phytochelatin synthase (PCS) activity increased more significantly during As(III) stress. However, PCs content seems inadequate in response to As accumulation leading to lower PC-SH:As molar ratio and higher As phytotoxicity during As(III) stress. N. indica may prove useful plant species for phytoremediation purpose in moderately As contaminated water bodies due to high As accumulation and tolerance potential.

Arsenite tolerance in rice (Oryza sativa L.) involves coordinated role of metabolic pathways of thiols and amino acids.

Thiolic ligands and several amino acids (AAs) are known to build up in plants against heavy metal stress. In the present study, alteration of various AAs in rice and its synchronized role with thiolic ligand was explored for arsenic (As) tolerance and detoxification. To understand the mechanism of As tolerance and stress response, rice seedlings of one tolerant (Triguna) and one sensitive (IET-4786) cultivar were exposed to arsenite (0-25 µM) for 7 days for various biochemical analyses using spectrophotometer, HPLC and ICPMS. Tolerant and sensitive cultivars respond differentially in terms of thiol metabolism, essential amino acids (EEAs) and nonessential amino acids (NEEAs) vis-á-vis As accumulation. Thiol biosynthesis-related enzymes were positively correlated to As accumulation in Triguna. Conversely, these enzymes, cysteine content and GSH/GSSG ratio declined significantly in IET-4786 upon As exposure. The level of identified phytochelatin (PC) species (PC(2), PC(3) and PC(4)) and phytochelatin synthase activity were also more pronounced in Triguna than IET-4786. Nearly all EAAs were negatively affected by As-induced oxidative stress (except phenylalanine in Triguna), but more significantly in IET-4786 than Triguna. However, most of the stress-responsive NEAAs like glutamic acid, histidine, alanine, glycine, tyrosine, cysteine and proline were enhanced more prominently in Triguna than IET-4786 upon As exposure. The study suggests that IET-4786 appears sensitive to As due to reduction of AAs and thiol metabolic pathway. However, a coordinated response of thiolic ligands and stress-responsive AAs seems to play role for As tolerance in Triguna to achieve the effective complexation of As by PCs.

Genome-wide identification of rice class I metallothionein gene: tissue expression patterns and induction in response to heavy metal stress.

Metallothioneins (MTs) are members of a family of cysteine-rich low molecular weight polypeptides which play an important role in heavy metal detoxification and homeostasis of intracellular metal ions in plant. Though MT genes from some selected plants have been characterized with respect to their protein sequences, kinetic properties and tissue-specific localization, no detailed study has been carried out in rice. Here, we present genome-wide identification, structural and expression analyses of rice MT gene family. Our analysis suggests presence of 11 class I MT genes in rice genome (Release 7 of the MSU Rice Genome Annotation Project) which are differentially expressed during growth and development, in various tissues and during biotic and abiotic stresses. Our analyses suggest that class I MT proteins in rice differ in tissue localization as well as in heavy metal coordination chemistry. We also suggest that some MTs have a predominant role in detoxification of As (V) in arsenic-tolerant rice cultivars. Our analysis suggests that apart from transcriptional regulation, post-transcriptional alternative splicing in some members of this family takes place during growth and development, in various tissues and during biotic and abiotic stresses.

Arsenic affects essential and non-essential amino acids differentially in rice grains: inadequacy of amino acids in rice based diet.

Recent breakthroughs in rice arsenic (As) research demonstrate that As accumulation significantly affects trace nutrients in rice grain. In the present study we analyzed the amino acid (AA) profile of sixteen rice genotypes differing in grain As accumulation, grown at three sites with different soil As concentrations, in ascending order, Chinsurah

Arsenic tolerances in rice (Oryza sativa) have a predominant role in transcriptional regulation of a set of genes including sulphur assimilation pathway and antioxidant system.

World wide arsenic (As) contamination of rice has raised much concern as it is the staple crop for millions. Four most commonly cultivated rice cultivars, Triguna, IR-36, PNR-519 and IET-4786, of the West Bengal region were taken for a hydroponic study to examine the effect of arsenate (As(V)) and arsenite (As(III)) on growth response, expression of genes and antioxidants vis-à-vis As accumulation. The rice genotypes responded differentially under As(V) and As(III) stress in terms of gene expression and antioxidant defences. Some of the transporters were up-regulated in all rice cultivars at lower doses of As species, except IET-4786. Phytochelatin synthase, GST and γ-ECS showed considerable variation in their expression pattern in all genotypes, however in IET-4786 they were generally down-regulated in higher As(III) stress. Similarly, most of antioxidants such as superoxide dismutase (SOD), ascorbate peroxidase (APX), guaiacol peroxidase (GPX), catalase (CAT), monodehydroascorbate reductase (MDHAR) and dehydroascorbate reductase (DHAR) increased significantly in Triguna, IR-36 and PNR-519 and decreased in IET-4786. Our study suggests that Triguna, IR-36 and PNR-519 are tolerant rice cultivars accumulating higher arsenic; however IET-4786 is susceptible to As-stress and accumulates less arsenic than other cultivars.