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Introduction: Nodulin-26-like intrinsic proteins (NIPs) are integral membrane proteins belonging to the aquaporin family, that facilitate the transport of neutral solutes across the bilayer. The OsNIP2;1 a member of NIP-III class of aquaporins is permeable to beneficial elements like silicon and hazardous arsenic. However, the atomistic cross-talk of these molecules traversing the OsNIP2;1 channel is not well understood. Objective: Due to the lack of genomic variation but the availability of high confidence crystal structure, this study aims to highlight structural determinants of metalloid permeation through OsNIP2;1. Methods: The molecular simulations, combined with site-directed mutagenesis were used to probe the role of specific residues in the metalloid transport activity of OsNIP2;1. Results: We drew energetic landscape of OsNIP2;1, for silicic and arsenous acid transport. Potential Mean Force (PMF) construction illuminate three prominent energetic barriers for metalloid passage through the pore. One corresponds to the extracellular molecular entry in the channel, the second located on ar/R filter, and the third size constriction in the cytoplasmic half. Comparative PMF for silicic acid and arsenous acid elucidate a higher barrier for silicic acid at the cytoplasmic constrict resulting in longer residence time for silicon. Furthermore, our simulation studies explained the importance of conserved residues in loop-C and loop-D with a direct effect on pore dynamics and metalloid transport. Next we assessed contribution of predicted key residues for arsenic uptake, by functional complementation in yeast. With the aim of reducing arsenic uptake while maintaining beneficial elements uptake, we identified novel OsNIP2;1 mutants with substantial reduction in arsenic uptake in yeast. Conclusion: We provide a comprehensive assessment of pore lining residues of OsNIP2;1 with respect to metalloid uptake. The findings will expand mechanistic understanding of aquaporin’s metalloid selectivity and facilitate variant interpretation to develop novel alleles with preference for beneficial metalloid species and reducing hazardous ones.

This study provides intriguing mechanistic insights into the innate immunity of the pigeonpea wild relative, Cajanus platycarpus, in comparison to the cultivated Cajanus cajan, based on biochemical and metabolic changes during Helicoverpa armigera infestation. Over a 96 h herbivory challenge, both species exhibited 164 metabolites, with 54 undergoing significant alterations. In C. platycarpus, primary carbohydrates such as sucrose, glucose, galactose, and mannose decreased, while structural carbohydrates like xylose, talose, and tagatose accumulated, indicating cell wall damage in C. cajan. Notably, C. platycarpus down-regulated most amino acids except for phenylalanine, which is crucial for the synthesis of defense compounds. The linoleic/linolenic acid pathway, which produces jasmonic acid, was exclusively identified in C. platycarpus, highlighting active defense. As herbivory continued, levels of galactinol, mannitol, and pinitol significantly increased in C. platycarpus, while sorbitol and xylitol levels rose in C. cajan. Essentially, C. platycarpus reduced nutrient availability to insects, enhanced specific defense hormones and pathways, and maintained reactive oxygen species (ROS) equilibrium. These findings offer significant potential for understanding the biology of the wild relative and developing innovative strategies for herbivore control and food sustainability.

Abstract Global mean temperature is increasing at a rapid pace due to the rapid emission of greenhouse gases majorly from anthropogenic practices and predicted to rise up to 1.5°C above the pre‐industrial level by the year 2050. The warming climate is affecting global crop production by altering biochemical, physiological, and metabolic processes resulting in poor growth, development, and reduced yield. Maize is susceptible to heat stress, particularly at the reproductive and early grain filling stages. Interestingly, heat stress impact on crops is closely regulated by associated environmental covariables such as humidity, vapor pressure deficit, soil moisture content, and solar radiation. Therefore, heat stress tolerance is considered as a complex trait, which requires multiple levels of regulations in plants. Exploring genetic diversity from landraces and wild accessions of maize is a promising approach to identify novel donors, traits, quantitative trait loci (QTLs), and genes, which can be introgressed into the elite cultivars. Indeed, genome wide association studies (GWAS) for mining of potential QTL(s) and dominant gene(s) is a major route of crop improvement. Conversely, mutation breeding is being utilized for generating variation in existing populations with narrow genetic background. Besides breeding approaches, augmented production of heat shock factors (HSFs) and heat shock proteins (HSPs) have been reported in transgenic maize to provide heat stress tolerance. Recent advancements in molecular techniques including clustered regularly interspaced short palindromic repeats (CRISPR) would expedite the process for developing thermotolerant maize genotypes.

High soil salinity has an unfavorable consequence on the growth and productivity of rice crop. However, some salt-tolerant plant growth-promoting bacteria (ST-PGPB) regulate specific physiological, biochemical, and molecular properties to promote crop growth while minimizing the detrimental effects of salt stress. In this regard, we isolated ST-PGPB from rhizospheric soil and examined it to mitigate the salinity stress in rice seedlings. The growth of the bacterium at 3 M NaCl demonstrated its halotolerance, and 16S rRNA sequencing identified it as Bacillus siamensis, and the isolated strain was named BW. Further study indicated that biopriming with BW strain helps plant growth promotion-related phenotype and significantly mitigates salinity stress in rice seedlings. Treatment of rice seeds with BW resulted in significantly improved germination of seedlings at 75 mM to 150 mM NaCl, along with better physiology and biochemical parameters than the untreated ones. Furthermore, Bacillus sp. BW efficiently colonizes rice roots and produces auxin and siderophore, via forming biofilm under different salt concentrations. Under 100–200 mM NaCl treatment conditions, the extracellular metabolite profile from BW showed a substantial abundance in specific metabolites, such as osmoprotective chemicals, suggesting the likely protective mechanism against salinity stress damage. This study demonstrates the role and potential of a halotolerant- BW strain in supporting the growth of rice plants under salinity conditions.

Measurement(s) Genome Assembly Sequence Technology Type(s) PacBio Sequel System, Illumina sequencing Factor Type(s) Lathyrus Pusa-24 Sample Characteristic - Organism Lathyrus sativus Sample Characteristic - Environment leaf Sample Characteristic - Location India

Abstract Orphan crops, also known as minor crops, smart foods, and superfoods, have attracted great attention recently because of their unique ability to grow in resource‐poor marginal lands, and under harsh environmental conditions without any intensive agricultural care. These crops possess inherent tolerance against different abiotic stresses such as drought, salinity, cold, and heat. Recent advancements in genomic resources and high‐throughput phenotyping platforms have provided opportunities to explore the untapped potential of orphan crops to identify novel gene source(s) and mechanism(s) for developing abiotic stress‐tolerant crops. Moreover, genomics‐assisted investigations into the various physiological and molecular mechanism(s) could provide useful insights into stress tolerance mechanisms in these plants. Nevertheless, translating the hidden power of the tolerant gene pools from the orphan crops into major staple crops for enhancing their stress tolerance while maintaining yield is a challenging task. The contemporary tools of genomics can be used to unravel the secret of stress tolerance in orphan crops and employ these untapped genes for tailoring stress‐tolerant crop varieties to ensure global food security in the era of climate change.

Abstract Camelina sativa (L.) Crantz is an oilseed crop with favorable potentials for biodiesel production, such as the high plant yield, high oil content in the seed, high net energy ratio, and low oil production cost. This review paper deals with the present state and perspectives of biodiesel production from camelina oil. First, important issues of camelina seed pretreatment and biodiesel production are reviewed. Emphasis is given to different biodiesel technologies that have been used so far worldwide, the economic assessment of the camelina oil biodiesel (COB) production, the camelina‐based biorefineries for the integrated biodiesel production, the COB life cycle analysis, and impact human health and ecosystem. Finally, the perspectives of COB production from the techno‐economic and especially genetic engineering points of view are discussed.

On the occasion of the 90th birthday of Govindjee, Professor Emeritus of Plant Biology, Biochemistry, and Biophysics, the University of Illinois at Urbana-Champaign (UIUC), over 100 celebrants have sent felicitations and messages to thank him for mentoring, nurturing, and building the community of photosynthesis researchers belonging to four generations; and in making the scientific knowledge accessible to students and young researchers via his monumental writings and editorial contributions. Govindjee joined UIUC in September of 1956 to study as a graduate student in the laboratory of Robert Emerson. In 1961, he joined UIUC as an Assistant Professor and retired as a full professor in 1999. He is well-known for pioneering work in oxygenic photosynthesis, leading to the current Z-scheme, and for his breakthrough advances concerning light harvesting, primary charge separation, the role of bicarbonate on the two-electron gate of photosystem II, water oxidation, nonphotochemical quenching, and the use of biophysical techniques, such as prompt fluorescence, delayed fluorescence, thermoluminescence, and nuclear magnetic resonance. Today, despite his retirement, Govindjee continues to explore several important questions in the field of photosynthesis and documents the history of science. This tribute, in turn, attempts to capture scientific collaborations, as well as scholarly and personal contributions made by Govindjee to the lives of hundreds of scholars and students worldwide.

Salinity is one of the major abiotic stresses which impose constraints to plant growth and production. Rice (Oryza sativa L.) is one of the most important staple food crops and a model monocot plant. Its production is expanding into regions that are affected by soil salinity, requiring cultivars more tolerant to saline conditions. Understanding the molecular mechanisms of such tolerance could lay a foundation for varietal improvement of salt tolerance in rice. In spite of extensive studies exploring the mechanism of salt tolerance, there has been limited progress in breeding for increased salinity tolerance. In this review, we summarize the information about the major molecular mechanisms underlying salinity tolerance in rice and further discuss the limitations in breeding for salinity tolerance. We show that numerous gene families and interaction networks are involved in the regulation of rice responses to salinity, prompting a need for a comprehensive functional analysis. We also show that most studies are based on whole-plant level analyses with only a few reports focused on tissue- and/or cell-specific gene expression. More details of salt-responsive channel and transporter activities at tissue- and cell-specific level still need to be documented before these traits can be incorporated into elite rice germplasm. Thus, future studies should focus on diversity of available genetic resources and, particular, wild rice relatives, to re-incorporate salinity tolerance traits lost during domestication.

Abstract Lysine cannot be synthesized by the human body, and it is, therefore, an indispensable amino acid in the human that must be consumed in adequate amounts to prevent disease. Unfortunately, lysine is not abundant in many important food sources such as rice grains. Efforts to fortify rice and other monocotyledonous crops with high lysine have proved to be challenging because of their effects on plant growth. The present study was designed to avoid the problems that are often encountered in engineering lysine metabolism. We generated different over‐expression constructs for the key anabolic enzyme, dihydrodipicolinate synthase (DHDPS and cdapA) and knockdown (KD) constructs for the catabolic enzyme—lysine ketoglutarate reductase/saccharopine dehydrogenase (LKR/SDH), with expression under the control of either the CaMV35S promoter or the endosperm‐specific glutelinD1 promoter. The use of the endosperm‐specific promoter together with the lysine feedback‐insensitive cdapA for over‐expression provides distinct advantages, as does silencing of LKR/SDH under the control of this promoter. Rice plants produced by over‐expressing cdapA together with silencing of LKR/SDH showed a 58% increase in grain lysine content, as well as higher amounts of total seed protein levels. Moreover, the transgenic seedlings were more tolerant to salinity. These results demonstrate that it is possible to generate high lysine stress‐tolerant rice varieties, which have the potential to reduce the need for dietary supplementation.

Abstract Intensive breeding programs have increased rice yields, strongly contributing to increasing global food security during the post‐green revolution period. However, rice productivity has reached a yield barrier where further yield improvement is restricted by inadequate information on the association of yield components, and morphological and physiological traits with yield. We conducted a field experiment to evaluate (i) the contribution of morphological and physiological traits to yield and (ii) quantify the trade‐off effect between the yield components in rice, using a mini‐core collection of 362 rice genotypes comprising geographically distinct landraces and breeding lines. Our data point towards multiscale coordination of physiological and morphological traits associated with yield and biomass. Considerable trait variations across the genotypes in yield ranging from 0.5 to 78.5 g hill−1 and harvest index ranging from 0.7% to 60.7% highlight enormous diversity in rice across the globe. The natural elimination of trade‐off between yield components revealed the possibility to enhance rice yield in modern cultivars. Furthermore, our study demonstrated that genotypes with larger sink sizes could fix more carbon to achieve a higher yield. We propose that the knowledge thus generated in this study can be helpful for (a) trait‐based modeling and pyramiding alleles in rice‐breeding programs and (b) assisting breeders and physiologists in their efforts to improve crop productivity under a changing climate, thus harnessing the potential for sustainable productivity gains.

Abstract Background A structural phenomenon seen in certain lineages of angiosperms that has captivated many scholars including Charles Darwin is the evolution of plant carnivory. Evidently, these structural features collectively termed carnivorous syndrome, evolved to aid nutritional acquisition from attracted, captured and digested prey. We now understand why plant carnivory evolved but how carnivorous plants acquired these attributes remains a mystery. In an attempt to understand the evolution of Nepenthes pitcher and to shed more light on its role in prey digestion, we analyzed the transcriptome data of the highly specialized Nepenthes khasiana leaf comprising the leaf base lamina, tendril and the different parts/zones of the pitcher tube viz. digestive zone, waxy zone and lid. Results In total, we generated around 262 million high-quality Illumina reads. Reads were pooled, normalized and de novo assembled to generate a reference transcriptome of about 412,224 transcripts. We then estimated transcript abundance along the N. khasiana leaf by mapping individual reads from each part/zone to the reference transcriptome. Correlation-based hierarchical clustering analysis of 27,208 commonly expressed genes indicated functional relationship and similar cellular processes underlying the development of the leaf base and the pitcher, thereby implying that the Nepenthes pitcher is indeed a modified leaf. From a list of 2386 differentially expressed genes (DEGs), we identified transcripts encoding key enzymes involved in prey digestion and protection against pathogen attack, some of which are expressed at high levels in the digestive zone. Interestingly, many of these enzyme-encoding genes are also expressed in the unopened N. khasiana pitcher. Transcripts showing homology to both bacteria and fungi were also detected; and in the digestive zone, fungi are more predominant as compared to bacteria. Taking cues from histology and scanning electron microscopy (SEM) photomicrographs, we found altered expressions of key regulatory genes involved in leaf development. Of particular interest, the expression of class III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII) and ARGONAUTE (AGO) genes were upregulated in the tendril. Conclusions Our findings suggest that N. khasiana pitchers employ a wide range of enzymes for prey digestion and plant defense, harbor microbes and probably evolved through altered expression of leaf polarity genes.

Plant carnivory is often manifested as dramatic changes in the structure and morphology of the leaf. These changes appear to begin early in leaf development. For example, the development of the Sarracenia purpurea leaf primordium is associated with the formation of an adaxial ridge, whose growth along with that of the leaf margin resulted in a hollow structure that later developed into a pitcher. In Nepenthes khasiana, pitcher formation occurs during the initial stages of leaf development, although this has not been shown at the primordial stage. The formation of the Utricularia gibba trap resulted from the growth of the dome-shaped primordium in both the longitudinal and transverse directions. Recent research has begun to unfold the genetic basis of the development of the carnivorous leaf. We review these findings and discuss them in relation to the flat-shaped leaves of the model plant Arabidopsis.

Abstract Background Rice productivity is adversely affected by environmental stresses. Transcription factors (TFs), as the regulators of gene expression, are the key players contributing to stress tolerance and crop yield. Histone gene binding protein-1b (OsHBP1b) is a TF localized within the Saltol QTL in rice. Recently, we have reported the characterization of OsHBP1b in relation to salinity and drought tolerance in a model system tobacco. In the present study, we over-express the full-length gene encoding OsHBP1b in the homologous system (rice) to assess its contribution towards multiple stress tolerance and grain yield. Results We provide evidence to show that transgenic rice plants over-expressing OsHBP1b exhibit better survival and favourable osmotic parameters under salinity stress than the wild type counterparts. These transgenic plants restricted reactive oxygen species accumulation by exhibiting high antioxidant enzyme activity (ascorbate peroxidase and superoxide dismutase), under salinity conditions. Additionally, these transgenic plants maintained the chlorophyll concentration, organellar structure, photosynthesis and expression of photosynthesis and stress-related genes even when subjected to salinity stress. Experiments conducted for other abiotic stresses such as drought and high temperature revealed improved tolerance in these transgenic plants with better root and shoot growth, better photosynthetic parameters, and enhanced antioxidant enzyme activity, in comparison with WT. Further, the roots of transgenic lines showed large cortical cells and accumulated a good amount of callose, unlike the WT roots, thus enabling them to penetrate hard soil and prevent the entry of harmful ions in the cell. Conclusion Collectively, our results show that rice HBP1b gene contributes to multiple abiotic stress tolerance through several molecular and physiological pathways and hence, may serve as an important gene for providing multiple stress tolerance and improving crop yield in rice.

Abstract Background To delineate the adaptive mechanisms operative under salinity stress, it is essential to study plant responses at the very early stages of stress which are very crucial for governing plant survival and adaptation. We believe that it is the initial perception and response phase which sets the foundation for stress adaptation in rice seedlings where plants can be considered to be in a state of osmotic shock and ion buildup. Results An isobaric Tags for Relative and Absolute Quantitation (iTRAQ) approach was used to analyze the pre-existing differences as well as the very early salt shock responsive changes in the proteome of seedlings of contrasting rice genotypes, viz salt-sensitive IR64 and salt-tolerant Pokkali. In response to a quick salt shock, shoots of IR64 exhibited hyperaccumulation of Na+, whereas in Pokkali, these ions accumulated more in roots. Interestingly, we could find 86 proteins to be differentially expressed in shoots of Pokkali seedlings under non-stress conditions whereas under stress, 63 proteins were differentially expressed in Pokkali shoots in comparison to IR64. However, only, 40 proteins under non-stress and eight proteins under stress were differentially expressed in Pokkali roots. A higher abundance of proteins involved in photosynthesis (such as, oxygen evolving enhancer proteins OEE1 & OEE3, PsbP) and stress tolerance (such as, ascorbate peroxidase, superoxide dismutase, peptidyl-prolyl cis-trans isomerases and glyoxalase II), was observed in shoots of Pokkali in comparison to IR64. In response to salinity, selected proteins such as, ribulose bisphosphate carboxylase/oxygenase activase, remained elevated in Pokkali shoots. Glutamate dehydrogenase - an enzyme which serves as an important link between Krebs cycle and metabolism of amino acids was found to be highly induced in Pokkali in response to stress. Similarly, other enzymes such as peroxidases and triose phosphate isomerase (TPI) were also altered in roots in response to stress. Conclusion We conclude that Pokkali rice seedlings are primed to face stress conditions where the proteins otherwise induced under stress in IR64, are naturally expressed in high abundance. Through specific alterations in its proteome, this proactive stress machinery contributes towards the observed salinity tolerance in this wild rice germplasm.

Abstract Leaves are the primary food‐producing organs for a plant that carry out photosynthesis and contribute to biomass and grain yield. Leaf senescence is a developmentally regulated physiological process but early leaf senescence is known to negatively affect plant yield. The cuticle is an outer waxy protective layer on the leaf surface which protects plants from pathogens attack as well as dehydration. Our understanding of the molecular mechanisms underlying cuticle development and leaf senescence is still immature. The present study reports the role of the DEGENERATED PANICLE AND PARTIAL STERILITY 1 (DPS1) gene encoding a cystathionine β‐synthase (CBS) domain‐containing protein in cuticle development and leaf senescence in rice. The dps1 loss‐of‐function mutant showed leaf senescence phenotype with twisted leaves, significantly reduced chlorophyll content and degenerated chloroplasts characterized by a reduced number of starch granules and an abundance of osmiophilic bodies. Furthermore, dps1 leaves displayed defective cuticle development, reduced wax and cutin compounds, and lower relative water content as compared with wild type. Physiological assays showed significantly higher accumulation of reactive oxygen species (ROS) accompanied by enhanced DNA fragmentation in dps1 leaves, which could be associated with chloroplast degeneration and defective cuticle development. Transcriptome analysis revealed altered expression of several critical genes related to photosynthesis and wax/cutin pathway. This study revealed a crucial role of DPS1 in regulating leaf cuticle development and senescence by affecting the expression of several genes. Thus, a moderate expression of DPS1 is necessary for better plant growth and productivity.

Improving grain yield in the staple food crop rice has been long sought goal of plant biotechnology. One of the traits with significant impact on rice breeding programs is peduncle elongation at the time of heading failing which leads to significant reduction in grain yield due to incomplete panicle exsertion. To decipher transcriptional dynamics and molecular players underlying peduncle elongation, we performed RNA sequencing analysis of elongating and non-elongating peduncles in two Indian cultivars, Swarna and Pokkali, at the time of heading. Along with genes associated with cell division and cell wall biosynthesis, we observed significant enrichment of genes associated with auxins, gibberellins, and brassinosteroid biosynthesis/signaling in the elongating peduncles before heading in both the genotypes. Similarly, genes associated with carbohydrate metabolism and mobilization, abiotic stress response along with cytokinin, abscisic acid, jasmonic acid, and ethylene biosynthesis/signaling were enriched in non-elongating peduncles post heading. Significant enrichment of genes belonging to key transcription factor families highlights their specialized roles in peduncle elongation and grain filling before and after heading, respectively. A comparison with anther/pollen development-related genes provided 76 candidates with overlapping roles in anther/pollen development and peduncle elongation. Some of these are important for carbohydrate remobilization to the developing grains. These can be engineered to combat with incomplete panicle exsertion in male sterile lines and manipulate carbohydrate dynamics in grasses. Overall, this study provides baseline information about potential target genes for engineering peduncle elongation with implications on plant height, biomass composition and grain yields in rice.

Drought is a critical factor limiting the productivity of legumes worldwide. Legumes can enter into a unique tripartite symbiotic relationship with root-nodulating bacteria of genera Rhizobium, Bradyrhizobium, or Sinorhizobium and colonization by arbuscular mycorrhizal fungi (AMF). Rhizobial symbiosis provides nitrogen necessary for growth. AMF symbiosis enhances uptake of diffusion-limited nutrients such as P, Zn, Cu, etc., and also water from the soil via plant-associated fungal hyphae. Rhizobial and AMF symbioses can act synergistically in promoting plant growth and fitness, resulting in overall yield benefits under drought stress. One of the approaches that rhizobia use to survive under stress is the accumulation of compatible solutes, or osmolytes, such as trehalose. Trehalose is a non-reducing disaccharide and an osmolyte reported to accumulate in a range of organisms. High accumulation of trehalose in bacteroids during nodulation protects cells and proteins from osmotic shock, desiccation, and heat under drought stress. Manipulation of trehalose cell concentrations has been directly correlated with stress response in plants and other organisms, including AMF. However, the role of this compound in the tripartite symbiotic relationship is not fully explored. This review describes the biological importance and the role of trehalose in the tripartite symbiosis between plants, rhizobia, and AMF. In particular, we review the physiological functions and the molecular investigations of trehalose carried out using omics-based approaches. This review will pave the way for future studies investigating possible metabolic engineering of this biomolecule for enhancing abiotic stress tolerance in plants.

Abstract Background Camelina sativa has attracted much interest as alternative renewable resources for biodiesel, other oil-based industrial products and a source for edible oils. Its unique oil attributes attract research to engineering new varieties of improved oil quantity and quality. The overexpression of enzymes catalyzing the synthesis of the glycerol backbone and the sequential conjugation of fatty acids into this backbone is a promising approach for increasing the levels of triacylglycerol (TAG). In a previous study, we co-expressed the diacylglycerol acyltransferase (DGAT1) and glycerol-3-phosphate dehydrogenase (GPD1), involved in TAG metabolism, in Camelina seeds. Transgenic plants exhibited a higher-percentage seed oil content, a greater seed mass, and overall improved seed and oil yields relative to wild-type plants. To further increase seed oil content in Camelina, we utilized metabolite profiling, in conjunction with transcriptome profiling during seed development to examine potential rate-limiting step(s) in the production of building blocks for TAG biosynthesis. Results Transcriptomic analysis revealed approximately 2518 and 3136 transcripts differentially regulated at significant levels in DGAT1 and GPD1 transgenics, respectively. These transcripts were found to be involved in various functional categories, including alternative metabolic routes in fatty acid synthesis, TAG assembly, and TAG degradation. We quantified the relative contents of over 240 metabolites. Our results indicate major metabolic switches in transgenic seeds associated with significant changes in the levels of glycerolipids, amino acids, sugars, and organic acids, especially the TCA cycle and glycolysis intermediates. Conclusions From the transcriptomic and metabolomic analysis of DGAT1, GPD1 and DGAT1 + GPD1 expressing lines of C. sativa, we conclude that TAG production is limited by (1) utilization of fixed carbon from the source tissues supported by the increase in glycolysis pathway metabolites and decreased transcripts levels of transcription factors controlling fatty acids synthesis; (2) TAG accumulation is limited by the activity of lipases/hydrolases that hydrolyze TAG pool supported by the increase in free fatty acids and monoacylglycerols. This comparative transcriptomics and metabolomics approach is useful in understanding the regulation of TAG biosynthesis, identifying bottlenecks, and the corresponding genes controlling these pathways identified as limitations, for generating Camelina varieties with improved seed and oil yields.

Abstract Saffron is one of the most expensive spices of the world. Since this spice is triploid and meiosis is unusual, it cannot reproduce sexually like other plants; rather, it is propagated vegetatively via an underground corm, which can withstand a long dry dormant period before sprouting. Thus, corms are indispensable to saffron propagation. To identify and analyse signature metabolites associated with the ‘dormancy-sprouting’ process, non-targeted GC-MS was performed at different stages of corm development. Comparative metabolite profiling reflected dissimilar profiles among the stages as portrayed by differential cluster patterns of metabolites in the PCA and PLS-DA analysis. Correlation analysis revealed the interdependencies of individual metabolites and metabolic pathway. At the onset of stage 2, characterized by the initiation and differentiation of leaf primordia, a shift from dormancy to active metabolism occurred as derived from the increased abundance of sugars and other metabolites involved in the tricarboxylic acid cycle, glycolytic, amino acid and fatty acid pathways. These changes contribute to sprouting and vegetative growth of the corm. The present study provides new insights into saffron corm composition and metabolite changes associated with various stages of corm development and may pave the way for achieving agronomical improvements in this economically important spice.

Glyoxalase pathway is the primary route for metabolism of methylglyoxal (MG), a toxic ubiquitous metabolite that affects redox homeostasis. It neutralizes MG using Glyoxalase I and Glyoxalase II (GLYI and GLYII) enzymes in the presence of reduced glutathione. In addition, there also exists a shorter route for the MG detoxification in the form of Glyoxalase III (GLYIII) enzymes, which can convert MG into D-lactate in a single-step without involving glutathione. GLYIII proteins in different systems demonstrate diverse functional capacities and play a vital role in oxidative stress response. To gain insight into their evolutionary patterns, here we studied the evolution of GLYIII enzymes across prokaryotes and eukaryotes, with special emphasis on plants. GLYIII proteins are characterized by the presence of DJ-1_PfpI domains thereby, belonging to the DJ-1_PfpI protein superfamily. Our analysis delineated evolution of double DJ-1_PfpI domains in plant GLYIII. Based on sequence and structural characteristics, plant GLYIII enzymes could be categorized into three different clusters, which followed different evolutionary trajectories. Importantly, GLYIII proteins from monocots and dicots group separately in each cluster and the each of the two domains of these proteins also cluster differentially. Overall, our findings suggested that GLYIII proteins have undergone significant evolutionary changes in plants, which is likely to confer diversity and flexibility in their functions.

There are many ways to detect polymorphism. In this study we use the microsatellite markers to detect the polymorphism for the salt tolerance. This method has been successfully conducted in Oryza sativa and Brassica juncea. The results are reproducible. In contrast to previous methods, our method is simple and quite accurate for detecting the polymorphic bands. In this study instead of using agarose gel and ethidium bromide staining, we used non-denaturing polyacrylamide gel and a low-cost improved method for silver staining when we compare it to 11 other methods for their ability to detect simple sequence repeat polymorphisms as small as 50 bp in denaturing polyacrylamide gels. All methods detected the same alleles and banding pattern. However, important differences in sensitivity, contrast, time consumption and background were observed.

The GATA gene family is one of the most conserved families of transcription factors, playing a significant role in different aspects of cellular processes, in organisms ranging from fungi to angiosperms. GATA transcription factors are DNA-binding proteins, having a class IV zinc-finger motif CX2CX17−20CX2C followed by a highly basic region and are known to bind a consensus sequence WGATAR. In plants, GATAs are known to be involved in light-dependent gene regulation and nitrate assimilation. However, a comprehensive analysis of these GATA gene members has not yet been highlighted in rice when subjected to environmental stresses. In this study, we present an overview of the GATA gene family in rice (OsGATA) in terms of, their chromosomal distribution, domain architecture, and phylogeny. Our study has revealed the presence of 28 genes, encoding 35 putative GATA transcription factors belonging to seven subfamilies in the rice genome. Transcript abundance analysis in contrasting genotypes of rice—IR64 (salt sensitive) and Pokkali (salt tolerant), for individual GATA members indicated their differential expression in response to various abiotic stresses such as salinity, drought, and exogenous ABA. One of the members of subfamily VII—OsGATA23a, emerged as a multi-stress responsive transcription factor giving elevated expression levels in response to salinity and drought. ABA also induces expression of OsGATA23a by 35 and 55-folds in IR64 and Pokkali respectively. However, OsGATA23b, an alternative splice variant of OsGATA23 did not respond to above-mentioned stresses. Developmental regulation of the OsGATA genes based on a publicly available microarray database showed distinct expression patterns for most of the GATA members throughout different stages of rice development. Altogether, our results suggest inherent roles of diverse OsGATA factors in abiotic stress signaling and also throw some light on the tight regulation of the spliced variants of OsGATA genes in response to different environmental conditions.

DNA damage is one of the common consequences of exposure to various stress conditions. Different methods have been developed to accurately assess DNA damage and fragmentation in cells and tissues exposed to different stress agents. However, owing to the presence of firm cellulosic cell wall and phenolics, plant cells and tissues are not easily amenable to be subjected to these assays. Here, we describe an optimized TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling) assay-based protocol to determine the extent of DNA fragmentation and programmed cell death in plant root cells subjected to various stress conditions. The method described here has the advantages of simplicity, reliability and reproducibility.

Shrinking arable land due to soil salinization and, depleting fresh water resources pose serious worldwide constraints to crop productivity. A vision of using plant feedstock for biofuel production can only be realized if we can identify alternate species that can be grown on saline soils and therefore, would not compete for the resources required for conventional agriculture. Halophytes have remarkable ability to grow under high salinity conditions. They can be irrigated with seawater without compromising their biomass and seed yields making them good alternate candidates as bioenergy crops. Both oil produced from the seeds and the lignocellulosic biomass of halophytes can be utilized for biofuel production. Several researchers across the globe have recognized this potential and assessed several halophytes for their tolerance to salt, seed oil contents and composition of their lignocellulosic biomass. Here, we review current advances and highlight the key species of halophytes analyzed for this purpose. We have critically assessed the challenges and opportunities associated with using halophytes as bioenergy crops.

Increasing vulnerability of plants to a variety of stresses such as drought, salt and extreme temperatures poses a global threat to sustained growth and productivity of major crops. Of these stresses, drought represents a considerable threat to plant growth and development. In view of this, developing staple food cultivars with improved drought tolerance emerges as the most sustainable solution towards improving crop productivity in a scenario of climate change. In parallel, unraveling the genetic architecture and the targeted identification of molecular networks using modern OMICS analyses, that can underpin drought tolerance mechanisms, is urgently required. Importantly, integrated studies intending to elucidate complex mechanisms can bridge the gap existing in our current knowledge about drought stress tolerance in plants. It is now well established that drought tolerance is regulated by several genes, including transcription factors (TFs) that enable plants to withstand unfavorable conditions, and these remain potential genomic candidates for their wide application in crop breeding. These TFs represent the key molecular switches orchestrating the regulation of plant developmental processes in response to a variety of stresses. The current review aims to offer a deeper understanding of TFs engaged in regulating plant’s response under drought stress and to devise potential strategies to improve plant tolerance against drought.

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Drought is an important abiotic factor which has a huge detrimental impact on crop productivity. Study of plant responses towards drought stress and investigating the mechanism of drought tolerance is crucial for achieving the target of developing drought-tolerant plants. Phenotyping is a cost effective approach which can be adopted to evaluate the severity of drought stress in a plant. Next to phenotyping parameters, biochemical parameters such as the study of antioxidant enzyme activity play significant roles in assessing the extent of drought stress caused injury in a plant. Among the antioxidant enzymes, ascorbate peroxidase is an enzyme which plays a crucial role in drought tolerance in plants. It has been well established that the activity of this enzyme increases under drought stress. Here, we present a simple and reproducible protocol to investigate the response of tobacco plants towards drought stress through measurement of phenotypic parameters and antioxidant enzyme activity. Though, these experiments have been conducted with tobacco plants, this protocol could be adopted for other crop species.

Stress tolerance is a multigenic trait that depends on the coordinated action of several genes. Various physiological parameters, such as plant height and weight, total yield, chlorophyll content, photosynthesis rate, level of reactive oxygen species (ROS) and anti-oxidant activity could be correlated directly with the level of stress tolerance potential of any particular genotype. To evaluate the stress tolerance potential of a plant, leaf disc stress tolerance assay is a very rapid and widely acceptable experiment with minimum instrumentation facilities.

Stress tolerance of plants is a complex phenomenon that depends on the inter-related action of several morphological, physiological and biochemical parameters. Although stress affects normal physiological growth of a plant irrespective of its developmental stage, seed germination and seed setting are considered to be the most sensitive two. Therefore, to evaluate the stress tolerance potential of a particular plant species or variety, rate of seed germination in presence of stress is an important agronomic trait. This will provide a clear indication about the stress tolerance potential with minimum instrumentation facilities. The method is very simple, effective and highly reproducible that would provide quick and reliable results to the researchers.

Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars for salinity tolerance, B. juncea and B. nigra. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52.

Cyclophilins, which bind to immunosuppressant cyclosporin A (CsA), are ubiquitous proteins and constitute a multigene family in higher organisms. Several members of this family are reported to catalyze cis-trans isomerisation of the peptidyl-prolyl bond, which is a rate limiting step in protein folding. The physiological role of these proteins in plants, with few exceptions, is still a matter of speculation. Although Arabidopsis genome is predicted to contain 35 cyclophilin genes, biochemical characterization, imperative for understanding their cellular function(s), has been carried only for few of the members. The present study reports the biochemical characterization of an Arabidopsis cyclophilin, AtCyp19-3, which demonstrated that this protein is enzymatically active and possesses peptidyl-prolyl cis-trans isomerase (PPIase) activity that is specifically inhibited by CsA with an inhibition constant (Ki) of 18.75 nM. The PPIase activity of AtCyp19-3 was also sensitive to Cu(2+), which covalently reacts with the sulfhydryl groups, implying redox regulation. Further, using calmodulin (CaM) gel overlay assays it was demonstrated that in vitro interaction of AtCyp19-3 with CaM is Ca(2+)-dependent, and CaM-binding domain is localized to 35-70 amino acid residues in the N-terminus. Bimolecular fluorescence complementation assays showed that AtCyp19-3 interacts with CaM in vivo also, thus, validating the in vitro observations. However, the PPIase activity of the Arabidopsis cyclophilin was not affected by CaM. The implications of these findings are discussed in the context of Ca(2+) signaling and cyclophilin activity in Arabidopsis.