National Institute for Biotechnology and Genetic Engineering

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the ∼730-megabase Sorghum bicolor (L.) Moench genome, placing ∼98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the ∼75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization ∼70 million years ago, most duplicated gene sets lost one member before the sorghum–rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum’s drought tolerance. The Sorghum bicolor genome sequence is published this week. Sorghum is a cereal grown widely as food, animal feed, fibre and fuel. Tolerant to hot, dry conditions, it is a staple for large populations in the West African Sahel region. Comparisons of the genome with those of maize and rice shed light on the evolution of grasses and of C4 photosynthesis, which is particularly efficient at assimilating carbon at high temperatures. In addition, protein coding genes and miRNAs that could contribute to sorghum's drought tolerance may also be found. Sorghum yield improvement has lagged behind that of other crops and the availability of the genome sequence could provide a vital boost to work on its improvement. Sorghum is an African grass that is grown for food, animal feed and fuel. The current paper presents an initial analysis of the ∼730 megabase genome of Sorghum bicolor. Genome analysis and its comparison with maize and rice shed light on grass genome evolution and also provide insights into the evolution of C4 photosynthesis, as well as protein coding genes and miRNAs that might contribute to sorghum's drought tolerance.

Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. The global genetic and molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo–assembled genomes for these two cultivated allotetraploid species with pronounced improvement in repetitive-DNA-enriched centromeric regions. Whole-genome comparative analyses revealed that species-specific alterations in gene expression, structural variations and expanded gene families were responsible for speciation and the evolutionary history of these species. These findings help to elucidate the evolution of cotton genomes and their domestication history. The information generated not only should enable breeders to improve fiber quality and resilience to ever-changing environmental conditions but also can be translated to other crops for better understanding of their domestication history and use in improvement. High-quality de novo–assembled genomes of two cultivated allotetraploid cotton species and whole-genome comparative analyses provide insights into the evolution of cotton genomes and improvement of fiber quality and resilience to stress.

The geminiviruses are a family of small, non-enveloped viruses with single-stranded, circular DNA genomes of 2500-5200 bases. Geminiviruses are transmitted by various types of insect (whiteflies, leafhoppers, treehoppers and aphids). Members of the genus Begomovirus are transmitted by whiteflies, those in the genera Becurtovirus, Curtovirus, Grablovirus, Mastrevirus and Turncurtovirus are transmitted by specific leafhoppers, the single member of the genus Topocuvirus is transmitted by a treehopper and one member of the genus Capulavirus is transmitted by an aphid. Geminiviruses are plant pathogens causing economically important diseases in most tropical and subtropical regions of the world. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Geminiviridae which is available at www.ictv.global/report/geminiviridae.

Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly. Generating larger amounts of sequence data more quickly does not address the difficulties of sequencing and assembling complex genomes de novo. The cotton ( Gossypium spp.)

The rhizosphere is undoubtedly the most complex microhabitat, comprised of an integrated network of plant roots, soil, and a diverse consortium of bacteria, fungi, eukaryotes, and archaea. The rhizosphere conditions have a direct impact on crop growth and yield. Nutrient-rich rhizosphere environments stimulate plant growth and yield and vice versa. Extensive cultivation exhaust most of the soils which need to be nurtured before or during the next crop. Chemical fertilizers are the major source of crop nutrients but their uncontrolled and widespread usage has posed a serious threat to the sustainability of agriculture and stability of an ecosystem. These chemicals are accumulated in the soil, drained in water, and emitted to the air where they persist for decades causing a serious threat to the overall ecosystem. Plant growth-promoting rhizobacteria (PGPR) present in the rhizosphere convert many plant-unavailable essential nutrients e.g., nitrogen, phosphorous, zinc, etc. into available forms. PGPR produces certain plant growth hormones (such as auxin, cytokinin, and gibberellin), cell lytic enzymes (chitinase, protease, hydrolases, etc.), secondary metabolites, and antibiotics, and stress alleviating compounds (e.g., 1-Aminocyclopropane-1- carboxylate deaminase), chelating agents (siderophores), and some signaling compounds (e.g., N-Acyl homoserine lactones) to interact with the beneficial or pathogenic counterparts in the rhizosphere. These multifarious activities of PGPR improve the soil structure, health, fertility, and functioning which directly or indirectly support plant growth under normal and stressed environments. Rhizosphere engineering with these PGPR has a wide-ranging application not only for crop fertilization but developing eco-friendly sustainable agriculture. Due to severe climate change effects on plants and rhizosphere biology, there is growing interest in stress-resilient PGPM and their subsequent application to induce stress (drought, salinity, and heat) tolerance mechanism in plants. This review describes the three components of rhizosphere engineering with an explicit focus on the broader perspective of PGPM that could facilitate rhizosphere engineering in selected hosts to serve as an efficient component for sustainable agriculture.

SAr) to organic substances. In these studies, electron-deficient carbon-centered fluoroalkyl radicals were successfully generated by the appropriate choice of fluoroalkyl source, photocatalyst, additives, and solvent. The redox potentials of the photocatalysts and the fluoroalkyl sources and the choice of sacrificial electron donor or acceptor as the additive affected the photocatalytic pathway, determining whether an oxidative or reductive quenching pathway was operative for the generation of key fluoroalkyl radicals. Notably, we have observed that additives significantly affect the efficiencies and selectivities of these reactions and can even change the outcome of the reaction by playing additional roles during its course. For instance, a tertiary amine as an additive in the reaction medium can act not only as a sacrificial electron donor in photoredox catalysis but also as a hydrogen atom source, an elimination base for dehydrohalogenation of the intermediate, and also a Brønsted base for deprotonation. In the same context, the selection of solvent is also critical since it affects the rate and selectivity of reactions depending upon its polarity and reagent solubilizing ability and plays additional roles in the process, for example, as a hydrogen atom source. By clearly understanding the roles of additives and solvent, we designed several controlled fluoroalkylation reactions where different products were formed selectively from the same starting substrates. In addition, we could exploit one of the most important advantages of radical reactions, that is, the use of unactivated π-systems such as alkenes, alkynes, arenes, and heteroarenes as radical acceptors without prefunctionalization. Furthermore, fluoroalkylation processes under mild room-temperature reaction conditions tolerate various functional groups and are therefore easily applicable to late-stage modifications of highly functionalized advanced intermediates.

The present study was conducted to characterize the native plant growth promoting (PGP) bacteria from wheat rhizosphere and root-endosphere in the Himalayan region of Rawalakot, Azad Jammu and Kashmir (AJK), Pakistan. Nine bacterial isolates were purified, screened in vitro for PGP characteristics and evaluated for their beneficial effects on the early growth of wheat (Triticum aestivum L.). Among nine bacterial isolates, seven were able to produce indole-3- acetic acid in tryptophan-supplemented medium; seven were nitrogen fixer, and four were able to solubilize inorganic phosphate in vitro. Four different morphotypes were genotypically identified based on IGS-RFLP fingerprinting and representative of each morphotype was identified by 16S rRNA gene sequencing analysis except Gram-positive putative Bacillus sp. Based on 16S rRNA gene sequence analysis, bacterial isolates AJK-3 and AJK-9 showing multiple PGP-traits were identified as Stenotrophomonas spp. while AJK-7 showed equal homologies to Acetobacter pasteurianus and Stenotrophomonas specie. Plant inoculation studies indicated that these Plant growth-promoting rhizobacteria (PGPR) strains provided a significant increase in shoot and root length, and shoot and root biomass. A significant increase in shoot N contents (up to 76%) and root N contents (up to 32%) was observed over the un-inoculated control. The study indicates the potential of these PGPR for inoculums production or biofertilizers for enhancing growth and nutrient content of wheat and other crops under field conditions. The study is the first report of wheat associated bacterial diversity in the Himalayan region of Rawalakot, AJK.

Tyrosinase is a copper-containing enzyme, which is widely distributed in microorganisms, animals and plants and is a key enzyme in melanin biosynthesis, involved in determining the color of mammalian skin and hair. In addition, unfavorable enzymatic browning of plant-derived foods by tyrosinase causes a decrease in nutritional quality and economic loss of food products. The inadequacy of current conventional methods to prevent tyrosinase action encourages researchers to seek new potent tyrosinase inhibitors for food and cosmetics. This article presents a study on the importance of tyrosinase, biochemical characteristics, type of inhibitions, activators from various natural sources with its clinical and industrial importance in recent prospects is discussed in this paper.

The type and amount of melanin synthesized by the melanocyte, and its distribution pattern in the surrounding keratinocytes, determines the actual color of the skin. Melanin forms through a series of oxidative reactions involving the amino acid tyrosine in the presence of the enzyme tyrosinase. Tyrosinase catalyses three different reactions in the biosynthetic pathway of melanin in melanocytes: the hydroxylation of tyrosine to l-DOPA and the oxidation of l-DOPA to dopaquinone; furthermore, in humans, dopaquinone is converted by a series of complex reactions to melanin. Among the skin-lightening and depigmenting agents, magnesium-l-ascorbyl-2-phosphate (MAP), hydroxyanisole, N-acetyl-4-S-cysteaminylphenol, arbutin (hydroquinone-beta-d-glucopyranoside) and hydroquinone (HQ) are the most widely prescribed worldwide. However, with reports of potential mutagenicity and epidemics of ochronosis, there has been an increasing impetus to find alternative herbal and pharmaceutical depigmenting agents. A review of the literature reveals that numerous other depigmenting or skin-lightening agents are either in use or in investigational stages. Some of these, such as kojic, glycolic and azelaic acids, are well known to most dermatologists. Others have been discovered and reported in the literature more recently. Several depigmentation and lightening agents are discussed, including their historical background, biochemical characteristics, type of inhibition and activators from various sources. In addition, the clinical importance of mushroom tyrosinase as a recent prospect is discussed in this paper.

Brain is a vital organ of the human body which performs very important functions such as analysis, processing, coordination, and execution of electrical signals. For this purpose, it depends on a complex network of nerves which are ensheathed in lipids tailored myelin; an abundant source of lipids in the body. The nervous system is enriched with important classes of lipids; sphingolipids and cholesterol which compose the major portion of the brain particularly in the form of myelin. Both cholesterol and sphingolipids are embedded in the microdomains of membrane rafts and are functional units of the neuronal cell membrane. These molecules serve as the signaling molecules; hold important roles in the neuronal differentiation, synaptogenesis, and many others. Thus, their adequate provision and active metabolism are of crucial importance in the maintenance of physiological functions of brain and body of an individual. In the present review, we have highlighted the physiological roles of cholesterol and sphingolipids in the development of the nervous system as well as the association of their altered metabolism to neurological and neurodegenerative diseases.

Paper-based microfluidics is the branch of microfluidics involving devices made out of paper, or other porous membranes, that wick fluids by capillary action. Paper-based microfluidic devices have several advantages over conventional microfluidic devices including simpler fabrication, lower cost, easier disposal, and the ability to operate without pumps or other supporting equipment. The most common application of paper-based microfluidic devices is in the development of point-of-care (POC) diagnostic devices, which could eliminate the need for costly and time-consuming laboratory-based analytical procedures. This review provides an overview of current methods of fabricating paper-based microfluidic devices, examples of applications of these devices, a discussion of their current limitations, and an outlook on their future.

We report here a simple one-step protocol for the preparation of near-monodisperse gold hydrosols in the small size regime (<5 nm). The particle size can be controlled by varying the concentration of the stabilizing polymer, which can be readily displaced by thiol ligands to yield monolayer protected clusters of the usual type.

With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a 'one size fits all' crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market.

Salinity is a growing problem affecting soils and agriculture in many parts of the world. The presence of salt in plant cells disrupts many basic metabolic processes, contributing to severe negative effects on plant development and growth. This review focuses on the effects of salinity on chloroplasts, including the structures and function of these organelles. Chloroplasts house various important biochemical reactions, including photosynthesis, most of which are considered essential for plant survival. Salinity can affect these reactions in a number of ways, for example, by changing the chloroplast size, number, lamellar organization, lipid and starch accumulation, and interfering with cross-membrane transportation. Research has shown that maintenance of the normal chloroplast physiology is necessary for the survival of the entire plant. Many plant species have evolved different mechanisms to withstand the harmful effects of salt-induced toxicity on their chloroplasts and its machinery. The differences depend on the plant species and growth stage and can be quite different between salt-sensitive (glycophyte) and salt-tolerant (halophyte) plants. Salt stress tolerance is a complex trait, and many aspects of salt tolerance in plants are not entirely clear yet. In this review, we discuss the different mechanisms of salt stress tolerance in plants with a special focus on chloroplast structure and its functions, including the underlying differences between glycophytes and halophytes.

Management of geminiviruses is a worldwide challenge because of the widespread distribution of economically important diseases caused by these viruses. Regardless of the type of agriculture, management is most effective with an integrated pest management (IPM) approach that involves measures before, during, and after the growing season. This includes starting with resistant cultivars and virus- and vector-free transplants and propagative plants. For high value vegetables, protected culture (e.g., greenhouses and screenhouses) allows for effective management but is limited owing to high cost. Protection of young plants in open fields is provided by row covers, but other measures are typically required. Measures that are used for crops in open fields include roguing infected plants and insect vector management. Application of insecticide to manage vectors (whiteflies and leafhoppers) is the most widely used measure but can cause undesirable environmental and human health issues. For annual crops, these measures can be more effective when combined with host-free periods of two to three months. Finally, given the great diversity of the viruses, their insect vectors, and the crops affected, IPM approaches need to be based on the biology and ecology of the virus and vector and the crop production system. Here, we present the general measures that can be used in an IPM program for geminivirus diseases, specific case studies, and future challenges.

Abiotic stresses, including drought, salinity, temperature, and heavy metals, pose a major challenge for crop production and cause substantial yield reduction worldwide. Breeding tolerant cultivars against these abiotic stresses is the most sustainable and eco-friendly approach to cope with this challenge. Advances in genome editing technologies provide new opportunities for crop improvement by employing precision genome engineering for targeted crop traits. However, the selection of the candidate genes is critical for the success of achieving the desired traits. Broadly speaking, these genes could fall into two major categories, structural and regulatory genes. Structural genes encode proteins that provide stress tolerance directly, whereas regulatory genes act indirectly by controlling the expression of other genes involved in different cellular processes. Additionally, cis-regulatory sequences are also vital for achieving stress tolerance. We propose targeting of these regulatory and/or structural genes along with the cis-regulatory sequences via the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system as a robust, efficient, and practical approach for developing crop varieties resilient to climate change. We also discuss the possibility of creating novel quantitative trait loci for abiotic stress tolerance via the CRISPR/Cas-mediated targeting of promoters. It is hoped that these genome editing tools will not only make a significant contribution towards raising novel plant types having tolerance to multiple abiotic stresses but will also aid in public acceptance of these products in years to come. This article is an attempt to critically evaluate the suitability of available tools and the target genes for obtaining plants with improved tolerance to abiotic stresses.

Deamination of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is a key plant-beneficial trait found in plant growth-promoting rhizobacteria (PGPR) and phytosymbiotic bacteria, but the diversity of the corresponding gene (acdS) is poorly documented. Here, acdS sequences were obtained by screening putative ACC deaminase sequences listed in databases, based on phylogenetic properties and key residues. In addition, acdS was sought in 71 proteobacterial strains by PCR amplification and/or hybridization using colony dot blots. The presence of acdS was confirmed in established AcdS+ bacteria and evidenced noticeably in Azospirillum (previously reported as AcdS-), in 10 species of Burkholderia and six Burkholderia cepacia genomovars (which included PGPR, phytopathogens and opportunistic human pathogens), and in five Agrobacterium genomovars. The occurrence of acdS in true and opportunistic pathogens raises new questions concerning their ecology in plant-associated habitats. Many (but not all) acdS+ bacteria displayed ACC deaminase activity in vitro, including two Burkholderia clinical isolates. Phylogenetic analysis of partial acdS and deduced AcdS sequences evidenced three main phylogenetic clusters, each gathering pathogens and plant-beneficial strains of contrasting geographic and habitat origins. The acdS phylogenetic tree was only partly congruent with the rrs tree. Two clusters gathered both Betaprotobacteria and Gammaproteobacteria, suggesting extensive horizontal transfers of acdS, noticeably between plant-associated Proteobacteria.

Wheat ( Triticum spp. L.) breeders have significantly improved wheat adaptation to stress‐prone environments around the world. This progress has largely been achieved using empirical selection and genetic variability within the primary wheat gene pool. As most stress tolerance traits are quantitatively inherited, expansion of the available genetic diversity for stress tolerance is necessary if rates of genetic progress are to be maintained. This review explores three sources of novel genetic variability, namely synthetic wheat, landrace cultivars, and alien introgressions and their applicability to applied wheat breeding. Synthetic hexaploid wheat, derived by crossing tetraploid wheat with Aegilops tauschii , provides new genetic variability for adaptation to drought, high temperature, salinity, waterlogging, and soil micronutrient imbalances from the secondary wheat gene pool. Synthetic‐derived materials have performed well in many stressed environments globally. There is significant unexploited variation among landraces and modern wheat cultivars to improve the stress adaptation of cultivated wheat. The tertiary gene pool, with a few significant exceptions, has been more difficult to exploit due to complex inheritance, meiotic instability, and linked deleterious effects. Nevertheless, there is sufficient genetic variation in the wheat gene pool to ensure the continued improvement of wheat adaptation to abiotic stress.

Salinity, a frequently occurring abiotic stress, is a major constraint for crop productivity worldwide. The present study was conducted to evaluate the ability of plant growth promoting rhizobacteria (PGPR) Bacillus cereus Pb25, isolated from soil irrigated with saline water, to promote Vigna radiate (mungbean) growth in the absence and presence of salt stress (9 dS m−1). Results demonstrated that B. cereus promoted V. radiate plant growth significantly even in the presence of salt. Inoculations with PGPR improved the plant growth, and increased the root, shoot fresh and dry biomass and yield as compared to plants with no bacterial treatment (control). Results showed that both chlorophyll content and plant growth were inhibited by saline stress and the salt-induced oxidative damage (measured by MDA, H2O2) was alleviated by PGPR inoculation. Furthermore, PGPR inoculation significantly increased the antioxidant enzymes (POD, SOD and CAT) activities and enhanced the accumulation of proline, potassium, nitrogen and phosphorus as well as decreased sodium accumulation in saline stressed plants. Regarding the soil biological activity, inoculated PGPR enhanced the activity of dehydrogenase, alkaline phosphatase, microbial biomass carbon, available phosphorus and total organic carbon under saline stress as compared to saline treatment alone. These results suggest that B. cereus can be used in salinized agricultural lands as bio-inoculant to increase crop productivity.

BACKGROUND: Viruses of the genus Begomovirus (family Geminiviridae) have genomes consisting of either one or two genomic components. The component of bipartite begomoviruses known as DNA-A is homologous to the genomes of all geminiviruses and encodes proteins required for replication, control of gene expression, overcoming host defenses, encapsidation and insect transmission. The second component, referred to as DNA-B, encodes two proteins with functions in intra- and intercellular movement in host plants. The origin of the DNA-B component remains unclear. The study described here was initiated to investigate the relationship between the DNA-A and DNA-B components of bipartite begomoviruses with a view to unraveling their evolutionary histories and providing information on the possible origin of the DNA-B component. RESULTS: Comparative phylogenetic and exhaustive pairwise sequence comparison of all DNA-A and DNA-B components of begomoviruses demonstrates that the two molecules have very distinct molecular evolutionary histories and likely are under very different evolutionary pressures. The analysis highlights that component exchange has played a far greater role in diversification of begomoviruses than previously suspected, although there are distinct differences in the apparent ability of different groups of viruses to utilize this "sexual" mechanism of genetic exchange. Additionally we explore the hypothesis that DNA-B originated as a satellite that was captured by the monopartite progenitor of all extant bipartite begomoviruses and subsequently evolved to become the integral (essential) genome component that we recognize today. The situation with present-day satellites associated with begomoviruses provides some clues to the processes and selection pressures that may have led to the "domestication" of a wild progenitor of the DNA-B component. CONCLUSIONS: The analysis has highlighted the greater genetic variation of DNA-B components, in comparison to the DNA-A components, and that component exchange is more widespread than previously demonstrated and confined to viruses from the Old World. Although the vast majority of New World and some Old World begomoviruses show near perfect co-evolution of the DNA-A and DNA-B components, this is not the case for the majority of Old World viruses. Genetic differences between Old and New World begomoviruses and the cultivation of exotic crops in the Old World are likely factors that have led to this dichotomy.