GENOME-WIDE ASSOCIATION AND EXPRESSION STUDIES FOR IDENTIFICATION OF QTLS AND CANDIDATE GENES UNDERLYING ABIOTIC STRESS TOLERANCE DURING GERMINATION STAGE OF RICE

Rice is one of the most important cereal crops feeding more than half of the world’s population. Due to extreme climatic condition, different abiotic stresses like hypoxia stress and chilling stress have been the biggest threat to rice production. Direct sowing method is the most preferred way of planting in Asian countries and in U.S. due to the lower cost of planting and less labor requirement. The major challenge associated with direct sowing is flash flooding that can happen immediately after sowing due to unpredicted rainfall. In this study, we evaluated more than 250 rice accessions belonging to different groups of rice for various traits related to chilling tolerance and hypoxia tolerance during germination stage. Compressed Mixed Linear Model (CMLM) of GAPIT was used to conduct GWAS analysis for the identification of QTLs. From the GWAS study conducted for chilling stress tolerance, we identified 41 QTLs associated with different chilling indices like low temperature germinability, germination index, coleoptile growth under cold condition, plumule length at 4 d recovery, and plumule growth rate after cold germination. Out of 41 QTLs identified in the whole panel, 14 QTLs were potentially colocalized with known genes/QTLs and 27 QTLs were found to be novel. From the GWAS analysis of hypoxia stress tolerance traits, there were 24 significant SNPs identified to be associated with different traits measured under hypoxia stress. Out of the 24 significant SNPs discovered in the whole panel, 11 QTLs were found to be potentially colocalized with previously identified candidate genes underlying flooding tolerance mechanism in rice. From the phenotypic evaluation of the whole panel for chilling stress tolerance and hypoxia stress tolerance, two lines with contrasting phenotypes under each stress condition were selected and used for global gene expression analysis. The results of these transcriptomics studies have provided new insights of underlying biological processes, molecular functions and cellular components related to the phenotypic differences of the contrasting lines. The findings of our study will help in identification of promising candidate genes underlying hypoxia stress and chilling stress tolerance and would eventually assist rice breeding program to develop improved tolerant rice cultivars

Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions

Amaranthus is a genus of C4 dicotyledonous herbaceous plants, and three New World species have been domesticated to produce grain crops with light colored seed which are classified as pseudo-cereals rich in protein and minerals. A core collection of grain amaranths and immediate precursor species has been established, representing the closest related species. The goal of this study was to evaluate the genetic diversity in that collection of cultivated and wild species, using competitive allele single nucleotide polymorphism markers. A secondary objective was to determine the relationships among the three cultivated species and non-domesticated Amaranthus, while a third objective was to evaluate the utility of the markers in detecting diversity in the 276 genotypes. The markers were found to be highly variable with an average polymorphism information content of 0.365. All markers were bi-allelic; and the major allele frequency ranged from 0.388 to 0.871. Population structure analysis of the cultigens revealed the presence of two sub populations. Phylogeny confirmed that the two Mesoamerican species, Amaranthus cruentus and Amaranthus hypochondriacus, were related and distant from the South American species Amaranthus caudatus, which in turn was very closely clustered with Amaranthus quitensis, even though this is considered a weedy relative. The first pair of species were likely to have inter-crossed, while the latter two likely exist in a wild-cultivated hybrid state. In conclusion, the results of this SNP study provided insights on amaranth cultivars and their relationship to wild species, the probable domestication events leading to the cultivars, and possible crop breeding or germplasm conservation strategies

GENOME-WIDE ASSOCIATION AND EXPRESSION STUDIES FOR IDENTIFICATION OF QTLS AND CANDIDATE GENES UNDERLYING ABIOTIC STRESS TOLERANCE DURING GERMINATION STAGE OF RICE

Rice is one of the most important cereal crops feeding more than half of the world’s population. Due to extreme climatic condition, different abiotic stresses like hypoxia stress and chilling stress have been the biggest threat to rice production. Direct sowing method is the most preferred way of planting in Asian countries and in U.S. due to the lower cost of planting and less labor requirement. The major challenge associated with direct sowing is flash flooding that can happen immediately after sowing due to unpredicted rainfall. In this study, we evaluated more than 250 rice accessions belonging to different groups of rice for various traits related to chilling tolerance and hypoxia tolerance during germination stage. Compressed Mixed Linear Model (CMLM) of GAPIT was used to conduct GWAS analysis for the identification of QTLs. From the GWAS study conducted for chilling stress tolerance, we identified 41 QTLs associated with different chilling indices like low temperature germinability, germination index, coleoptile growth under cold condition, plumule length at 4 d recovery, and plumule growth rate after cold germination. Out of 41 QTLs identified in the whole panel, 14 QTLs were potentially colocalized with known genes/QTLs and 27 QTLs were found to be novel. From the GWAS analysis of hypoxia stress tolerance traits, there were 24 significant SNPs identified to be associated with different traits measured under hypoxia stress. Out of the 24 significant SNPs discovered in the whole panel, 11 QTLs were found to be potentially colocalized with previously identified candidate genes underlying flooding tolerance mechanism in rice. From the phenotypic evaluation of the whole panel for chilling stress tolerance and hypoxia stress tolerance, two lines with contrasting phenotypes under each stress condition were selected and used for global gene expression analysis. The results of these transcriptomics studies have provided new insights of underlying biological processes, molecular functions and cellular components related to the phenotypic differences of the contrasting lines. The findings of our study will help in identification of promising candidate genes underlying hypoxia stress and chilling stress tolerance and would eventually assist rice breeding program to develop improved tolerant rice cultivars

Genetic diversity analysis of Amaranthus using molecular markers (SNPS) and morphological traits

Amaranths belonging to family Amaranthaceae and genus Amaranthus is a C4 dicotyledonous herbaceous plants comprising approximately 70 species. The genus Amaranthus contains both cultivated and grain types, where cultivated ones are used for food grains, leafy vegetables, forage, ornamental gardening etc. Amaranth grains are pseudocereals containing high amount of proteins and minerals. Genetic diversity analysis of Amaranthus is important for development of core set of germplasm with widely diverse population and effective utilization of plant genetic resources. Several methods like use of morphological markers, molecular markers like proteins and enzyme based markers, ISSR, RAPD, AFLP, SSR, SNPs have been employed so far for genetic characterization of Amaranthus. In this study, we had core collection of 260 accessions from United State Department of Agriculture (USDA) and 33 accessions from Seed Savers’ Exchange (SSE). We evaluated morphological traits like blade pigmentation, blade shape, petiole pigmentation, branching index, flower color, stem color, inflorescence density, inflorescence shape, terminal inflorescence attitude, plant height and yield characteristics across all 293 accessions. We did genetic characterization of 276 accessions (249 accessions from USDA and 27 accessions from SSE) using KASPar designed 45 SNP markers. Data analysis of morphological data showed significant difference of petiole pigmentation, stem color, blade pigmentation, blade shape and flower color across different clusters of 260 accessions of USDA unlike among different clusters of SSE where we found significant difference of only blade pigmentation, blade shape and flower color across different clusters. The average yield per plant across 260 accessions of USDA and 33 accessions of SSE was 25.30g and 40.18g respectively. The SNP markers used were found to be highly polymorphic with an average PIC value of 0.5837 except one SNP marker (A-AM19583). The major allele frequency ranged from 0.3877 to 0.8533 with an average value of 0.6776. Model-based structure analysis with 100,000 burn-in length revealed the presence of highly polymorphic three populations with some admixtures across 276 accessions. The genetic relationship depicted by neighbor-joining method of DARwin software was consistent with the structure-based membership assignments of each accessions. This results will provide insights on germplasm conservation and crop improvement of amaranths

Morphological Assessment of Cultivated and Wild Amaranth Species Diversity

Amaranthus L. is genus of C4 dicotyledonous herbaceous plants comprising approximately 70 species, with three subgenera, which contains both cultivated and wild types, where cultivated ones are used for food grains, leafy vegetables, potential forages and ornamentals. Grain amaranth are pseudocereals from three species domesticated in North and South America and are notable for containing high amount of protein and minerals and balanced amino acid in their small seeds. Genetic diversity analysis of amaranths is important for development of core set of germplasm with widely diverse population and effective utilization of plant genetic resources. In this study, we evaluated a germplasm collection of 260 amaranth accessions from United State Department of Agriculture (USDA) and 33 accessions from Seed Savers’ Exchange (SSE). We evaluated morphological traits like blade pigmentation, blade shape, petiole pigmentation, branching index, flower color, stem color, inflorescence density, inflorescence shape, terminal inflorescence attitude, plant height and yield characteristics across all 293 accessions. We compared clustering within the USDA and SSE collection and across both collections. Data analysis of morphological data showed significant difference of petiole pigmentation, stem color, blade pigmentation, blade shape and flower color across different clusters of accessions of USDA unlike among different clusters of SSE where we found significant difference of only blade pigmentation, blade shape and flower color. The relationship depicted by neighbor-joining dendogram using the morphological markers was consistent with some but not all of the differences observed between species. Some divisions were found between cultivated and weedy amaranths that was substantiated by morphological characteristics but no separation of South and Central American species was observed. Substantial phenotypic plasticity limits the use of morphological analysis for phylogenetic analysis but does show that important morphological traits such as inflorescence type and plant architecture can cross species boundaries. Similarly, color variants for leaves, flowers and seeds are not exclusive to one cluster in our study nor to one species and can be used widely for breeding any of the cultigens, but not to species identification. Our findings will help in germplasm conservation of grain amaranths and facilitate in this crop’s improvement. It will also help on developing effective breeding programs involving different plant characteristics and morphological traits of Amaranths

Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions

Amaranthus is a genus of C4 dicotyledonous herbaceous plants, and three New World species have been domesticated to produce grain crops with light colored seed which are classified as pseudo-cereals rich in protein and minerals. A core collection of grain amaranths and immediate precursor species has been established, representing the closest related species. The goal of this study was to evaluate the genetic diversity in that collection of cultivated and wild species, using competitive allele single nucleotide polymorphism markers. A secondary objective was to determine the relationships among the three cultivated species and non-domesticated Amaranthus, while a third objective was to evaluate the utility of the markers in detecting diversity in the 276 genotypes. The markers were found to be highly variable with an average polymorphism information content of 0.365. All markers were bi-allelic; and the major allele frequency ranged from 0.388 to 0.871. Population structure analysis of the cultigens revealed the presence of two sub populations. Phylogeny confirmed that the two Mesoamerican species, Amaranthus cruentus and Amaranthus hypochondriacus, were related and distant from the South American species Amaranthus caudatus, which in turn was very closely clustered with Amaranthus quitensis, even though this is considered a weedy relative. The first pair of species were likely to have inter-crossed, while the latter two likely exist in a wild-cultivated hybrid state. In conclusion, the results of this SNP study provided insights on amaranth cultivars and their relationship to wild species, the probable domestication events leading to the cultivars, and possible crop breeding or germplasm conservation strategies

Biochemical Analysis and Human Aldose Reductase Inhibition Activity of Selected Medicinal Plants of Nepal

Aldose reductase has received extensive research as a key enzyme in the development of long-term problems linked to diabetes mellitus. Overexpression of this enzyme or with exceeded glucose concentration in the blood increases sorbitol on the retina leading to retinopathy, which is the adverse effect of type II diabetes. Approximately 100 million people are suffering from diabetic retinopathy globally. This research is focused on studying the total phenolic content (TPC), total flavonoid content (TFC), antioxidant potential, and aldose reductase inhibiting properties of selected medicinal plants such as Anacyclus pyrethrum, Bergenia ciliata, Rhododendron arboreum, and Swertia chirayita. In addition, ADMET analysis and molecular docking of seven previously identified compounds from the chosen medicinal plants were carried out against human aldose reductase (PDB ID: 4JIR). The ethanol extract of S. chirayita exhibited the highest TPC (4.63 ± 0.16 mg GAE/g) and TFC (0.90 ± 0.06 mg QE/g). Analysis of 2,2-diphenyl-1-picrylhydrazyl (DPPH)-based antioxidant assay showed that IC50 of the ethanolic extract of B. cilata and R. arboreum showed a significant antioxidant activity with IC50 value of 0.05 mg/mL. The percentage inhibition of AR by extract of B. ciliata (94.74 ± 0.01%) was higher than other plant extracts. A molecular docking study showed that morin isolated from B. ciliata showed a good binding interaction with AR. This study showed that the extracts of A. pyrethrum, B. ciliata, and R. arboreum could be potential sources of inhibitors against AR to treat retinopathy

Current Research on Silver Nanoparticles: Synthesis, Characterization, and Applications

Over the past couple of decades, nanomaterials have advanced the research in materials; biomedical, biological, and chemical sciences; etc., owing to their peculiar properties at the nanoregime compared to their bulk composition. Applications of nanoparticles in the fields like medicine and agriculture have been boosted due to the development of different methodologies developed to synthesize specific shapes and sizes. Silver nanoparticles have tunable physical and chemical properties, so it has been studied widely to improve its applicability. The antimicrobial properties of Ag NPs are finding their application in enhancing the activity of drugs (like Amphotericin B, Nystatin, Fluconazole) and composite scaffolds for controlled release of drugs and targeted delivery of drugs due to their low toxicity and biocompatibility. Similarly, their surface plasmon resonance property makes Ag NPs a top-notch material for developing (bio)sensors, for instance, in surface-enhanced Raman spectroscopy, for detecting biomarkers, diseases, pollutants, and higher catalytic activity in photochemical reactions. Besides these, highly conducting Ag NPs are used in wearable and flexible sensors to generate electrocardiographs. Physicochemical or biological approaches are used to prepare Ag NPs; however, each method has its pros and cons. The prohibitive cost and use of hazardous chemicals hinder the application of physicochemical synthesis. Likewise, biological synthesis is not always reproducible for extensive use but can be a suitable candidate for therapeutic activities like cancer therapy. Excess use of Ag NPs is cytotoxic, and their unregulated discharge in the environment may have effects on both aquatic and terrestrial biota. The research in Ag NPs has always been driven by the need to develop a technology with potential benefits and minimal risk to environmental and human health. In this review, we have attempted to provide an insight into the application of Ag NPs in various sectors along with the recent synthetic and characterization techniques used for Ag NPs

Technological Advancements for the Detection of Antibiotics in Food Products

Antibiotics, nowadays, are not only used for the treatment of human diseases but also used in animal and poultry farming to increase production. Overuse of antibiotics leads to their circulation in the food chain due to unmanaged discharge. These circulating antibiotics and their residues are a major cause of antimicrobial resistance (AMR), so comprehensive and multifaceted measures aligning with the One Health approach are crucial to curb the emergence and dissemination of antibiotic resistance through the food chain. Different chromatographic techniques and capillary electrophoresis (CE) are being widely used for the separation and detection of antibiotics and their residues from food samples. However, the matrix present in food samples interferes with the proper detection of the antibiotics, which are present in trace concentrations. This review is focused on the scientific literature published in the last decade devoted to the detection of antibiotics in food products. Various extraction methods are employed for the enrichment of antibiotics from a wide variety of food samples; however, solid-phase extraction (SPE) techniques are often used for the extraction of antibiotics from food products and biological samples. In addition, this review has scrutinized how changing instrumental composition, organization, and working parameters in the chromatography and CE can greatly impact the identification and quantification of antibiotic residues. This review also summarized recent advancements in other detection methods such as immunological assays, surface-enhanced Raman spectroscopy (SERS)-based assays, and biosensors which have emerged as rapid, sensitive, and selective tools for accurate detection and quantification of traces of antibiotics