Integrated omic techniques and their genomic features for invasive weeds.

Many emerging invasive weeds display rapid adaptation against different stressful environments compared to their natives. Rapid adaptation and dispersal habits helped invasive populations have strong diversity within the population compared to their natives. Advances in molecular marker techniques may lead to an in-depth understanding of the genetic diversity of invasive weeds. The use of molecular techniques is rapidly growing, and their implications in invasive weed studies are considered powerful tools for genome purposes. Here, we review different approach used multi-omics by invasive weed studies to understand the functional structural and genomic changes in these species under different environmental fluctuations, particularly, to check the accessibility of advance-sequencing techniques used by researchers in genome sequence projects. In this review-based study, we also examine the importance and efficiency of different molecular techniques in identifying and characterizing different genes, associated markers, proteins, metabolites, and key metabolic pathways in invasive and native weeds. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding invasive weeds traits. Although these techniques can provide robust insights about the molecular functioning, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. We conclude that different multi-omic techniques will provide long-term benefits in launching new genome projects to enhance the understanding of invasive weeds' invasion process.

Molecular cloning, characterization and expression analysis of two 12-oxophytodienoate reductases (NtOPR1 and NtOPR2) from Nicotiana tabacum.

BACKGROUND: 12-oxophytodienoic acid (OPDA) is a signaling molecule involved in defense and stress responses in plants. 12-oxophytodienoate reductase (OPR) is involved in the biosynthesis of jasmonic acid and trigger the conversion of OPDA into 3-oxo-2(2'[Z]-pentenyl)-cyclopentane-1-octanoic acid (OPC-8:0). METHODS AND RESULTS: Sequence analysis revealed that Nicotiana tabacum 12-oxophytodienoate reductase 1 (OPR1) and OPR2 encoded polypeptides of 375 and 349 amino acids with molecular masses of 41.67 and 39.04 kilodaltons (kDa), respectively, while the deduced protein sequences of NtOPR1 and NtOPR2 showed high homology with other 12-oxophytodienoate reductases. BLAST (Basic local alignment search tool) analysis revealed that both NtOPRs belong to the family of Old Yellow Enzymes (OYE), and analysis of genomic DNA structure indicated that both genes include 5 exons and 4 introns. Phylogenetic analysis using MEGA X showed that NtOPR1 and NtOPR2 shared a close evolutionary relationship with Nicotiana attenuata 12-oxophytodienoate reductases. In silico analysis of subcellular localization indicated the probable locations of NtOPR1 and NtOPR2 to be the cytoplasm and the peroxisome, respectively. Tissue-specific expression assays via qRT-PCR revealed that NtOPR1 and NtOPR2 genes were highly expressed in Nicotiana tabacum roots, temperately expressed in leaves and flowers, while low expression was observed in stem tissue. CONCLUSIONS: Presently, two 12-oxophytodienoate reductase genes (NtOPR1 and NtOPR2) were cloned and comprehensively characterized. Our findings provide comprehensive analyses that may guide future deep molecular studies of 12-oxophytodienoate reductases in Nicotiana tabacum.

Pharmacological screening and GC-MS analysis of vegetative/reproductive parts of Nigella sativa L.

Nigella sativa is an extensively utilized herbal medicinal plant. Medicinal utilization of seeds and oil of N. sativa was common among all the ancient medicinal systems. Previously, the vegetative part of the plant was not utilized for pharmaceutical purposes. Therefore, the current study was aimed at determining the potential of the vegetative parts (leaves, branches and stem) of the plant to reduce the pressure on the reproductive part (seeds/oil) and to get a potential alternate source of pharmaceutical materials. The experiment was carried out in split block RCD design. The dried plant was extracted through partitioning method in a series of concentrations ranging from 200-1.562mg/ml in different solvents. Phyto-chemical screening, antibacterial and anti-oxidant assays and GC-MS analysis of the potent extracts were done. The green parts of N. sativa were shown to contain saponins, alkaloids, terpenoids, steroids, cardiac glycosides, tannins, and flavonoids, whereas phloba-tannins were absent. Evaluation of anti-aging properties through antioxidant assays yielded significant results in all the assays. Linoleic acid, palmitic acid, stearic acid, oleic acid and glyceryl linoleate were profiled through GC-MS analysis. Based on these results, it was concluded that the vegetative parts of N. sativa are effective alternatives to the reproductive part/seed for anti-aging and other phytochemicals needed to meet the present day requirements of the pharmaceutical industry.

Applications of the CRISPR/Cas9 System for Rice Grain Quality Improvement: Perspectives and Opportunities.

Grain quality improvement is a key target for rice breeders, along with yield. It is a multigenic trait that is simultaneously influenced by many factors. Over the past few decades, breeding for semi-dwarf cultivars and hybrids has significantly contributed to the attainment of high yield demands but reduced grain quality, which thus needs the attention of researchers. The availability of rice genome sequences has facilitated gene discovery, targeted mutagenesis, and revealed functional aspects of rice grain quality attributes. Some success has been achieved through the application of molecular markers to understand the genetic mechanisms for better rice grain quality; however, researchers have opted for novel strategies. Genomic alteration employing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) for reverse genetics has opened new avenues of research in the life sciences, including for rice grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting. Over the past few years many genes that are related to various aspects of rice grain quality have been successfully edited via CRISPR/Cas9 technology. Interestingly, studies on functional genomics at larger scales have become possible because of the availability of GETs. In this review, we discuss the progress made in rice by employing the CRISPR/Cas9 editing system and its eminent applications. We also elaborate possible future avenues of research with this system, and our understanding regarding the biological mechanism of rice grain quality improvement.

Understanding the role of magnetic (Fe3O4) nanoparticle to mitigate cadmium stress in radish (Raphanus sativus L.).

Heavy metals stress particularly cadmium contamination is hotspot among researchers and considered highly destructive for both plants and human health. Iron is examined as most crucial element for plant development, but it is available in inadequate amount because they are present in insoluble Fe3+ form in soil. Fe3O4 have been recently found as growth promoting factor in plants. To understand, a sand pot experiment was conducted in completely randomized design (control, cadmium, 20 mg/L Fe3O4 nanoparticles,40 mg/L Fe3O4 nanoparticles, 20 mg/L Fe3O4 nanoparticles + cadmium, 40 mg/L Fe3O4 nanoparticles + cadmium) to study the mitigating role of Fe3O4 nanoparticles on cadmium stress in three Raphanus sativus cultivars namely i.e., MOL SANO, MOL HOL PARI, MOL DAQ WAL. The plant growth, physiological and biochemical parameters i.e.,shoot length, shoot fresh weight, shoot dry weight, root length, root fresh and dry weight, MDA content, soluble protein contents, APX, CAT, POD activities and ion concentrations, membrane permeability, chlorophyll a, chlorophyll b and anthocyanin content, respectively were studied. The results displayed that cadmium stress remarkably reduces all growth, physiological and biochemical parameters for allcultivars under investigation. However, Fe3O4 nanoparticles mitigated the adverse effect of cadmium by improving growth, biochemical and physiological attributes in all radish cultivars. While, 20 mg/L Fe3O4 nanoparticles have been proved to be more useful against cadmium stress. The outcome of present investigation displayed that Fe3O4 nanoparticles can be utilized for mitigating heavy metal stress.

Effects of biochar on growth and yield of Wheat (Triticum aestivum L.) under salt stress.

Globally from abiotic stresses, salt stress is the major stress that limits crop production. One of them is wheat that has been utilized by more than 1/3 of the world population as staple food due to its nutritive value. Biochar is an activated carbon that can ameliorate the negative impacts on plants under saline conditions. The present study was conducted to examine the ameliorative impact of "Biochar application" to Triticum aestivum L. plant grown under salinity stress and evaluated on the basis of various growth, yield, physiological, biochemical attributes. Preliminary experiment was done to select the Triticum aestivum L. varieties with 90% germination rate for further experiment. The selected varieties, FSD08 and PUNJAB-11 of wheat were treated with two levels of sodium chloride (0 mM and 120 mM). Two varieties of wheat included FSD08 and PUNJAB-11 were treated with two levels of sodium chloride (0 mM and 120 mM). To address the impact of salt stress two levels of biochar 0% and 5% was used as exogenous application. A three way completely randomized experimentation was done in 24 pots of two wheat varieties with three replicates. The results demonstrated that salt stress affected growth, physiological attributes, yield and inorganic mineral ions (Ca2+ and K+) in roots and shoots parameters of wheat negatively while biochar overall improved the performance of plant. SOD, CAT, APX and POD activities enhanced during salt stress as the plant self-defense mechanism against salinity to minimize the damaging effect. Salt stress also significantly increased the membrane permeability, and levels of H2O2, MDA, Cl and Na ions. Biochar treatment nullified negative impacts of NaCl and improved the plant growth and yield significantly. Hence, biochar amendment can be suggested as suitable supplement for sustainable crop production under salinization.

Recent trends and perspectives in the application of metal and metal oxide nanomaterials for sustainable agriculture.

Sustainable ecosystem management leads to the use of eco-friendly agricultural techniques for crop production. One of them is the use of metal and metal oxide nanomaterials and nanoparticles, which have proven to be a valuable option for the improvement of agricultural food systems. Moreover, the biological synthesis of these nanoparticles, from plants, bacteria, and fungi, also contributes to their eco-friendly and sustainable characteristics. Nanoparticles, which vary in size from 1 to 100 nm have a variety of mechanisms that are safer and more efficient than conventional fertilizers. Their usage as fertilizers and insecticides in agriculture is gaining favor in the scientific community to maximize crop output. More studies in this field will increase our understanding of this new technology and its broad acceptance in terms of performance, affordability, and environmental protection, as certain nanoparticles may outperform conventional fertilizers and insecticides. Accordingly, to the information gathered in this review, nanoparticles show remarkable potential for enhancing crop production, improving soil quality, and protecting the environment, however, metal and metal oxide NPs are not widely employed in agriculture. Many features of nanoparticles are yet left over, and it is necessary to uncover them. In this sense, this review article provides an overview of various types of metal and metal oxide nanoparticles used in agriculture, their characterization and synthesis, the recent research on them, and their possible application for the improvement of crop productivity in a sustainable manner.

Effect of Qiangdi 863 Nanosynergids Treated Water, Nitrogen, Phosphorous and Potassium Fertilizers on Rice Growth Physiology and Grain Quality.

Nanotechnology is an emerging technique that helps in solving the biotic and abiotic agricultural issues leading to enhance crop productivity. Therefore, it was hypothesized to check the effect of Qiangdi 863 nano synergids biological-assisted growth apparatus and nitrogen, phosphorous, and potassium (NPK) fertilizers improving rice germination, early growth, physiology, and yield. An experiment was performed on five rice varieties for three consecutive years (2017-2019). The nanosynergids-treated water (NTW) significantly improved the speed of germination (25.3, 35.6, and 32.3%), final emergence percentage (100%) and seed emergence energy percentage (80, 95, and 90%), radical (1.25, 1.7, and 2.35 cm) and plumule growth (1.29, 1.24, and 1.66 cm), soil plant analysis development (46, 45, and 47), antioxidant enzymatic activities, such as catalase activity (34,376 µg-1FW h-1, 33,264 µg-1FW h-1, and 34,453 µg-1F W h-1), superoxide dismutase (18,456 µg-1F W h-1, 19,445 µg-1F W h-1, and 19,954 µg-1F W h-1), peroxide (745 Ug-1F W, 734 Ug-1F W, and 752 Ug-1F W), production and declined malondialdehyde (4.5 µmolg-1F W, 5.1 µmolg-1F W, and 4.2 µmolg-1F W) for all years respectively in KSK 133. The application of nano-treated irrigated water enriched the biomass of rice seedlings. The overall nano synergid treatments successfully enhanced the endogenous hormones as salicylic acid (6,016.27 p mol/L, 5823.22 p mol/L, and 5922.12 p mol/L), jasmonates (JA) (5,175.6 p mol/L, 4231 p mol/L, and 5014.21 p mol/L) brassinosteroids (BR) (618.2 p mol/L, 546.83 p mol/L, and 582.1 p mol/L) quantification and yield 1000 grain weight (22.3, 22, and 23.2 g) of KSK 133. Hence, the overall results proved that NTW could effectively enhance the early growth and yield of rice varieties.

Assessment of Mineral Nutrient Efficiency in Genetically Diverse Spinach Accessions by Biochemical and Functional Marker Strategies.

Leafy vegetable crops are considered as a natural source of mineral nutrients that could decrease the risk factor of many growth issues in children and adults. Spinach is globally considered as the most desirable leafy crop, due to its taste and nutrient richness along with greater nitrate contents and better nitrogen use efficiency. To evaluate the mineral nutrient efficiency of this crop, thirty genetically diverse spinach accessions were analyzed through nutritional and functional marker strategies. The accession 163,310 from Pakistan was found to be rich in minerals (sodium, calcium, potassium, zinc, and manganese) and nitrates. However, the oxalate contents were lesser in the accessions that had greater quantity of nutrients. These represented a negative correlation between mineral availability and oxalate accumulation in the leaves. To study the relationship of oxalates and minerals in the accessions, a functional marker analysis was performed, based on the genes involved in oxalate metabolism and disease resistance in spinach. High level of genetic polymorphism was observed among the accessions represented with 115 polymorphic bands out of 130 bands. Heat map clustering represented the accessions from Asian countries (Pakistan, India, China, and Iran) as the most adaptable accessions to the local environment. The correlation between nutritional and genetic analysis also revealed the nutrient richness of these accessions along with good oxalate metabolism and disease resistance. Hence, these accessions could be considered as useful genotypes in future breeding programs.

Genome-wide analysis of potassium transport genes in Gossypium raimondii suggest a role of GrHAK/KUP/KT8, GrAKT2.1 and GrAKT1.1 in response to abiotic stress.

Potassium (K+) is an important macro-nutrient for plants, which comprises almost 10% of plant's dry mass. It plays a crucial role in the growth of plants as well as other important processes related to metabolism and stress tolerance. Plants have a complex and well-organized potassium distribution system (channels and transporters). Cotton is the most important economic crop, which is the primary source of natural fiber. Soil deficiency in K+ can negatively affect yield and fiber quality of cotton. However, potassium transport system in cotton is poorly studied. Current study identified 43 Potassium Transport System (PTS) genes in Gossypium raimondii genome. Based on conserved domains, transmembrane domains, and motif structures, these genes were classified as K+ transporters (2 HKTs, 7 KEAs, and 16 KUP/HAK/KTs) and K+ channels (11 Shakers and 7 TPKs/KCO). The phylogenetic comparison of GrPTS genes from Arabidopsis thaliana, Glycine max, Oryza sativa, Medicago truncatula and Cicer arietinum revealed variations in PTS gene conservation. Evolutionary analysis predicted that most GrPTS genes were segmentally duplicated. Gene structure analysis showed that the intron/exon organization of these genes was conserved in specific-family. Chromosomal localization demonstrated a random distribution of PTS genes across all the thirteen chromosomes except chromosome six. Many stress responsive cis-regulatory elements were predicted in promoter regions of GrPTS genes. The RNA-seq data analysis followed by qRT-PCR validation demonstrated that PTS genes potentially work in groups against environmental factors. Moreover, a transporter gene (GrHAK/KUP/KT8) and two channel genes (GrAKT2.1 and GrAKT1.1) are important candidate genes for plant stress response. These results provide useful information for further functional characterization of PTS genes with the breeding aim of stress-resistant cultivars.

Apomixis and strategies to induce apomixis to preserve hybrid vigor for multiple generations.

Hybrid seeds of several important crops with supreme qualities including yield, biotic and abiotic stress tolerance have been cultivated for decades. Thus far, a major challenge with hybrid seeds is that they do not have the ability to produce plants with the same qualities over subsequent generations. Apomixis, an asexual mode of reproduction by avoiding meiosis, exists naturally in flowering plants, and ultimately leads to seed production. Apomixis has the potential to preserve hybrid vigor for multiple generations in economically important plant genotypes. The evolution and genetics of asexual seed production are unclear, and much more effort will be required to determine the genetic architecture of this phenomenon. To fix hybrid vigor, synthetic apomixis has been suggested. The development of MiMe (mitosis instead of meiosis) genotypes has been utilized for clonal gamete production. However, the identification and parental origin of genes responsible for synthetic apomixis are little known and need further clarification. Genome modifications utilizing genome editing technologies (GETs), such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (cas), a reverse genetics tool, have paved the way toward the utilization of emerging technologies in plant molecular biology. Over the last decade, several genes in important crops have been successfully edited. The vast availability of GETs has made functional genomics studies easy to conduct in crops important for food security. Disruption in the expression of genes specific to egg cell MATRILINEAL (MTL) through the CRISPR/Cas genome editing system promotes the induction of haploid seed, whereas triple knockout of the Baby Boom (BBM) genes BBM1, BBM2, and BBM3 cause embryo arrest and abortion, which can be fully rescued by male-transmitted BBM1. The establishment of synthetic apomixis by engineering the MiMe genotype by genome editing of BBM1 expression or disruption of MTL leads to clonal seed production and heritability for multiple generations. In the present review, we discuss current developments related to the use of CRISPR/Cas technology in plants and the possibility of promoting apomixis in crops to preserve hybrid vigor. In addition, genetics, evolution, epigenetic modifications, and strategies for MiMe genotype development are discussed in detail.

Development of Carrot Nutraceutical Products as an Alternative Supplement for the Prevention of Nutritional Diseases.

Nutraceuticals can serve as an alternative supplement to overcome nutritional deficiency for a healthy lifestyle. They can also play a key role in disease management. To develop carrot nutraceutical products, 64 genotypes from four different continents were evaluated for a range of morpho-nutrition variables. Genetic variability, heritability, strength and direction of association among variables, and direct and indirect relationships among physiochemical and nutritional traits with ß-carotene content were evaluated. Core diameter, foliage weight, root weight and shoulder weight showed significant association with ß-carotene accumulation. Principal component analysis for physiochemical and nutritional assessment divided these genotypes into two distinctive groups, Eastern carrots and Western carrots. Caloric and moisture content had high positive associations with ß-carotene content while carbohydrate content was negatively associated. Five genotypes (T-29, PI 634658, PI 288765, PI 164798, and Ames 25043) with the highest ß-carotene contents were selected for making three nutraceutical supplements (carrot-orange juice, carrot jam and carrot candies). These nutraceutical supplements retained high ß-carotene content coupled with antioxidant properties. Carrot jam (6.5 mg/100 g) and carrot candies (4.8 mg/100 g) had greater concentrations of ß-carotene than carrot-orange juice (1.017 mg/100 g). Carrot jam presented high antioxidant activity with the highest values in T-29 (39% inhibition of oxidation) followed by PI 634658 (37%), PI 164798 (36.5%), Ames 25043 (36%) and PI 288765 (35.5%). These nutraceutical products, with 4-6.5 mg/100 g ß-carotene content, had higher values than the USDA recommended dietary intake of 3-6 mg ß-carotene/day can be recommended for daily use to lower the risk of chronic disease.

Phytochemical relationship of Euphorbia helioscopia and Euphorbia pulcherrima with Lactuca sativa.

Allelopathy is an important phenomenon that modifies the ecosystem. A plant can enhance or reduce the growth of other plant due to the presence of a number of allelochemicals in its different parts. Euphorbia helioscopia and Euphorbia pulcherrima are medicinal plant species. Both these species are collected from wild resources for various purposes. To reduce the pressure on wild population, it is important to bring them into cultivation. Therefore, the allelopathic effects of E. helioscopia and E. pulcherrima on the growth of lettuce seeds were studied. Three different concentrations (2%, 4% and 6%) of five different solvents (methanol, acetone, ethyl acetate, n-hexane and distilled water) were used to estimate the allelopathic potential of the above-mentioned Euphorbia species. Results indicated a non-significant growth inhibitory effect of both plants on lettuce seeds. Different extracts reduced the growth of test plant to some extent but this inhibition was not significant. From the observed results, it was concluded that the studied Euphorbia species, being medicinally important crops, can be introduced as intercrop with other cash crops.