Comparative adaptability assessment of bread wheat and synthetic hexaploid genotypes under saline conditions using physiological, biochemical, and genetic indices.

The tolerance to salinity stress is an intricate phenomenon at cellular and whole plant level that requires the knowledge of contributing physiological and biochemical processes and the genetic control of participating traits. In this context, present study was conducted with objective to evaluate the physiological, biochemical, and genetic responses of different wheat genotypes including bread wheat (BW) and synthetic hexaploids (SHs) under saline and control environment. The experiment was conducted in two factorial arrangement in randomized complete block design (RCBD), with genotypes as one factor and treatments as another factor. A significant decline in physiological traits (chlorophyll, photosynthesis, stomatal conductance, transpiration, and cell membrane stability) was observed in all genotypes due to salt stress; however, this decline was higher in BW genotypes as compared to four SH genotypes. In addition, the biochemical traits including enzymes [superoxide dismutase, catalase, and peroxidase (POD)] activity, proline, and glycine betaine (GB) illustrated significant increase along with increase in the expression of corresponding genes (TaCAT1, TaSOD, TaPRX2A, TaP5CS, and TaBADH-A1) due to salt stress in SHs as compared to BW. Correspondingly, highly overexpressed genes, TaHKT1;4, TaNHX1, and TaAKT1 caused a significant decline in Na+/K+ in SH as compared to BW genotypes under salt stress. Moreover, correlation analysis, principal component analysis (PCA), and heatmap analysis have further confirmed that the association and expression of physiological and biochemical traits varied significantly with salinity stress and type of genotype. Overall, the physiological, biochemical, and genetic evaluation proved SHs as the most useful stock for transferring salinity tolerance to other superior BW cultivars via the right breeding program.

Physiomorphic and molecular-based evaluation of wheat germplasm under drought and heat stress.

Drought and heat stress are potential problems that can reduce wheat yield, particularly during the terminal growth stages in arid and semiarid regions of the world. The current study intended to examine the impact of individual and combined drought and heat stress on the biochemical contents (antioxidant enzymes, proline, soluble proteins, and soluble sugars), physiological parameters (chlorophyll content, cell membrane stability, photosynthesis, stomatal conductance, and transpiration), plant-water relations (relative water content, water potential, osmotic potential, and pressure potential), agronomic traits (flag leaf area, plant height, number of tillers per plant, spike length, grains per spike, and thousand-grain weight), and gene expression (TaHSF1a, TaWRKY-33, TaNAC2L, and TaGASR1) in four different thermostable and drought-tolerant wheat genotypes (i.e., Gold-16, HS-240, Suntop, and Hemai-13) collected from different countries. The tri-replicate experiment was conducted using two factorial arrangements in a randomized complete block design (RCBD). All measured traits, except total soluble sugars, proline, and cell membrane stability index, showed significant reduction under both combined and individual treatments. Furthermore, correlation analysis revealed a significant association between biochemical and physiological characteristics and crop agronomic productivity. Furthermore, principal component analysis (PCA) and heatmap analysis demonstrated significant levels of variation in traits according to the type of stress and nature of wheat genotype. The spectrographs and micrographs generated by scanning electron microscopy for the selected high- and low- tolerance samples revealed clear differences in mineral distribution and starch granulation. All studied genes showed comparatively high levels of relative expression under combined treatments of drought and heat stress in all wheat genotypes, but this expression was the highest in 'Gold-16' followed by 'HS-240', 'Suntop', and 'Hemai-13'. Overall, this study concluded that plants are proactive entities and they respond to stresses at all levels; however, the tolerant plants tend to retain the integrity of their biochemical, physiological, and molecular equilibrium.

Optimization of soybean physiochemical, agronomic, and genetic responses under varying regimes of day and night temperatures.

Soybean is an important oilseed crop worldwide; however, it has a high sensitivity to temperature variation, particularly at the vegetative stage to the pod-filling stage. Temperature change affects physiochemical and genetic traits regulating the soybean agronomic yield. In this regard, the current study aimed to comparatively evaluate the effects of varying regimes of day and night temperatures (T1 = 20°C/12°C, T2 = 25°C/17°C, T3 = 30°C/22°C, T4 = 35°C/27°C, and T5 = 40°C/32°C) on physiological (chlorophyll, photosynthesis, stomatal conductance, transpiration, and membrane damage) biochemical (proline and antioxidant enzymes), genetic (GmDNJ1, GmDREB1G;1, GmHSF-34, GmPYL21, GmPIF4b, GmPIP1;6, GmGBP1, GmHsp90A2, GmTIP2;6, and GmEF8), and agronomic traits (pods per plant, seeds per plant, pod weight per plant, and seed yield per plant) of soybean cultivars (Swat-84 and NARC-1). The experiment was performed in soil plant atmosphere research (SPAR) units using two factorial arrangements with cultivars as one factor and temperature treatments as another factor. A significant increase in physiological, biochemical, and agronomic traits with increased gene expression was observed in both soybean cultivars at T4 (35°C/27°C) as compared to below and above regimes of temperatures. Additionally, it was established by correlation, principal component analysis (PCA), and heatmap analysis that the nature of soybean cultivars and the type of temperature treatments have a significant impact on the paired association of agronomic and biochemical traits, which in turn affects agronomic productivity. Furthermore, at corresponding temperature regimes, the expression of the genes matched the expression of physiochemical traits. The current study has demonstrated through extensive physiochemical, genetic, and biochemical analyses that the ideal day and night temperature for soybeans is T4 (35°C/27°C), with a small variation having a significant impact on productivity from the vegetative stage to the grain-filling stage.

Pharmacological properties and preliminary phytochemical analysis of Pseudocaryopteris foetida (D.Don) P.D. Cantino leaves.

Medicinal plants have significant contribution in pharmaceutical industries being producers of compounds utilized as precursors for drug development. A plant of Lamiaceae family; Pseudocaryopteris foetida had not been investigated for its biomedical potential. Current research was aimed to investigate phytochemical analysis, cytotoxic potential and antioxidant activity of crude methanolic extract and fractions of Pseudocaryopteris foetida (leaves). The preliminary phytochemical analysis of crude methanolic extracts and fractions of Pseudocaryopteris foetida revealed that plant is rich in phenolic and flavonoid classes of secondary metabolites while presence of tannin was observed only in crude methanolic extract. The cytotoxicity was determined using brine shrimp lethality test. Different concentrations (25, 50, 100, 150, 200 and 250 µg/mL) of crude methanolic extract and fractions exhibited dose dependent cytotoxicity. However, The LD50 for all the extracts was more than 200 µg/mL indicating weak cytotoxic potential of Pseudocaryopteris foetida. The antioxidant capabilities of crude methanolic extract and fraction of Pseudocaryopteris foetida were analyzed by in vitro bio assays including DPPH, ABTS, Reducing power and phosphomolybdate antioxidant assays using ascorbic acid as standard. The crude methanolic extract showed IC50 (256.38 ± 0.6 and 314.95 ± 1.1 µg/mL) for DPPH and ABTS respectively, while total antioxidant capacity was calculated as 55.79 ± 0.5 µg/mL for crude methanolic extract of Pseudocaryopteris foetida while ascorbic acid indicated total antioxidant capacity of 71.89 ± 2.3 µg/mL. Study concluded that leaves of Pseudocaryopteris foetida were the rich source of antioxidant phytochemicals. Based on preliminary investigations further research should be focused to isolate bioactive phytochemicals as leading source of clinical medicines in future.

Determination of ROS Scavenging, Antibacterial and Antifungal Potential of Methanolic Extract of Otostegia limbata (Benth.) Boiss.

Wide spectrum medicinal significance augments plant utilization as the primary source of significant pharmaceutical agents. In vitro investigation of antioxidant and antimicrobial activity highlights the therapeutic potential of Otostegia limbata. Methanol extract of the plant (MEP) shows considerable dose dependent antioxidant ability at six concentrations (7.81 µg/mL to 250 µg/mL) in 2.2-diphenyl-1-picrylhydrazyl (DPPH) assay, phosphomolybdate assay (PMA) and reducing power assay (RPA). The plant capability to scavenge free radicals in the mixture ranged from 37.89% to 63.50% in a concentration-dependent manner. MEP was active against five tested bacterial strains in the agar-well diffusion method. Staphylococcus aureus, gram-positive bacteria was found to be most susceptible followed by S. epidermidis with 18.80 mm and 17.47 mm mean zone of inhibition. The mean inhibition zone against gram-negative strains Klebsiella pneumonia, Pseudomonas spp. and Escherichia coli were 15.07 mm, 14.73 mm, and 12.17 mm. MEP revealed potential against Alternaria spp. and Aspergillus terreus fungal strains evaluated through agar-tube dilution assay. Aspergillus terreus was more sensitive than Alternaria spp. with an average 78.45% and 68.0% inhibition. These findings can serve as a benchmark for forthcoming scrutiny such as bioactive components discovery and drug development.

Using HPLC-DAD and GC-MS Analysis Isolation and Identification of Anticandida Compounds from Gui Zhen Cao Herbs (Genus Bidens): An Important Chinese Medicinal Formulation.

Gui Zhen Cao is an herbal formulation that has been documented in Chinese traditional medicine as a remedy for diarrhea, dysentery, inflammation, and toxicity. The sources of this formulation (Bidens pilosa L., Bidens biternata (Lour.) Merr. & Sherff, Bidens bipinnata L.) are also listed in ethnomedicinal reports all over the world. In this study, all these plants are tested for in vitro anticandida activity. A quantitative evaluation of the phytochemicals in all these plants indicated that their vegetative parts are rich in tannins, saponins, oxalates, cyanogenic glycoside and lipids; moreover, the roots have high percentages of alkaloids, flavonoids, and phenols. The results indicated significant anticandida activity, especially for the hexane extract of B. bipinnata leaves which inhibited C. albicans (42.54%), C. glabrata (46.98%), C. tropicalis (50.89%), C. krusei (40.56%), and C. orthopsilosis (50.24%). The extract was subjected to silica gel chromatography and 220 fractions were obtained. Purification by High Performance Liquid Chromatography with Diode-Array Detection (HPLC-DAD) and Gas Chromatography tandem Mass Spectrometry (GC-MS/MS) analysis led to the identification of two anticandida compounds: dehydroabietic and linoleic acid having an inhibition of 85 and 92%, respectively.

Isolation of biotic stress resistance genes from cotton (Gossypium arboreum) and their analysis in model plant tobacco (Nicotiana tabacum) for resistance against cotton leaf curl disease complex.

Cotton production is widely effected by Cotton Leaf Curl Virus (CLCuV) in world posing serious losses to cotton yield.The CRT genes from CLCuV resistant G. arboreum and CLCuV susceptible G. hirsutum were cloned and sequenced to know the differences of protein composition in both species. Molecular techniques were used to isolate full length putative biotic stress resistance genes from G. arboreum besides the analysis of identified novel genes in model plant tobacco (Nicotiana tabacum) for resistance to cotton leaf curl disease complex. It was found that transgenic plants over expressing Hydroperoxidelyase (HPL) genes exhibited higher enzyme activity than wild type. In addition the genome sequence information was used for the purpose of gene isolation. Even for the enhanced expression of Calreticulin (CRT), AOS and HPL in G. hirsutum, it still showed susceptibility against CLCuV suggesting alternative genes and pathways involved for the expression of resistance.

Exploration of cotton leaf curl virus resistance genes and their screening in Gossypium arboreum by targeting resistance gene analogues.

Cotton leaf curl virus (CLCuV) disease is one of the major limiting factors in cotton production, particularly in widely cultivated Gossypium hirsutum varieties that are susceptible to attack by this virus. Several approaches have been employed to explore putative resistance genes in another cotton species, G. arboreum. However, the exact mechanisms conferring disease resistance in cotton are still unknown. In the current study, we used various approaches to identify possible resistance genes against CLCuV infection. We report the identification and isolation of a set of genes involved in the resistance response to viral infestation. PCR products containing genomic DNA gave multiple amplifications with a single primer in most reactions, and 38 fragments were cloned from G. arboreum and G. hirsutum. The sequences of cloned fragments belonged to various pathway genes and uncharacterized proteins. However, five amplified fragments (RM1, RM6, RM8, RM12 and RM31) showed similarity with R genes. Maximum homology (94 %) was observed with G. raimondii toll/interleukin receptor-like protein. BLAST search showed the homology of all resistance gene analogues (RGAs) with more than one chromosome, and multiple hits were observed on each chromosome for each RGA. Expression analysis through RT-PCR identified variable expression levels of the different RGAs in all tested genotypes. The expression level of RGAs differed between symptomatic and asymptomatic plants, with the exception of RGA 395, whose expression level was the same in both diseased and healthy plants. Knowledge of the interaction of these genes with various cotton pathogens could be utilized to improve the resistance of susceptible G. hirsutum and other plant species.

Boosting Alfalfa (Medicago sativa L.) Production With Rhizobacteria From Various Plants in Saudi Arabia.

This study focused on rhizobacteria to promote sustainable crop production in arid regions of Saudi Arabia. The study isolated 17 tightly root-adhering rhizobacteria from various plants at Hada Al Sham in Saudi Arabia. All 17 rhizobacterial isolates were confirmed as plant growth promoting rhizobacteria by classical biochemical tests. Using 16S rDNA gene sequence analyses, the strains were identified as Bacillus, Acinetobacter and Enterobacter. Subsequently, the strains were assessed for their ability to improve the physiology, nutrient uptake, growth, and yield of alfalfa plants grown under desert agriculture conditions. The field trials were conducted in a randomized complete block design. Inoculation of alfalfa with any of these 17 strains improved the relative water content; chlorophyll a; chlorophyll b; carotenoid contents; nitrogen (N), phosphorus, and potassium contents; plant height; leaf-to-stem ratio; and fresh and dry weight. Acinetobacter pittii JD-14 was most effective to increase fresh and dry weight of alfalfa by 41 and 34%, respectively, when compared to non-inoculated control plants. Nevertheless, all strains enhanced crop traits when compared to controls plants, indicating that these desert rhizobacterial strains could be used to develop an eco-friendly biofertilizer for alfalfa and possibly other crop plants to enhance sustainable production in arid regions.

Author Correction: Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Humic Substances: Determining Potential Molecular Regulatory Processes in Plants.

Humic substances (HSs) have considerable effects on soil fertility and crop productivity owing to their unique physiochemical and biochemical properties, and play a vital role in establishing biotic and abiotic interactions within the plant rhizosphere. A comprehensive understanding of the mode of action and tissue distribution of HS is, however, required, as this knowledge could be useful for devising advanced rhizospheric management practices. These substances trigger various molecular processes in plant cells, and can strengthen the plant's tolerance to various kinds of abiotic stresses. HS manifest their effects in cells through genetic, post-transcriptional, and post-translational modifications of signaling entities that trigger different molecular, biochemical, and physiological processes. Understanding of such fundamental mechanisms will provide a better perspective for defining the cues and signaling crosstalk of HS that mediate various metabolic and hormonal networks operating in plant systems. Various regulatory activities and distribution strategies of HS have been discussed in this review.

Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation.

In plants, UGTs (UDP-glycosyltransferases) glycosylate various phytohormones and metabolites in response to biotic and abiotic stresses. Little is known about stress-responsive glycosyltransferases in plants. Therefore, it is important to understand the genomic and transcriptomic portfolio of plants with regard to biotic and abiotic stresses. Here, we identified 140, 154, and 251 putative UGTs in Brassica rapa, Brassica oleracea, and Brassica napus, respectively, and clustered them into 14 major phylogenetic groups (A-N). Fourteen major KEGG pathways and 24 biological processes were associated with the UGTs, highlighting them as unique modulators against environmental stimuli. Putative UGTs from B. rapa and B. oleracea showed a negative selection pressure and biased gene fractionation pattern during their evolution. Polyploidization increased the intron proportion and number of UGT-containing introns among Brassica. The putative UGTs were preferentially expressed in developing tissues and at the senescence stage. Differential expression of up- and down-regulated UGTs in response to phytohormone treatments, pathogen responsiveness and abiotic stresses, inferred from microarray and RNA-Seq data in Arabidopsis and Brassica broaden the glycosylation impact at the molecular level. This study identifies unique candidate UGTs for the manipulation of biotic and abiotic stress pathways in Brassica and Arabidopsis.

Functional characterization of naturally occurring wild soybean mutant (sg-5) lacking astringent saponins using whole genome sequencing approach.

Triterpenoid saponins are one of the most highly accumulated groups of functional components in soybean (Glycine max) and the oxidative reactions during their biosynthesis are required for their aglycone diversity. Natural mutants of soyasaponins in wild soybean (Glycine soja) are valuable resources for establishing the soyasaponin biosynthesis pathway and breeding new soybean varieties. In this study, we investigated the genetic mechanism behind the absence of group A saponins in a Korean wild soybean mutant, CWS5095. Whole genome sequencing (WGS) of CWS5095 identified four point mutations [Val6 → Asp, Ile231 → Thr, His294 → Gln, and Arg376 → Lys] in CYP72A69 (Glyma15g39090), which oxygenate the C-21 position of soyasapogenol B or other intermediates to produce soyasapogenol A, leading to group A saponin production. An in vitro enzyme activity assay of single-sited mutated clones indicated that the Arg376 > Lys mutation (a highly conserved mutation based on a nucleotide change from G → A at the 1,127th position) may lead to loss of gene function in the sg-5 mutant. A very high normalized expression value of 377 reads per kilo base per million (RPKM) of Glyma15g39090 in the hypocotyl axis at the early maturation seed-development stage confirmed their abundant presence in seed hypocotyls. A molecular dynamics analysis of the Arg376 > Lys mutation based on the CYP3A4 (a human CYP450) protein structure found that it was responsible for the increase in axis length toward the heme (active site), which is critically important for biological activity and ligand binding. Our results provide important information on how to eradicate bitter and astringent saponins in soybean by utilizing the reported mutation in Glyma15g39090, and its importance for seed hypocotyl development based on transcript abundance.

Redox and Ionic Homeostasis Regulations against Oxidative, Salinity and Drought Stress in Wheat (A Systems Biology Approach).

Systems biology and omics has provided a comprehensive understanding about the dynamics of the genome, metabolome, transcriptome, and proteome under stress. In wheat, abiotic stresses trigger specific networks of pathways involved in redox and ionic homeostasis as well as osmotic balance. These networks are considerably more complicated than those in model plants, and therefore, counter models are proposed by unifying the approaches of omics and stress systems biology. Furthermore, crosstalk among these pathways is monitored by the regulation and streaming of transcripts and genes. In this review, we discuss systems biology and omics as a promising tool to study responses to oxidative, salinity, and drought stress in wheat.

In-Depth Genomic and Transcriptomic Analysis of Five K+ Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation.

Plants have evolved a sophisticated network of K+ transport systems to regulate growth and development. Limited K+ resources are now forcing us to investigate how plant demand can be satisfied. To answer this complex question, we must understand the genomic and transcriptomic portfolio of K+ transporters in plants. Here, we have identified 70 putative K+ transporter genes from soybean, including 29 HAK/KT/KUP genes, 16 genes encoding voltage-gated K+ channels, 9 TPK/KCO genes, 4 HKT genes, and 12 KEA genes. To clarify the molecular evolution of each family in soybean, we analyzed their phylogeny, mode of duplication, exon structures and splice sites, and paralogs. Additionally, ortholog clustering and syntenic analysis across five other dicots further explored the evolution of these gene families and indicated that the soybean data is suitable as a model for all other legumes. Available microarray data sets from Genevestigator about nodulation was evaluated and further confirmed with the RNA sequencing data available by a web server. For each family, expression models were designed based on Transcripts Per Kilobase Million (TPM) values; the outcomes indicated differential expression linked to nodulation and confirmed the genes' putative roles. In-depth studies such as ours provides the basis for understanding K+ inventories in all other plants.

Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana.

The cell wall (CW) as a first line of defense against biotic and abiotic stresses is of primary importance in plant biology. The proteins associated with cell walls play a significant role in determining a plant's sustainability to adverse environmental conditions. In this work, the genes encoding cell wall proteins (CWPs) in Arabidopsis were identified and functionally classified using geneMANIA and GENEVESTIGATOR with published microarrays data. This yielded 1605 genes, out of which 58 genes encoded proline-rich proteins (PRPs) and glycine-rich proteins (GRPs). Here, we have focused on the cellular compartmentalization, biological processes, and molecular functioning of proline-rich CWPs along with their expression at different plant developmental stages. The mined genes were categorized into five classes on the basis of the type of PRPs encoded in the cell wall of Arabidopsis thaliana. We review the domain structure and function of each class of protein, many with respect to the developmental stages of the plant. We have then used networks, hierarchical clustering and correlations to analyze co-expression, co-localization, genetic, and physical interactions and shared protein domains of these PRPs. This has given us further insight into these functionally important CWPs and identified a number of potentially new cell-wall related proteins in A. thaliana.

Transcriptomics and Biochemical Profiling: Current Dynamics in Elucidating the Potential Attributes of Olive.

Various transcriptome studies have remained useful in unraveling the complexity of molecular pathways regulating the oil biochemical contents and fruit characteristics of agronomic value in olive. Genes networks associated with plant architect and abiotic stress tolerance have been constructed due to robust genomic data generated by the tools of genomics. This, familiarity will accelerate the breeding programmes in making the selection of high yielding olive genotypes promptly and efficiently. Moreover, comparative transcriptome studies for endogeneous enzymes at different expression sites explicate the contribution of various pathways in phenol and lipid oxidation in olive. Recently, non-targeted metabolomics and metabolic profiling techniques have not only made the understanding of metabolic changes easy but also elucidate biomarkers in fruits related to agronomic parameters and abiotic stresses. However, the alteration in the architectural build up of phenotypes auth-enticates the conservation of their potential genetic links that will invoke interest for future olive breeding.

Genomics: A Hallmark to Monitor Molecular and Biochemical Processes Leading Toward a Better Perceptive of Seed Aging and ex-situ Conservation.

For human food security, the preservation of 7.4 million ex-situ germplasm is a global priority. However, ex-situ-conserved seeds are subject to aging, which reduces their viability and ultimately results in the loss of valuable genetic material over long periods. Recent progress in seed biology and genomics has revealed new opportunities to improve the long-term storage of ex-situ seed germplasm. This review summarizes the recent improvements in seed physiology and genomics, with the intention of developing genomic tools for evaluating seed aging. Several lines of seed biology research have shown promise in retrieving viability signal from various stages of seed germination. We conclude that seed aging is associated with mitochondrial alteration and programmed cell death, DNA and enzyme repair, anti-oxidative genes, telomere length, and epigenetic regulation. Clearly, opportunities exist for observing seed aging for developing genomic tools to increment the traditional germination test for effective conservation of ex-situ germplasm.

Molecular markers based identification of diversity for drought tolerance in bread wheat varieties and synthetic hexaploids.

The complexity of the wheat genome has delayed the development and application of molecular markers to this species and wheat now lies behind barley, maize and rice in marker development. However, improvements in marker detection systems and in the techniques used to identify markers linked to useful traits has allowed considerable advances to be made in recent years. To evaluate the genetic diversity 53 genotypes of Richard's selection, were studied at National Agriculture Reseach Center (NARC) Islamabad. The present study found that RAPD analysis is a valuable diagnostic tool. Different sets of RAPD primers were used to study the polymorphism at molecular level. Highest number of amplifications was shown by primer OpG-2 in Richard's material. Coefficient of similarity as well as genetic distances among these three sets of materials was calculated by using Unweighted Pair Group of Arithamatic Means (UPGMA) function (Nei and Li, 1979). The SHs derived genotypes of Richard's selection were highly polymorphic with a polymorphism percentage of 69.70 as compared to NUYT (rainfed) and elite Pakistani bread wheat varieties with a polymorphism of 44.44% and 61.11% respectively. Cluster analysis was done in which grouping of genotypes was done on the basis of genetic distances. Cluster analysis revealed that genotypes of Richard's genotypes are showing high level of among cultivar variation as compared to NUYT (Rainfed) and elite Pakistani drought tolerant bread wheat varieties. These genotypes were also phenotypically evaluated.