Genetic diversity analysis in wheat cultivars using SCoT and ISSR markers, chloroplast DNA barcoding and grain SEM.

BACKGROUND: Wheat is a major cereal that can narrow the gap between the increasing human population and food production. In this connection, assessing genetic diversity and conserving wheat genetic resources for future exploitation is very important for breeding new cultivars that may withstand the expected climate change. The current study evaluates the genetic diversity in selected wheat cultivars using ISSR and SCoT markers, the rbcL and matK chloroplast DNA barcoding, and grain surface sculpture characteristics. We anticipate that these objectives may prioritize using the selected cultivars to improve wheat production. The selected collection of cultivars may lead to the identification of cultivars adapted to a broad spectrum of climatic environments. RESULTS: Multivariate clustering analyses of the ISSR and SCoT DNA fingerprinting polymorphism grouped three Egyptian cultivars with cultivar El-Nielain from Sudan, cultivar Aguilal from Morocco, and cultivar Attila from Mexico. In the other group, cultivar Cook from Australia and cultivar Chinese-166 were differentiated from four other cultivars: cultivar Cham-10 from Syria, cultivar Seri-82 from Mexico, cultivar Inqalab-91 from Pakistan, and cultivar Sonalika from India. In the PCA analysis, the Egyptian cultivars were distinct from the other studied cultivars. The rbcL and matK sequence variation analysis indicated similarities between Egyptian cultivars and cultivar Cham-10 from Syria and cultivar Inqalab-91 from Pakistan, whereas cultivar Attila from Mexico was distinguished from all other cultivars. Combining the data of ISSR and SCoT with the rbcL and matK results retained the close resemblance among the two Egyptian cultivars EGY1: Gemmeiza-9 and EGY3: Sakha-93, and the Moroccan cultivar Aguilal, and the Sudanese cultivar El-Nielain and between Seri-82, Inqalab-91, and Sonalika cultivars. The analysis of all data distinguished cultivar Cham-10 from Syria from all other cultivars, and the analysis of grain traits indicated a close resemblance between cv. Cham-10 from and the two Egyptian cultivars Gemmeiza-9 and Sakha-93. CONCLUSIONS: The analysis of rbcL and matK chloroplast DNA barcoding agrees with the ISSR and the SCoT markers in supporting the close resemblance between the Egyptian cultivars, particularly Gemmeiza-9 and Sakha-93. The ISSR and SCoT data analyses significantly expressed high differentiation levels among the examined cultivars. Cultivars with closer resemblance may be recommended for breeding new wheat cultivars adapted to various climatic environments.

Growth, physiological, and molecular responses of three phaeophyte extracts on salt-stressed pea (Pisum sativum L.) seedlings.

BACKGROUND: Seaweeds are a viable bioresource for suffering plants against salt stress, as they abundant in nutrients, hormones, vitamins, secondary metabolites, and many other phytochemicals that sustain plants' growth under both typical and stressful situations. The alleviating capacity of extracts from three brown algae (Sargassum vulgare, Colpomenia sinuosa, and Pandia pavonica) in pea (Pisum sativum L.) was investigated in this study. METHODS: Pea seeds were primed for 2 h either with seaweed extracts (SWEs) or distilled water. Seeds were then subjected to salinity levels of 0.0, 50, 100, and 150 mM NaCl. On the 21st day, seedlings were harvested for growth, physiological and molecular investigations. RESULTS: SWEs helped reduce the adverse effects of salinity on pea, with S. vulgare extract being the most effective. Furthermore, SWEs diminished the effect of NaCl-salinity on germination, growth rate, and pigment content and raised the osmolytes proline and glycine betaine levels. On the molecular level, two low-molecular-weight proteins were newly synthesized by the NaCl treatments and three by priming pea seeds with SWEs. The number of inter-simple sequence repeats (ISSR) markers increased from 20 in the control to 36 in 150 mM NaCl-treated seedlings, including four unique markers. Priming with SWEs triggered more markers than the control, however about ten of the salinity-induced markers were not detected following seed priming before NaCl treatments. By priming with SWEs, seven unique markers were elicited. CONCLUSION: All in all, priming with SWEs alleviated salinity stress on pea seedlings. Salinity-responsive proteins and ISSR markers are produced in response to salt stress and priming with SWEs.

Ultrastructural and molecular implications of ecofriendly made silver nanoparticles treatments in pea (Pisum sativum L.).

BACKGROUND: Silver nanoparticles (AgNPs) are the most widely used nanomaterial in agricultural and environmental applications. In this study, the impact of AgNPs solutions at 20 mg/L, 40 mg/L, 80 mg/L, and 160 mg/L on cell ultrastructure have been examined in pea (Pisum sativum L) using a transmission electron microscope (TEM). The effect of AgNPs treatments on the α, ß esterase (EST), and peroxidase (POX) enzymes expression as well as gain or loss of inter-simple sequence repeats (ISSRs) markers has been described. RESULTS: Different structural malformations in the cell wall and mitochondria, as well as plasmolysis and vacuolation were recorded in root cells. Damaged chloroplast and mitochondria were frequently observed in leaves and the osmiophilic plastoglobuli were more observed as AgNPs concentration increased. Starch grains increased by the treatment with 20 mg/L AgNPs. The expressions of α, ß EST, and POX were slightly changed but considerable polymorphism in ISSR profiles, using 17 different primers, were scored indicating gain or loss of gene loci as a result of AgNPs treatments. This indicates considerable variations in genomic DNA and point mutations that may be induced by AgNPs as a genotoxic nanomaterial. CONCLUSION: AgNPs may be used to induce genetic variation at low concentrations. However, considerations should be given to the uncontrolled use of nanoparticles and calls for evaluating their impact on plant growth and potential genotoxicity are justified.

Genetic diversity of a global collection of maize genetic resources in relation to their subspecies assignments, geographic origin, and drought tolerance.

The genetic diversity among an international collection of 40 maize accessions has been evaluated using DNA ISSR fingerprinting. Among the 180 ISSR markers scored by 15 primers, 161 markers (89.59%) were polymorphic and 19 were unique in 16 accessions. A cluster tree based on the average distance coefficients and the Dice similarity indices divided the accessions into three major groups, each including clusters of accessions assigned to their subspecies. However, a low level of genetic differentiation among the accessions was demonstrated by the STRUCTURE analysis of ISSR data in agreement with the low gene flow (Nm) value among the accessions. A scatter diagram of the principal component analysis (PCA) based on ISSR data analysis revealed that the accessions were differentiated into three groups comparable to those produced by the cluster analysis, in which some accessions of the same subspecies showed a close similarity to each other. A scatter diagram of the principal coordinate analysis (PCoA) based on the drought tolerance indices (DTIs) showed that nine genetically similar accessions share drought tolerance characteristics; these include four of subsp. indurata, three of subsp. everata, and two of subsp. indentata. An abundance of unique ISSR alleles found in the 16 accessions, including the nine drought-tolerant accessions, represents rich untapped genetic resources and these accessions may be exploited in the future breeding of maize commercial lines.

Genetic diversity and volatile oil components variation in Achillea fragrantissima wild accessions and their regenerated genotypes.

BACKGROUND: Wild medicinal plants are suffering natural environmental stresses and habitat destruction. The genetic diversity evaluation of wild accessions and their in vitro raised genotypes using molecular markers, as well as the estimation of substances of pharmaceutical value in wild plants and their regenerated genotypes are convenient approaches to test the genetic fidelity of regenerated plants as a source of substances of pharmaceutical value. In this study, the genetic diversity of 12 accessions of the medicinal plant Achillea fragrantissima, representing five sites in the mountains of South Sinai, Egypt, were estimated by the inter simple sequence repeats (ISSR) fingerprinting and their volatile oil components were identified using gas chromatography-mass spectrometry (GC-MS) analysis. The same accessions were regenerated in vitro and the genetic diversity and volatile oil components of propagated genotypes were determined and compared to their wild parents. RESULTS: Clustering and principal component analyses indicated that the wild accessions and their regenerated genotypes were genetically differentiated, but the regenerated plants are relatively more diverse compared to their wild parents. However, genetic variation between wild accessions is inherited to their in vitro propagated genotypes indicating genotypic differentiation of the examined accessions. The number of volatile oil compounds in the wild A. fragrantissima accessions was 31 compounds while in the in vitro propagated plants only 24 compounds were detected. Four major compounds are common to both wild and regenerated plants; these are artemisia ketone, alpha-thujone, dodecane, and piperitone. CONCLUSIONS: Genome profiling and essential oil components analysis showed variations in A. fragrantissima accessions from different populations. Genetic differences between wild and regenerated genotypes were analyzed and validated with the final conclusion that in vitro conditions elicited higher genetic variation that is associated with reduced amount and diversity in the essential oil components.

Molecular Phylogeny of Trifolium L. Section Trifolium with Reference to Chromosome Number and Subsections Delimitation.

The genus Trifolium is one of the largest genera of the legume family Fabaceae with ca. 255 species. The genus is divided into eight sections; the section Trifolium is a major section of the genus, comprising 73 species mainly distributed in the Mediterranean region. We used nuclear ribosomal DNA internal transcribed spacer (ITS) and morphological variation to reconsider the delimitation and phylogenetic relationships of species in the section Trifolium with reference to chromosomal variations. Bayesian analysis of ITS data delimited the species as three clades based on the analysis of ITS sequence and informative indels in combination with morphological variation. The phylogeny of the species by different analyses methods does not support their current delimitation in 17 subsections. The basic chromosome number x = 8 is the number for the genus Trifolium, from which x = 7, 6 and 5 were derived through successive aneuploidy events. With reference to the distribution of these numbers in the species of the section Trifolium, species in clade III and clade II are more evolved than species in clade I.

Nanobiotechnological advancements in agriculture and food industry: Applications, nanotoxicity, and future perspectives.

The high demand for sufficient and safe food, and continuous damage of environment by conventional agriculture are major challenges facing the globe. The necessity of smart alternatives and more sustainable practices in food production is crucial to confront the steady increase in human population and careless depletion of global resources. Nanotechnology implementation in agriculture offers smart delivery systems of nutrients, pesticides, and genetic materials for enhanced soil fertility and protection, along with improved traits for better stress tolerance. Additionally, nano-based sensors are the ideal approach towards precision farming for monitoring all factors that impact on agricultural productivity. Furthermore, nanotechnology can play a significant role in post-harvest food processing and packaging to reduce food contamination and wastage. In this review, nanotechnology applications in the agriculture and food sector are reviewed. Implementations of nanotechnology in agriculture have included nano- remediation of wastewater for land irrigation, nanofertilizers, nanopesticides, and nanosensors, while the beneficial effects of nanomaterials (NMs) in promoting genetic traits, germination, and stress tolerance of plants are discussed. Furthermore, the article highlights the efficiency of nanoparticles (NPs) and nanozymes in food processing and packaging. To this end, the potential risks and impacts of NMs on soil, plants, and human tissues and organs are emphasized in order to unravel the complex bio-nano interactions. Finally, the strengths, weaknesses, opportunities, and threats of nanotechnology are evaluated and discussed to provide a broad and clear view of the nanotechnology potentials, as well as future directions for nano-based agri-food applications towards sustainability.

Efficacy of metal oxide nanoparticles as novel antimicrobial agents against multi-drug and multi-virulent Staphylococcus aureus isolates from retail raw chicken meat and giblets.

Staphylococcus aureus is among the most common zoonotic pathogens originating from animals consumed as food, especially raw chicken meat (RCM). As far as we know, this might be the first report that explores the efficacy of metal oxide nanoparticles (MONPs), such as zinc peroxide nanoparticles (ZnO2-NPs), zinc oxide nanoparticles (ZnO-NPs), and titanium dioxide nanoparticles (TiO2-NPs) against multidrug resistant (MDR) and/or pandrug resistant (PDR) S. aureus strains with a strong biofilm-producing ability isolated from RCM and giblets. The overall prevalence of coagulase-positive staphylococci was 21%, with a contamination level range between 102 and 104 CFU/g. The incidence of virulence genes See (21/36), pvl (16/36), clfA (15/36), sec (12/36), tst (12/36), and sea (11/36) among S. aureus strains were relatively higher those of seb, sed, fnbA, and fnbB. For antimicrobial resistance gene distribution, most strains harbored the blaZ gene (25/36), aacA-aphD gene (24/36), mecA gene (22/36), vanA gene (20/36), and apmA gene (20/36) confirmed the prevalence of MDR among S. aureus of RCM products. However, cfr (11/36), spc (9/36), and aadE (7/36) showed a relatively lower existence. The data of antibiogram resistance profiles was noticeably heterogeneous (25 patterns) with 32 MDR and four PDR S. aureus strains. All tested strains had a very high MAR index value (>0.2) except the P11 pattern (GEN, MXF, PMB), which showed a MAR index of 0.19. Among the strong biofilm-producing ability (BPA), 14 (70%) strains were isolated from wet markets, while only six strong BPA strains were isolated from supermarkets. The mean values of BPA ranged from 2.613 ± 0.04 to 11.013 ± 0.05. Clearly, ZnO2-NPs show significant inhibitory activity against S. aureus strains compared with those produced by the action of ZnO-NPs and TiO2-NPs. The results of anti-inflammatory activity suggest ZnO2-NPs as a lead compound for designing an alternative antimicrobial agent against drug-resistant and strong biofilm-producing S. aureus isolates from retail RCM and giblets.

Genetic Diversity among Selected Medicago sativa Cultivars Using Inter-Retrotransposon-Amplified Polymorphism, Chloroplast DNA Barcodes and Morpho-Agronomic Trait Analyses.

Alfalfa (Medicago sativa L.) is a major forage crop of family Fabaceae and is frequently cultivated in Egypt. The present study is concerned with the genetic discrimination of fifteen alfalfa cultivars from three different countries (Egypt, Australia, and USA) using two molecular approaches: inter-retrotransposon-amplified polymorphism (IRAP) markers and two chloroplast DNA barcodes matK and the trnH in addition to the analysis of fifteen morpho-agronomic traits. The genetic relatedness, based on analysis of IRAP marker polymorphism and produced using eleven primers by clustering via principal component analysis (PCA) and multivariate heatmap biostatistical methods differentiated the two Egyptian cultivars EGY1-Ismailia1 and EGY2-Nubaria1 from the three Australian and seven American cultivars, with some distinction of the cv. USA6-SW9720 and cv. AUS4-SuperFast. The results were also supported by the sequence analysis of the matK and the trnH genes on the genetic relatedness between eight cultivars. Moreover, it might be suggested that breeding lines from M. sativa cultivars may provide novel insights and a better understanding of the domestication of M. sativa genetic diversity. The classification of the eight cultivars, as revealed by morpho-agronomic traits, confirmed the close genetic relationship between the two Egyptian cultivars and indicated some resemblance between them and the AUS2-Siri Nafa, whereas the two American cultivars, USA1-Super supreme and USA4-Cuf101, were clearly isolated from a cluster of other three cultivars USA7-SW9628, USA8-Magna901, and USA9-Perfect. The results are useful sources of genetic information for future breeding programs in crop development and open new possibilities of producing M. sativa lines harboring high forage quality, productivity, and resistance to biotic and abiotic stresses.

Screening for Drought Tolerance in Maize (Zea mays L.) Germplasm Using Germination and Seedling Traits under Simulated Drought Conditions.

Maize is known to be susceptible to drought stress, which negatively affects vegetative growth and biomass production, as well as the formation of reproductive organs and yield parameters. In this study, 27 responsive traits of germination (G) and seedlings growth were evaluated for 40 accessions of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) germplasm collection, under no stress and simulated drought stress treatments by 10%, 15%, and 20% of polyethylene glycol (PEG). The three treatments significantly reduced G% and retarded seedlings growth, particularly the 15% and 20% PEG treatments; these two treatments also resulted in a significant increase of abnormal seedlings (AS). The heritability (H2) and correlations of the traits were estimated, and drought tolerance indices (DTIs) were calculated for traits and accessions. The H2 of G% values were reduced, and H2 for AS% increased as the PEG stress increased. Positive correlations were found between most trait pairs, particularly shoot and root traits, with 48 highly significant correlations under no stress and 25 highly significant correlations under the 10% PEG treatments, particularly for shoot and root traits. The medium to high heritability of shoot and root seedling traits provides a sound basis for further genetic analyses. PCA analysis clearly grouped accessions with high DTIs together and the accessions with low DTIs together, indicating that the DTI indicates the stress tolerance level of maize germplasm. However, the resemblance in DTI values does not clearly reflect the origin or taxonomic assignments to subspecies and varieties of the examined accessions.

Seed coat color, weight and eye pattern inheritance in gamma-rays induced cowpea M2-mutant line.

Gamma radiation is a very effective tool for inducing genetic variation in characters of many plants. Black seeds of M2 mutant were obtained after exposure of an Egyptian cowpea cultivar (Kaha 1) to a low dose of gamma rays. Segregation of seed coat color, weight of 100 seeds and seed eye pattern of the black seeds of this mutant line were further examined in this study. Four colors were observed for seed coat in the M3 plants ranging from cream to reddish brown and three eye patterns were distinguished from each other. SDS-PAGE of the seed storage proteins showed 18 protein bands; five of these bands disappeared in the seeds of M3 plants compared to M2 and M0 controls while other 5 protein bands were specifically observed in seeds of M3 plants. PCR analysis using twelve ISSR primers showed 47 polymorphic and 8 unique amplicons. The eight unique amplicons were characteristic of the cream coat color and brown wide eye pattern (M03-G10) while the polymorphic bands were shared by 6 coat-color groups. A PCR fragment of 850 bp was amplified, using primer HB-12, in M3-G04 which showed high-100 seed weight. These results demonstrated the mutagenic effects of gamma rays on seed coat color, weight of 100 seeds and eye pattern of cowpea M3 mutant plants.

Floristic composition and vegetation analysis in Hail region north of central Saudi Arabia.

In this study, 19 sites representing different habitats in Hail region were regularly visited for two years, in each site 2-5 stands were selected for investigating floristic composition and vegetation types in the area. A total of 124 species representing 34 families were recorded. The family Asteraceae is represented by the highest number of species (21 species) followed by the Poaceae (17 species) and the Brassicaceae (10 species) whereas, 15 families including Acanthaceae, Convolvulaceae, Moraceae, Nyctaginaceae and Primulaceae, are represented by a single species each. Chronological analysis of the vegetation in the area revealed the domination of Saharo-Sindian elements in the wild vegetations and of weedy species in the cultivated plots. Therophytes and chamaephytes are the dominating life forms of the vegetation spectra; therophytes represent 49.20% and chamaephytes represent 29.00% of the total species in the study area. Application of TWINISPAN and DECORANA classification and ordination techniques to the data produced seven vegetation groups. Ruderal habitats comprised two small groups A and F dominated by Phragmites australis and Imperata cylindrical (A), Euphorbia peplus and Sisymbrium irio (F), respectively. Two vegetation groups (B and G) have been recognized in the mountains and slopes dominated by Launaea mucronata, Trigonella stellata (B) and Ficus palmate and Fagonia bruguieri (G). Other two groups (C and E) inhabit the desert and mountainous wadies; these are represented by Gymnocarpos decandrus and Ochradenus baccatus (C) and Senecio glaucus subsp. coronopifolius and Rumex equisetiforme (E). On the other hand, one group (D) inhabits the cultivated plots and is represented by Plantago albicans and Rumex vesicarius, the last group also includes species restricted to the sand dune habitat of the Al-Nafud desert north of Hail city and represented by Calligonum polygonoides and Halyxolon salicornicum. The vegetation analysis indicated the invasion of Hail Flora by some foreign weeds such as Solanum nigrum, Lactuca serriola and Amaranthus lividus. The presence of these weeds points out the need to monitor the vegetation change in Hail region, and also other regions of Saudi Arabia, in order to elucidate the human impact on the wild plants diversity as human activities change with the fast development in the kingdom.

Determination of functional gamma-GTase genes and investigation of the biological activity of proteins in Arabidopsis thaliana at different stages of growth.

The results in the present study emphasize that in Arabidopsis thaliana genome, gamma-GTase encoded by a gene family comprised of four genes. Three of these genes are functionally expressed while the fourth is a pseudogene. The three functional genes express different active protein isoforms that appeared to have different functions. Two genes (GGT1 and GGT2) are structurally similar and expresses proteins with the same molecular weight and both target to the same cellular compartment (plasma membrane). However, both demonstrated different tissue localization, physiological activities and different patterns of response to environmental stress. The majority of GGTI encoded by the first gene was localized in the rosette leaves, It is also expressed throughout the whole plant.