Exploring the genetic potential of Pakistani soybean cultivars through RNA-seq based transcriptome analysis.

BACKGROUND: Soybean is largely grown and considered among the top oilseed crops. Three Pakistani cultivars, NARC-II (N), Swat-84 (S), and Rawal-I (R) were employed for RNA-Seq based transcriptome analysis to explore their genetic potential and performance in our local environment. METHODS AND RESULTS: We grew the plants in glass house at same conditions and sampled leaves for RNA-Seq analysis in triplicate for each variety. We retrieved 2225 differentially expressed genes (DEGs) between S vs R, 2591 DEGs between S vs N, and 1221 DEGs between R vs N cultvars. These genes consist of transcription factors representing Basic Helix-loop Helix, myeloblastosis, ethylene response factors, and WRKY amino acid motif (WRKY) type major families that were up-regulated. KEGG pathway analysis revealed that MAPK, plant hormone signal transduction, and Phenylpropanoid biosynthesis pathways were the most dominant pathways involved in plant defense and growth. Comparative analysis showed that Swat-84 (S) cultivar had better gene expression among these varieties having higher number of DEGs, where mostly genes related to important phenotypic traits were up regulated. CONCLUSIONS: This is a pilot study to investigate and functionally characterise the DEG involved in the stress response in the cultivars studied.

Systematic analysis of HD-ZIP transcription factors in sesame genome and gene expression profiling of SiHD-ZIP class I entailing drought stress responses at early seedling stage.

BACKGROUND: Sesame is an ancient oilseed crop, known for its high oil content and quality. Its sensitivity to drought at early seedling stage is one of the limiting factors affecting its world-wide growth and productivity. Among plant specific transcription factors, the association of HD-ZIPs with sesame drought responses at early seedling stage is not well-established yet and is very important to develop our molecular understanding on sesame drought tolerance. METHODS AND RESULTS: In this study, total 61 sesame HD-ZIP proteins were identified, based on their protein sequence homology with Arabidopsis and protein domain(s) architecture prediction, followed by their phylogenetic, conserved domain(s) motifs and gene structure analyses to classify them into four classes (HD-ZIP Class I-IV). HD-ZIP Class I was also subdivided into four subgroups: α (SiHZ25, SiHZ43, SiHZ9 and SiHZ16), ß1 (SiHZ10, SiHZ30, SiHZ32 and SiHZ26), ß2 (SiHZ42 and SiHZ45) and γ (SiHZ17, SiHZ7 and SiHZ35) by a comparative phylogenetic analysis of sesame with Arabidopsis and maize. Afterwards, twenty-one days old sesame seedlings were exposed to drought stress by withholding water for 7 days (when soil moisture content reduced to ~16%) and gene expression of HD-ZIP Class I (13 members) was performed in well- watered (control) and drought stressed seedlings. The gene expression analysis showed that the expressions of SiHZ7 (6.8 fold) and SiHZ35 (2.6 fold) from γ subgroup were significantly high in drought seedlings. CONCLUSIONS: This study is useful in demonstrating the role of SiHD-ZIP Class I in sesame drought responses at early seedling stage and to develop its novel drought tolerant varieties.

Isolation and characterization of culturable endophytic bacterial community of stripe rust-resistant and stripe rust-susceptible Pakistani wheat cultivars.

In this study, endophytic bacteria isolated from root, stem, and leaf tissues of stripe rust-susceptible (Inqilab 91, Galaxy 2013, and 15BT023) and stripe rust-resistant (NARC 2011, Ujala 2015, TW1410) cultivars were identified and characterized. Abundance of endophytes was found in roots as compared with stems and leaves. Resistant and susceptible cultivars significantly differed in abundance of endophytic bacteria. Restriction analysis of 16S rRNA genes amplified from 100 bacterial isolates produced 17 unique patterns. Representatives of each of the 17 unique patterns were sequenced and identified. Among the sequenced bacteria, 8 belonged to Firmicutes, 7 were Proteobacteria, and 2 were Actinobacteria. Most of the isolates have plant growth-promoting properties and a few have the potential of producing hydrolytic enzymes. Two isolates showed significant inhibition of rust spore germination. These endophytic bacteria not only can be helpful in growth-promoting activities but also can assist in biocontrol of stripe rust disease.

Genome and proteome analysis of Pseudomonas chloritidismutans†AW-1T that grows on n-decane with chlorate or oxygen as electron acceptor.

Growth of Pseudomonas chloritidismutans AW-1T on C7 to C12 n-alkanes with oxygen or chlorate as electron acceptor was studied by genome and proteome analysis. Whole genome shotgun sequencing resulted in a 5 Mbp assembled sequence with a G + C content of 62.5%. The automatic annotation identified 4767 protein-encoding genes and a putative function could be assigned to almost 80% of the predicted proteins. The distinct phylogenetic position of P. chloritidismutans AW-1T within the Pseudomonas stutzeri cluster became clear by comparison of average nucleotide identity values of sequenced genomes. Analysis of the proteome of P. chloritidismutans AW-1T showed the versatility of this bacterium to adapt to aerobic and anaerobic growth conditions with acetate or n-decane as substrates. All enzymes involved in the alkane oxidation pathway were identified. An alkane monooxygenase was detected in n-decane-grown cells, but not in acetate-grown cells. The enzyme was found when grown in the presence of oxygen or chlorate, indicating that under both conditions an oxygenase-mediated pathway is employed for alkane degradation. Proteomic and biochemical data also showed that both chlorate reductase and chlorite dismutase are constitutively present, but most abundant under chlorate-reducing conditions.

An Inventory of Anthelmintic Plants across the Globe.

A wide range of novelties and significant developments in the field of veterinary science to treat helminth parasites by using natural plant products have been assessed in recent years. To the best of our knowledge, to date, there has not been such a comprehensive review of 19 years of articles on the anthelmintic potential of plants against various types of helminths in different parts of the world. Therefore, the present study reviews the available information on a large number of medicinal plants and their pharmacological effects, which may facilitate the development of an effective management strategy against helminth parasites. An electronic search in four major databases (PubMed, Scopus, Web of Science, and Google Scholar) was performed for articles published between January 2003 and April 2022. Information about plant species, local name, family, distribution, plant tissue used, and target parasite species was tabulated. All relevant studies meeting the inclusion criteria were assessed, and 118 research articles were included. In total, 259 plant species were reviewed as a potential source of anthelmintic drugs. These plants can be used as a source of natural drugs to treat helminth infections in animals, and their use would potentially reduce economic losses and improve livestock production.

Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes.

Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.

Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers.

BACKGROUND: Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. RESULTS: In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from - 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. CONCLUSIONS: Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

Control of stripe rust of wheat using indigenous endophytic bacteria at seedling and adult plant stage.

Stripe rust (caused by Puccinia striiformis tritici) is one of the most devastating diseases of wheat. The most effective ways to control stripe rust are the use of resistant cultivars and the timely use of an appropriate dose of fungicide. However, the changing nature of rust pathogen outwits the use of resistant cultivars, and the use of a fungicide is associated with environmental problems. To control the disease without sacrificing the environment, we screened 16 endophytic bacteria, which were isolated from stripe rust-resistant wheat cultivars in our previous study, for their biocontrol potential. A total of 5 bacterial strains Serratia marcescens 3A, Bacillus megaterium 6A, Paneibacillus xylanexedens 7A, Bacillus subtilis 11A, and Staphyloccus agentis 15A showed significant inhibition of Puccinia striiformis f. sp. tritici (Pst) urediniospores germination. Two formulations i.e., fermented liquid with bacterial cell (FLBC) and fermented liquid without bacterial cells (FL) of each bacterial strain, were evaluated against the urediniospores germination. Formulations of five selected endophytic bacteria strains significantly inhibited the uredinioospores germination in the lab experiments. It was further confirmed on seedlings of Pakistani susceptible wheat cultivar Inqilab-91 in the greenhouse, as well as in semi-field conditions. FLBC and FL formulations applied 24 h before Pst inoculation (hbi) displayed a protective mode. The efficacy of FLBC was between 34.45 and 87.77%, while the efficacy of FL was between 39.27 and 85.16% when applied 24 hbi. The inoculated wheat cultivar Inqilab-91 was also tested under semi-field conditions during the 2017-2018 cropping season at the adult plant stage. The strains Bacillus megaterium 6A and Paneibacillus xylanexedens 7A alone significantly reduced the disease severity of stripe rust with the efficacy of 65.16% and 61.11% for the FLBC in protective effect, while 46.07% and 44.47% in curative effect, respectively. Inoculated seedlings of Inqilab-91 showed higher activities of antioxidant enzymes, superoxide dismutase (SOD), peroxidase (POD), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL). The treated seedlings also showed higher expressions of pathogenesis-related (PR) protein genes, antifungal protein (PR-1), ß-1,3-endoglucanases (PR-2), endochitinases (PR-4), peroxidase (PR-9), and ribonuclease-like proteins (PR-10). These results indicated that endophytic bacteria have the biocontrol potential, which can be used to manage stripe rust disease. High production antioxidant enzymes, as well as high expression of PR protein genes, might be crucial in triggering the host defense mechanism against Pst.

Leaf size modulation by cytokinins in sesame plants.

Phytohormones play important roles in controlling leaf size and in the modulation of various stress responses, including drought. In this study, hormone profiling analyses by ultra high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry (UHPLC-MS/MS) was performed in leaves collected at three stages of active leaf growth to unravel which phytohormones modulate leaf size in sesame (Sesamum indicum L.) plants, an important oil-rich crop. Furthermore, endogenous contents of phytohormones were measured in parallel to various stress markers in sesame plants exposed to mild water deficit conditions by withholding water in potted plants for one week. Results revealed a major role of cytokinins and auxin in the modulation of leaf growth in sesame plants (which increased by 21.5 and 2.1-fold, respectively, with leaf growth), as well as a putative antagonistic response between jasmonic acid and salicylic acid during leaf development. Furthermore, growth arrest during water deficit stress appeared to be modulated by cytokinins, the endogenous contents of which decreased (by 48%) in parallel with ABA increases (by 59%). Reductions in the contents of the active cytokinin trans-zeatin occurred in parallel with increases in isopentenyladenine contents under drought, which suggests a partial metabolic limitation in cytokinin biosynthesis in leaves upon water deficit stress. These results provide useful information for the hormonal modulation of leaf size and the improvement of leaf growth and production in sesame plants through manipulation of the levels of key regulatory phytohormones.

Protein quantification and enzyme activity estimation of Pakistani wheat landraces.

Wheat is a major food grain in Pakistan having a prominent role in agriculture as well as the economic status of the country. In the current study, seeds of 99 wheat landraces were characterized for the quantification of seed storage proteins (Albumins, Globulin, Gliadins, and Glutenin), enzyme activities of antioxidant enzymes i.e. Ascorbate peroxidase (APX), Catalase (CAT), Superoxide dismutase (SOD), Peroxidase (POD), one hydrolytic enzyme Protease (PROT) and non-enzymatic antioxidant enzyme Ascorbic acid (AsA). The landraces were categorized into low, medium, and high based on protein concentration and enzymes activities/content. The majority of the landraces were placed in the medium category. However, for the AsA parameter majority of the landraces were placed in the low category. The highest concentration of total extracted protein (184.88±0.7 mg/g. wt.), globulins (21.35±0.43 mg/g. wt.) and glutenin (20±0.04 mg/g. wt.) as well as the high activity of SOD (303±16.80 Units/g. wt.), and Ascorbic acid (533±36.1 Units/g. wt.) was identified in the wheat landrace "11757" collected from district Panjgur (Balochistan). The wheat landrace "11760", collected from district Kech (Balochistan), contained the highest albumins concentration (65.42±0.02 mg/g. wt.) and highest activity for CAT (589.5±61.20 Units/g. wt.). The highest activity of POD (32341± 91.3) and PROT was observed in seeds of the wheat landrace "11618" collected from the Gilgit Baltistan region of Pakistan. The principal component analysis showed that the great variations existed for the tested parameters among the wheat landraces. The landraces with a high concentration of seed storage proteins and antioxidant enzyme activities can be used for breeding purposes to improve the nutrimental quality of wheat cultivars.

Knowledge, attitudes and practices related to cystic echinococcosis endemicity in Pakistan.

BACKGROUND: Cystic echinococcosis (CE) is a human and animal health problem in many endemic areas worldwide. It is considered a neglected zoonotic disease caused by the larval form (hydatid cyst) of Echinococcus spp. tapeworm. There are limited studies on echinococcosis in Pakistan. METHODS: A cross-sectional survey was conducted to find out recent knowledge, attitudes and practices on the occurrence of cystic echinococcosis in butchers and dog owners in both urban and rural areas of Rawalpindi/Islamabad regions, Pakistan. The quantitative data was collected in the form of questionnaires to investigate the knowledge and awareness of CE among community members and their routine practices that  were behind the factors involved in hydatid cyst infection. The practices and infrastructure of abattoirs/butcher shops and their role in transmission of cystic echinococcosis were also evaluated in the present study. RESULTS: The participants involved in the study were dog owners and people who kept animals. A total of 400 people were interviewed and 289 questionnaires were received. The results showed that only 4.1% of people have heard about the disease, and 58.1% were closely associated with dogs. Sixty-three percent of dogs in study area were consuming uncooked organs (e.g. liver, lung, etc.) of slaughtered animals, while 100% of dogs at butcher shops were consuming uncooked organs. Home slaughtering was common in 20.06%. Among butchers, 32.3% had heard about zoonoses and 7.61% knew about CE. The statistical analysis showed that there was highly significant difference (P < 0.05) among most of the practices that were associated with the prevalence of CE. CONCLUSIONS: It  was concluded from the present study that, the knowledge and awareness of CE among people of Rawalpindi/Islamabad were low. Because of dogs and poor knowledge of CE among community members and butchers, the transmission of echinococcosis is facilitated. Therefore, there is urgent need to strengthen awareness and health education among people, as well as proper practices related to the CE not only in the study area, but also in other areas of Pakistan.

Isolation and characterization of culturable endophytic bacterial community of stripe rust-resistantand striperust-susceptible Pakistani wheat cultivars

In this study, endophytic bacteria isolated from root, stem, and leaf tissues of stripe rust-susceptible (Inqilab 91, Galaxy 2013, and 15BT023) and stripe rust-resistant (NARC 2011, Ujala 2015, TW1410) cultivars were identified and characterized. Abundance of endophytes was found in roots as compared with stems and leaves. Resistant and susceptible cultivars significantly differed in abundance of endophytic bacteria. Restriction analysis of 16S rRNA genes amplified from 100 bacterial isolates produced 17 unique patterns. Representatives of each of the 17 unique patterns were sequenced and identified. Among the sequenced bacteria, 8 belonged to Firmicutes, 7 were Proteobacteria, and 2 were Actinobacteria. Most of the isolates have plant growth-promoting properties and a few have the potential of producing hydrolytic enzymes. Two isolates showed significant inhibition of rust spore germination. These endophytic bacteria not only can be helpful in growth-promoting activities but also can assist in biocontrol of stripe rust disease

No disponible