ORCID Profile
0000-0002-9544-8259
Current Organisations
University of Adelaide
,
University of Nottingham
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Publisher: Cold Spring Harbor Laboratory
Date: 10-02-2020
DOI: 10.1101/2020.02.09.940775
Abstract: Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici is a major threat to wheat production worldwide. The breakdown in resistance of certain major genes and new emerging aggressive races of stripe rusts are causing serious concerns in all main wheat growing areas of the world. To search for new sources of resistance genes and associated QTL for effective utilization in future breeding programs an association mapping panel comprising of 600 bread wheat landraces collected from eight different countries conserved at ICARDA gene bank were evaluated for seedling and adult plant resistance against PstS2 and Warrior races of stripe rust at the Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey during 2016, 2018 and 2019. A set of 25,169 informative SNP markers covering the whole genome were used to examine the population structure, linkage disequilibrium and marker-trait associations in the association mapping panel. The genome-wide association study (GWAS) was carried out using a Mixed Linear Model (MLM). We identified 47 SNP markers at 19 genomic regions with significant SNP-trait associations for both seedling and adult plant stage resistance, the threshold of significance for all SNP-trait associations was determined by the false discovery rate (q) ≤ 0.05. Three genomic regions ( QYr.1D_APR, QYr.3A_seedling and QYr.7D_seedling ) identified in this study are far away from any previously reported Yr gene or QTL hence, tagging novel genomic regions. The In-silico analysis of the novel QTL regions identified candidate resistance genes encoding proteins putative to plants disease resistance and defense mechanism.
Publisher: Frontiers Media SA
Date: 18-02-2020
Publisher: Wiley
Date: 07-12-2020
DOI: 10.1002/TPG2.20066
Abstract: Stripe or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici is a major threat to bread wheat production worldwide. The breakdown in resistance of certain major genes and newly emerging aggressive races of stripe rusts pose serious concerns in all main wheat growing areas of the world. To identify new sources of resistance and associated QTL for effective utilization in future breeding programs an association mapping (AM) panel comprising of 600 bread wheat landraces collected from eight different countries conserved at ICARDA gene bank were evaluated for seedling and adult plant resistance against the PstS2 and Warrior races of stripe rust at the Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey during 2016, 2018 and 2019. A set of 25,169 informative SNP markers covering the whole genome were used to examine the population structure, linkage disequilibrium and marker‐trait associations in the AM panel. The genome‐wide association study (GWAS) was carried out using a Mixed Linear Model (MLM). We identified 47 SNP markers across 19 chromosomes with significant SNP‐trait associations for both seedling stage and adult plant resistance. The threshold of significance for all SNP‐trait associations was determined by the false discovery rate (q) ≤ 0.05. Three genomic regions ( QYr.1D_APR, QYr.3A_seedling and QYr.7D_seedling ) identified in this study do not correspond to previously reported Yr genes or QTL, suggesting new genomic regions for stripe rust resistance.
Publisher: Oxford University Press (OUP)
Date: 09-2020
Abstract: Chlorophyll biosynthesis and chloroplast development are crucial to photosynthesis and plant growth, but their regulatory mechanism remains elusive in many crop species. We isolated a Brassica napus yellow-virescent leaf (yvl) mutant, which exhibited yellow-younger-leaf and virescent-older-leaf with decreased chlorophyll accumulation and delayed chloroplast development. We mapped yvl locus to a 70-kb interval between molecular markers yvl-O10 and InDel-O6 on chromosome A03 in BC2F2 population using whole genome re-sequencing and bulked segregant analysis. The mutant had a ‘C’ to ‘T’ substitution in the coding sequence of BnaA03.CHLH, which encodes putative H subunit of Mg-protoporphyrin IX chelatase (CHLH). The mutation resulted in an imperfect protein structure and reduced activity of CHLH. It also h ered the plastid encoded RNA polymerase which transcribes regulatory genes of photosystem II and I. Consequently, the chlorophyll a/b and carotenoid contents were reduced and the chloroplast ultrastructure was degraded in yvl mutant. These results explain that a single nucleotide mutation in BnaA03.CHLH impairs PEP activity to disrupt chloroplast development and chlorophyll biosynthesis in B. napus.
Publisher: Wiley
Date: 23-12-2019
Abstract: Salinity has drastic effects on plant growth and productivity and is one of the major factors responsible for crop yield losses throughout the agricultural soils of the world. The mechanisms of salinity tolerance in plants are regulated by a set of inherent multigenes and prevalent environmental factors, which bring about a myriad of metabolic changes in each plant part. The stress-induced metabolic changes in the rice plant have been intensively studied, but extensively in plant parts such as stem, leaf, and root. However, little information exists in the literature about such stress-induced architectural and physiological changes in rice grain, a premier staple food of a large proportion of human population. Thus, the current review comprehensively describes the effects of salinity stress on rice grain composition including changes in carbohydrate, protein, fat, and mineral contents. Elucidation of salinity induced changes in rice grain composition would help to understand whether or not a nutritious and healthy staple food is available to human population from rice grown under saline environments.
Publisher: Wiley
Date: 24-06-2020
DOI: 10.1002/TPG2.20030
Publisher: Oxford University Press (OUP)
Date: 12-2020
DOI: 10.1038/S41438-020-00416-8
Abstract: The organoleptic qualities of watermelon fruit are defined by the sugar and organic acid contents, which undergo considerable variations during development and maturation. The molecular mechanisms underlying these variations remain unclear. In this study, we used transcriptome profiles to investigate the coexpression patterns of gene networks associated with sugar and organic acid metabolism. We identified 3 gene networks/modules containing 2443 genes highly correlated with sugars and organic acids. Within these modules, based on intramodular significance and Reverse Transcription Quantitative polymerase chain reaction (RT-qPCR), we identified 7 genes involved in the metabolism of sugars and organic acids. Among these genes, Cla97C01G000640 , Cla97C05G087120 and Cla97C01G018840 ( r 2 = 0.83 with glucose content) were identified as sugar transporters ( SWEET , EDR6 and STP ) and Cla97C03G064990 ( r 2 = 0.92 with sucrose content) was identified as a sucrose synthase from information available for other crops. Similarly, Cla97C07G128420 , Cla97C03G068240 and Cla97C01G008870 , having strong correlations with malic ( r 2 = 0.75) and citric acid ( r 2 = 0.85), were annotated as malate and citrate transporters ( ALMT7 , CS , and ICDH ). The expression profiles of these 7 genes in erse watermelon genotypes revealed consistent patterns of expression variation in various types of watermelon. These findings add significantly to our existing knowledge of sugar and organic acid metabolism in watermelon.
Publisher: Cold Spring Harbor Laboratory
Date: 05-09-2020
DOI: 10.1101/2020.09.04.283556
Abstract: Despite the economic importance of P utilization efficiency, information on genetic factors underlying this trait remains elusive. To address that, we performed a genome-wide association study in a spring wheat ersity panel ranging from landraces to elite varieties. We evaluated the phenotype variation for P utilization efficiency in controlled conditions and genotype variation using wheat 90K SNP array. Phenotype variables were transformed into a smaller set of uncorrelated principal components that captured the most important variation data. We identified two significant loci associated with both P utilization efficiency and the 1st principal component on chromosomes 3A and 4A: qPE1-3A and qPE2-4A . Annotation of genes at these loci revealed 53 wheat genes, among which 6 were identified in significantly enriched pathways. The expression pattern of these 6 genes indicated that TraesCS4A02G481800 , involved in pyruvate metabolism and TCA cycle, had a significantly higher expression in the P efficient variety under limited P conditions. Further characterization of these loci and candidate genes can help stimulate P utilization efficiency in wheat. We report two new loci for P utilization efficiency on chromosomes 3A and 4A of wheat. The prioritized candidate genes at these loci can be investigated by molecular biology techniques to improve P efficiency in wheat and grass relatives.
Publisher: MDPI AG
Date: 11-03-2021
DOI: 10.3390/MOLECULES26061548
Abstract: Green synthesis of nanomaterials is advancing due to its ease of synthesis, inexpensiveness, nontoxicity and renewability. In the present study, an eco-friendly biogenic method was developed for the green synthesis of nickel oxide nanoparticles (NiONPs) using phytochemically rich Berberis balochistanica stem (BBS) extract. The BBS extract was rich in phenolics, flavonoids and berberine. These phytochemicals successfully reduced and stabilised the NiNO3 (green) into NiONPs (greenish-gray). BBS-NiONPs were confirmed by using UV-visible spectroscopy (peak at 305 nm), X-ray diffraction (size of 31.44 nm), Fourier transform infrared spectroscopy (identified -OH group and Ni-O formation), energy dispersive spectroscopy (showed specified elemental nature) and scanning electron microscopy (showed rhombohedral agglomerated shape). BBS-NiONPs were exposed to multiple in vitro bioactivities to ascertain their beneficial biological applications. They exhibited strong antioxidant activities: total antioxidant capacity (64.77%) and 2, 2-diphenyl-1-picrylhydrazyl (71.48%) and cytotoxic potential: Brine shrimp cytotoxicity assay with IC50 (10.40 µg/mL). BBS-NiONPs restricted the bacterial and fungal pathogenic growths at 1000, 500 and 100 µg/mL. Additionally, BBS-NiONPs showed stimulatory efficacy by enhancing seed germination rate and seedling growth at 31.25 and 62.5 µg/mL. In aggregate, BBS extract has a potent antioxidant activity which makes the green biosynthesis of NiONPs easy, economical and safe. The biochemical potential of BBS-NiONPs can be useful in various biomedical and agricultural fields.
Publisher: MDPI AG
Date: 23-03-2022
DOI: 10.3390/MOLECULES27072064
Abstract: An eco-friendly biogenic method for the synthesis of nickel oxide nanoparticles (NiONPs) using phytochemically rich Berberis pachyacantha leaf extract (BPL) was established. To achieve this purpose, 80 mL of BPL extract was used as a suitable reducing and capping agent for the synthesis of NiONPs. The synthesis of BPL-based nickel oxide nanoparticles (BPL@NiONPs) was confirmed using different microscopic and spectroscopic techniques: UV Visible spectroscopy (UV-Vis), Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), energy dispersive X-ray (EDX), dynamic light scattering (DLS) and scanning electron microscopy (SEM) analysis. Spectroscopically, BPL-NiONPs was found with a pure elemental composition (oxygen and nickel), average size (22.53 nm) and rhombohedral structure with multiple functional groups (-OH group and Ni-O formation) on their surface. In the next step, the BPL extract and BPL@NiONPs were further investigated for various biological activities. As compared to BPL extract, BPL@NiONPs exhibited strong biological activities. BPL@NiONPs showed remarkable antioxidant activities in terms of 2,2-diphenyl-1-picrylhydrazyl (76.08%) and total antioxidant capacity (68.74%). Antibacterial action was found against Pseudomonas aeruginosa (27 mm), Staphylococcus aureus (20 mm) and Escherichia coli (19.67 mm) at 500 µg/mL. While antifungal potentials were shown against Alternaria alternata (81.25%), Fusarium oxysporum (42.86%) and Aspergillus niger (42%) at 1000 µg/mL. Similarly, dose-dependent cytotoxicity response was confirmed against brine shrimp with IC50 value (45.08 µg/mL). Additionally, BPL@NiONPs exhibited stimulatory efficacy by enhancing seed germination rate at low concentrations (31.25 and 62.5 µg/mL). In conclusion, this study depicted that BPL extract has important phytochemicals with remarkable antioxidant activities, which successfully reduced and stabilized the BPL@NiONPs. The overall result of this study suggested that BPL@NiONPs could be used as nanomedicines and nanofertilizers in biomedical and agrarian fields.
Publisher: Oxford University Press (OUP)
Date: 26-08-2022
Abstract: The trans-Golgi network (TGN) acts as a central platform for sorting and secreting various cargoes to the cell surface, thus being essential for the full execution of plant immunity. However, the fine-tuned regulation of TGN components in plant defense and stress response has been not fully elucidated. Our study revealed that despite largely compromising penetration resistance, the loss-of-function mutation of the TGN component protein ECHIDNA (ECH) induced enhanced postinvasion resistance to powdery mildew in Arabidopsis thaliana. Genetic and transcriptome analyses and hormone profiling demonstrated that ECH loss resulted in salicylic acid (SA) hyperaccumulation via the ISOCHORISMATE SYNTHASE 1 biosynthesis pathway, thereby constitutively activating SA-dependent innate immunity that was largely responsible for the enhanced postinvasion resistance. Furthermore, the ech mutant displayed accelerated SA-independent spontaneous cell death and constitutive POWDERY MILDEW RESISTANCE 4-mediated callose depositions. In addition, ECH loss led to a chronically prolonged endoplasmic reticulum stress in the ech mutant. These results provide insights into understanding the role of TGN components in the regulation of plant immunity and stress responses.
Publisher: Elsevier BV
Date: 04-2020
Publisher: Informa UK Limited
Date: 10-10-2022
Publisher: Elsevier BV
Date: 10-2023
Publisher: Wiley
Date: 09-2023
DOI: 10.1002/FES3.498
Publisher: Elsevier BV
Date: 12-2020
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Luqman Bin Safdar.