Publications by authors named "Muhammad Hafeez Ullah Khan"

12 Publications

  • Page 1 of 1

Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using different GWAS models.

Sci Rep 2021 Mar 24;11(1):6767. Epub 2021 Mar 24.

State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China.

Wheat is a major food crop worldwide. The plant architecture is a complex trait mostly influenced by plant height, tiller number, and leaf morphology. Plant height plays a crucial role in lodging and thus affects yield and grain quality. In this study, a wheat population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by ML-GWAS and SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were consistently detected, including seven across multiple environments and 36 across multiple methods. Interestingly, five SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, played a role in modulating both plant height and flag leaf length. Furthermore, candidate SNPs (BS00068592_51, Kukri_c4750_452 and BS00022127_51) constantly repeated in different years and methods associated with flag leaf width and number of tillers. We also detected several SNPs (Jagger_c6772_80, RAC875_c8121_1490, BS00089954_51, Excalibur_01167_1207, and Ku_c5191_340) having common associations with more than one trait across multiple environments. By further appraising these GWAS methods, the pLARmEB and FarmCPU models outperformed in SNP detection compared to the other ML-GWAS and SL-GWAS methods, respectively. Totally, 152 candidate genes were found to be likely involved in plant growth and development. These finding will be helpful for better understanding of the genetic mechanism of architectural traits in wheat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-021-86127-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7990932PMC
March 2021

A Revolution toward Gene-Editing Technology and Its Application to Crop Improvement.

Int J Mol Sci 2020 Aug 7;21(16). Epub 2020 Aug 7.

Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea.

Genome editing is a relevant, versatile, and preferred tool for crop improvement, as well as for functional genomics. In this review, we summarize the advances in gene-editing techniques, such as zinc-finger nucleases (ZFNs), transcription activator-like (TAL) effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) associated with the Cas9 and Cpf1 proteins. These tools support great opportunities for the future development of plant science and rapid remodeling of crops. Furthermore, we discuss the brief history of each tool and provide their comparison and different applications. Among the various genome-editing tools, CRISPR has become the most popular; hence, it is discussed in the greatest detail. CRISPR has helped clarify the genomic structure and its role in plants: For example, the transcriptional control of Cas9 and Cpf1, genetic locus monitoring, the mechanism and control of promoter activity, and the alteration and detection of epigenetic behavior between single-nucleotide polymorphisms (SNPs) investigated based on genetic traits and related genome-wide studies. The present review describes how CRISPR/Cas9 systems can play a valuable role in the characterization of the genomic rearrangement and plant gene functions, as well as the improvement of the important traits of field crops with the greatest precision. In addition, the speed editing strategy of gene-family members was introduced to accelerate the applications of gene-editing systems to crop improvement. For this, the CRISPR technology has a valuable advantage that particularly holds the scientist's mind, as it allows genome editing in multiple biological systems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms21165665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461041PMC
August 2020

Antimicrobial potentials of medicinal plant's extract and their derived silver nanoparticles: A focus on honey bee pathogen.

Saudi J Biol Sci 2019 Nov 21;26(7):1815-1834. Epub 2018 Feb 21.

Institute of Chemical Sciences, Gomal University Dera Ismail Khan, KPK, Pakistan.

Infectious (or Communicable) diseases are not only the past but also the present problem in developing as well as developed countries. It is caused by various pathogenic microbes like fungi, bacteria, parasites and virus etc. The medicinal plants and nano-silver have been used against the pathogenic microbes. Herbal medicines are generally used for healthcare because they have low price and wealthy source of antimicrobial properties. Like medicinal plants, silver nanoparticles also have emergent applications in biomedical fields due to their immanent therapeutic performance. Here, we also explore the various plant parts such as bark, stem, leaf, fruit and seed against Gram negative and Gram-positive bacteria, using different solvents for extraction i.e. methanol, ethyl acetate, chloroform, acetone, . hexane, butanol, petroleum ether and benzene. Since ancient to date most of the countries have been used herbal medicines, but in Asia, some medicinal plants are commonly used in rural and backward areas as a treatment for infectious diseases. In this review, we provide simple information about medicinal plants and Silver nanoparticles with their potentialities such as antiviral, bactericidal and fungicidal. Additionally, the present review to highlights the versatile applications of medicinal plants against honey bee pathogen such as fungi (), mites ( spp. and sp.), bacteria (), and microsporidia ( and ). In conclusion, promising nonchemical (plant extracts) are innocuous to adult bees. So, we strongly believed that this effort was made to evaluate the status of medicinal plants researches globally.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.sjbs.2018.02.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864162PMC
November 2019

Morpho-physiological traits, gaseous exchange attributes, and phytoremediation potential of jute (Corchorus capsularis L.) grown in different concentrations of copper-contaminated soil.

Ecotoxicol Environ Saf 2020 Feb 10;189:109915. Epub 2019 Nov 10.

MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. Electronic address:

Jute (Corchorus capsularis L.) is the most commonly used natural fiber as reinforcement in green composites and, due to its huge biomass, deep rooting system, and metal tolerance in stressed environments, it is an excellent candidate for the phytoremediation of different heavy metals. Therefore, the present study was carried out to examine the growth, antioxidant capacity, gaseous exchange attributes, and phytoremediation potential of C. capsularis grown at different concentrations of Cu (0, 100, 200, 300, and 400 mg kg) in a glass house environment. The results illustrate that C. capsularis can tolerate Cu concentrations of up to 300 mg kg without significant decreases in growth or biomass, but further increases in Cu concentration (i.e., 400 mg kg) lead to significant reductions in plant growth and biomass. The photosynthetic pigments and gaseous exchange attributes in the leaves of C. capsularis decreased as the Cu concentration in the soil increased. Furthermore, high concentrations of Cu in the soil caused lipid peroxidation by increasing the malondialdehyde content in the leaves. This implies that elevated Cu levels cause oxidative damage in C. capsularis. Antioxidants, such as superoxidase dismutase and peroxidase, come into play to scavenge the reactive oxygen species which are generated as a result of oxidative stress. In the present study, the concentrations of Cu in different parts of the plant (the roots, leaves, stem core, and fibers) were also investigated at four different stages of the life cycle of C. capsularis, i.e., 30, 60, 90, and 120 days after sowing (DAS). The results of this investigation reveal that, in the earlier stages of the growth, Cu was highly accumulated in the belowground parts of the plant while little was transported to the aboveground parts. Contrastingly, at a fully mature stage of the growth (120 DAS), it was observed that the majority of Cu was transported to the aboveground parts of the plant and very little accumulated in the belowground parts. The results also show a progressive increase in Cu uptake in response to increasing Cu concentrations in the soil, suggesting that C. capsularis is a potential bio-resource for the phytoremediation of Cu in Cu-contaminated soil.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ecoenv.2019.109915DOI Listing
February 2020

Targeted mutagenesis of BnTT8 homologs controls yellow seed coat development for effective oil production in Brassica napus L.

Plant Biotechnol J 2020 05 11;18(5):1153-1168. Epub 2019 Nov 11.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.

Yellow seed is a desirable trait with great potential for improving seed quality in Brassica crops. Unfortunately, no natural or induced yellow seed germplasms have been found in Brassica napus, an important oil crop, which likely reflects its genome complexity and the difficulty of the simultaneous random mutagenesis of multiple gene copies with functional redundancy. Here, we demonstrate the first application of CRISPR/Cas9 for creating yellow-seeded mutants in rapeseed. The targeted mutations of the BnTT8 gene were stably transmitted to successive generations, and a range of homozygous mutants with loss-of-function alleles of the target genes were obtained for phenotyping. The yellow-seeded phenotype could be recovered only in targeted mutants of both BnTT8 functional copies, indicating that the redundant roles of BnA09.TT8 and BnC09.TT8b are vital for seed colour. The BnTT8 double mutants produced seeds with elevated seed oil and protein content and altered fatty acid (FA) composition without any serious defects in the yield-related traits, making it a valuable resource for rapeseed breeding programmes. Chemical staining and histological analysis showed that the targeted mutations of BnTT8 completely blocked the proanthocyanidin (PA)-specific deposition in the seed coat. Further, transcriptomic profiling revealed that the targeted mutations of BnTT8 resulted in the broad suppression of phenylpropanoid/flavonoid biosynthesis genes, which indicated a much more complex molecular mechanism underlying seed colour formation in rapeseed than in Arabidopsis and other Brassica species. In addition, gene expression analysis revealed the possible mechanism through which BnTT8 altered the oil content and fatty acid composition in seeds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/pbi.13281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152602PMC
May 2020

Antagonist effects of strains of Bacillus spp. against Rhizoctonia solani for their protection against several plant diseases: Alternatives to chemical pesticides.

C R Biol 2019 Jun - Aug;342(5-6):124-135. Epub 2019 Aug 9.

Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.

Rhizoctonia solan Kühn (teleomorph: Thanatephorus cucumeris (Frank) Donk (R. solani) is a soil-borne phytopathogenic species complex as well as a necrotic fungus that causes significant crop yield losses worldwide. Agronomic practices (crop rotation), resistant cultivars, and chemical pesticides are widely used to control R. solani. However, these practices are insufficient to control the pest. Moreover, the application of chemical pesticides is harmful to both the environment and human health. Therefore, the use of biocontrol agents (BCAs) and that of plant-growth promoting bacteria (PGPB) are considered to be potentially sustainable, cost-effective, efficient, and eco-friendly ways to control R. solani. Several microorganisms have been used as biocontrol agents (BCAs) to manage R. solani. Among these, biocontrol agents (BCAs) Bacillus spp. are used to promote plant growth. Furthermore, due to its broad range of antibiotic-producing abilities, Bacillus spp. is widely used against R. solani. In this review, current and previous studies about the ability of Bacillus spp. to control diseases caused by R. solani are reported. It also focuses on the plant-growth promotion attributes of Bacillus spp. in response to the deleterious effects of R. solani.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.crvi.2019.05.002DOI Listing
December 2019

Promoter variations in a homeobox gene, BnA10.LMI1, determine lobed leaves in rapeseed (Brassica napus L.).

Theor Appl Genet 2018 Dec 15;131(12):2699-2708. Epub 2018 Sep 15.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.

Key Message: BnA10.LMI1 positively regulates the development of leaf lobes in Brassica napus, and cis-regulatory divergences cause the different allele effects. Leaf shape is an important agronomic trait, and large variations in this trait exist within the Brassica germplasm. The lobed leaf is a unique morphological characteristic for Brassica improvement. Nevertheless, the molecular basis of leaf lobing in Brassica is poorly understood. Here, we show that an incompletely dominant locus, BnLLA10, is responsible for the lobed-leaf shape in rapeseed. A LATE MERISTEM IDENTITY1 (LMI1)-like gene (BnA10.LMI1) encoding an HD-Zip I transcription factor is the causal gene underlying the BnLLA10 locus. Sequence analysis of parental alleles revealed no sequence variations in the coding sequences, whereas abundant variations were identified in the regulatory region. Consistent with this finding, the expression levels of BnLMI1 were substantially elevated in the lobed-leaf parent compared with its near-isogenic line. The knockout mutations of BnA10.LMI1 gene were induced using the CRISPR/Cas9 system in both HY (the lobed-leaf parent) and J9707 (serrated leaf) genetic backgrounds. BnA10.LMI1 null mutations in the HY background were sufficient to produce unlobed leaves, whereas null mutations in the J9707 background showed no obvious changes in leaf shape compared with the control. Collectively, our results indicate that BnA10.LMI1 positively regulates the development of leaf lobes in B. napus, with cis-regulatory divergences causing the different allelic effects, providing new insights into the molecular mechanism of leaf lobe formation in Brassica crops.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00122-018-3184-5DOI Listing
December 2018

In vitro biological screening of a critically endangered medicinal plant, Atropa acuminata Royle Ex Lindl of north western Himalaya.

Sci Rep 2018 07 23;8(1):11028. Epub 2018 Jul 23.

Department of Agriculture, University of Swabi, Swabi, Khyber Pakhtunkhwa, Pakistan.

Atropa acuminata Royle Ex Lindl (Atropa acuminata) under tremendous threat of extinction in its natural habitat. However, the antimicrobial, antileishmanial and anticancer effects of the plant's extracts have not been reported yet. In the current study, an attempt has been made to evaluate the pharmacological potential of this plant's extracts against microbes, Leishmania and cancer. The roots, stems and leaves of Atropa acuminata were ground; then, seven different solvents were used alone and in different ratios to prepare crude extracts, which were screened for pharmacological effects. The aqueous, methanolic and ethanolic extracts of all parts carried a broad spectrum of anti-bacterial activities, while no significant activity was observed with combined solvents. Three types of cytotoxicity assays were performed, i.e., haemolytic, brine shrimp and protein kinase assays. The aqueous extract of all the parts showed significant haemolytic activity while n-hexane extracts of roots showed significant activity against brine shrimp. The acetone extracts strongly inhibited protein kinase while the methanolic extracts exhibited significant cytotoxic activity of roots and stem. The anti-leishmanial assays revealed that the methanolic extract of leaves and roots showed significant activity. These findings suggest that this plant could be a potential source of natural product based drugs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-29231-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056422PMC
July 2018

Nanosilver: new ageless and versatile biomedical therapeutic scaffold.

Int J Nanomedicine 2018 2;13:733-762. Epub 2018 Feb 2.

College of Plant Sciences and Technology.

Silver nanotechnology has received tremendous attention in recent years, owing to its wide range of applications in various fields and its intrinsic therapeutic properties. In this review, an attempt is made to critically evaluate the chemical, physical, and biological synthesis of silver nanoparticles (AgNPs) as well as their efficacy in the field of theranostics including microbiology and parasitology. Moreover, an outlook is also provided regarding the performance of AgNPs against different biological systems such as bacteria, fungi, viruses, and parasites (leishmanial and malarial parasites) in curing certain fatal human diseases, with a special focus on cancer. The mechanism of action of AgNPs in different biological systems still remains enigmatic. Here, due to limited available literature, we only focused on AgNPs mechanism in biological systems including human (wound healing and apoptosis), bacteria, and viruses which may open new windows for future research to ensure the versatile application of AgNPs in cosmetics, electronics, and medical fields.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2147/IJN.S153167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799856PMC
April 2018

Induced mutation and epigenetics modification in plants for crop improvement by targeting CRISPR/Cas9 technology.

J Cell Physiol 2018 06 4;233(6):4578-4594. Epub 2018 Jan 4.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.

Clustered regularly interspaced palindromic repeats associated protein Cas9 (CRISPR-Cas9), originally an adaptive immunity system of prokaryotes, is revolutionizing genome editing technologies with minimal off-targets in the present era. The CRISPR/Cas9 is now highly emergent, advanced, and highly specific tool for genome engineering. The technology is widely used to animal and plant genomes to achieve desirable results. The present review will encompass how CRISPR-Cas9 is revealing its beneficial role in characterizing plant genetic functions, genomic rearrangement, how it advances the site-specific mutagenesis, and epigenetics modification in plants to improve the yield of field crops with minimal side-effects. The possible pitfalls of using and designing CRISPR-Cas9 for plant genome editing are also discussed for its more appropriate applications in plant biology. Therefore, CRISPR/Cas9 system has multiple benefits that mostly scientists select for genome editing in several biological systems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jcp.26299DOI Listing
June 2018

Bacillus safensis with plant-derived smoke stimulates rice growth under saline conditions.

Environ Sci Pollut Res Int 2017 Oct 3;24(30):23850-23863. Epub 2017 Sep 3.

College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.

Salinity is a worldwide environmental problem of agricultural lands. Smoke and plant growth-promoting bacteria (PGPR) are individually used to improve plant growth, but the combined effects of these have not been studied yet under saline conditions. The combined effect of plant growth-promoting bacteria Bacillus safensis and plant-derived smoke Cymbopogon jwarancusa was studied under different salinity level as 50, 100, and 150 mM on rice (cv. Basmati-385). Smoke dilutions of C. jwarancusa (C-500 and C-1000) and bacterial culture of B. safensis were used to soak seeds for 10 h. It was observed that the salt concentration decreases the germination percentage, vegetative growth, ion contents (K and Ca), and photosynthetic pigments (Chl "a," Chl "b," and carotene) while an increase occurred in Na, total soluble protein (TSP), proline, total soluble sugar, catalase (CAT), and peroxidase (POD) contents. The combined effect of B. safensis and smoke primed seeds increased the germination percentage, seedling growth, ion contents (K, Ca), and photosynthetic pigments (Chl "a," Chl "b," carotene) and reduced the Na ion content, total soluble protein, proline content, total soluble sugar, CAT, and POD activity by lowering the drastic effect of salt stress. It was concluded that combined effect of smoke and PGPR is more effective than individual effect.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11356-017-0026-yDOI Listing
October 2017