Publications by authors named "Sajid Fiaz"

13 Publications

  • Page 1 of 1

Characterization of Vascular plant One-Zinc finger (VOZ) in soybean (Glycine max and Glycine soja) and their expression analyses under drought condition.

PLoS One 2021 2;16(7):e0253836. Epub 2021 Jul 2.

Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China.

Vascular plant one-zinc-finger (VOZ) transcription factors regulate plant growth and development under drought conditions. Six VOZ transcription factors encoding genes exist in soybean genome (both in Glycine max and Glycine soja). Herein, GmVOZs and GsVOZs were identified through in silico analysis and characterized with different bioinformatics tools and expression analysis. Phylogenetic analysis classified VOZ genes in four groups. Sequence logos analysis among G. max and G. soja amino acid residues revealed higher conservation. Presence of stress related cis-elements in the upstream regions of GmVOZs and GsVOZs highlights their role in tolerance against abiotic stresses. The collinearity analysis identified 14 paralogous/orthologous gene pairs within and between G. max and G. soja. The Ka/Ks values showed that soybean VOZ genes underwent selection pressure with limited functional deviation arising from whole genome and segmental duplication. The GmVOZs and GsVOZs were found to express in roots and leaves at seedling stage. The qRT-PCR revealed that GmVOZs and GsVOZs transcripts can be regulated by abiotic stresses such as polyethylene glycol (PEG). The findings of this study will provide a reference to decipher physiological and molecular functions of VOZ genes in soybean.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0253836PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8253436PMC
July 2021

Exploration of Epigenetics for Improvement of Drought and Other Stress Resistance in Crops: A Review.

Plants (Basel) 2021 Jun 16;10(6). Epub 2021 Jun 16.

Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.

Crop plants often have challenges of biotic and abiotic stresses, and they adapt sophisticated ways to acclimate and cope with these through the expression of specific genes. Changes in chromatin, histone, and DNA mostly serve the purpose of combating challenges and ensuring the survival of plants in stressful environments. Epigenetic changes, due to environmental stress, enable plants to remember a past stress event in order to deal with such challenges in the future. This heritable memory, called "plant stress memory", enables plants to respond against stresses in a better and efficient way, not only for the current plant in prevailing situations but also for future generations. Development of stress resistance in plants for increasing the yield potential and stability has always been a traditional objective of breeders for crop improvement through integrated breeding approaches. The application of epigenetics for improvements in complex traits in tetraploid and some other field crops has been unclear. An improved understanding of epigenetics and stress memory applications will contribute to the development of strategies to incorporate them into breeding for complex agronomic traits. The insight in the application of novel plant breeding techniques (NPBTs) has opened a new plethora of options among plant scientists to develop germplasms for stress tolerance. This review summarizes and discusses plant stress memory at the intergenerational and transgenerational levels, mechanisms involved in stress memory, exploitation of induced and natural epigenetic changes, and genome editing technologies with their future possible applications, in the breeding of crops for abiotic stress tolerance to increase the yield for zero hunger goals achievement on a sustainable basis in the changing climatic era.
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http://dx.doi.org/10.3390/plants10061226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8235456PMC
June 2021

Advantage of Nanotechnology-Based Genome Editing System and Its Application in Crop Improvement.

Front Plant Sci 2021 28;12:663849. Epub 2021 May 28.

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

Agriculture is an important source of human food. However, current agricultural practices need modernizing and strengthening to fulfill the increasing food requirements of the growing worldwide population. Genome editing (GE) technology has been used to produce plants with improved yields and nutritional value as well as with higher resilience to herbicides, insects, and diseases. Several GE tools have been developed recently, including clustered regularly interspaced short palindromic repeats (CRISPR) with nucleases, a customizable and successful method. The main steps of the GE process involve introducing transgenes or CRISPR into plants via specific gene delivery systems. However, GE tools have certain limitations, including time-consuming and complicated protocols, potential tissue damage, DNA incorporation in the host genome, and low transformation efficiency. To overcome these issues, nanotechnology has emerged as a groundbreaking and modern technique. Nanoparticle-mediated gene delivery is superior to conventional biomolecular approaches because it enhances the transformation efficiency for both temporal (transient) and permanent (stable) genetic modifications in various plant species. However, with the discoveries of various advanced technologies, certain challenges in developing a short-term breeding strategy in plants remain. Thus, in this review, nanobased delivery systems and plant genetic engineering challenges are discussed in detail. Moreover, we have suggested an effective method to hasten crop improvement programs by combining current technologies, such as speed breeding and CRISPR/Cas, with nanotechnology. The overall aim of this review is to provide a detailed overview of nanotechnology-based CRISPR techniques for plant transformation and suggest applications for possible crop enhancement.
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http://dx.doi.org/10.3389/fpls.2021.663849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8194497PMC
May 2021

In Response to Abiotic Stress, DNA Methylation Confers EpiGenetic Changes in Plants.

Plants (Basel) 2021 May 30;10(6). Epub 2021 May 30.

Gansu Provincial Key Laboratory of Aridland Crop Science; Department of Crop Genetics & Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.

Epigenetics involves the heritable changes in patterns of gene expression determined by developmental and abiotic stresses, i.e., drought, cold, salinity, trace metals, and heat. Gene expression is driven by changes in DNA bases, histone proteins, the biogenesis of ncRNA, and changes in the nucleotide sequence. To cope with abiotic stresses, plants adopt certain changes driven by a sophisticated biological system. DNA methylation is a primary mechanism for epigenetic variation, which can induce phenotypic alterations in plants under stress. Some of the stress-driven changes in plants are temporary, while some modifications may be stable and inheritable to the next generations to allow them to cope with such extreme stress challenges in the future. In this review, we discuss the pivotal role of epigenetically developed phenotypic characteristics in plants as an evolutionary process participating in adaptation and tolerance responses to abiotic and biotic stresses that alter their growth and development. We emphasize the molecular process underlying changes in DNA methylation, differential variation for different species, the roles of non-coding RNAs in epigenetic modification, techniques for studying DNA methylation, and its role in crop improvement in tolerance to abiotic stress (drought, salinity, and heat). We summarize DNA methylation as a significant future research priority for tailoring crops according to various challenging environmental issues.
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http://dx.doi.org/10.3390/plants10061096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8227271PMC
May 2021

Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security.

Int J Mol Sci 2021 May 25;22(11). Epub 2021 May 25.

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

A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from and 1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.
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http://dx.doi.org/10.3390/ijms22115585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8197453PMC
May 2021

Novel plant breeding techniques to advance nitrogen use efficiency in rice: A review.

GM Crops Food 2021 May 25:1-20. Epub 2021 May 25.

College of Khurma, Taif University, Taif, Saudi Arabia.

Recently, there has been a remarkable increase in rice production owing to genetic improvement and increase in application of synthetic fertilizers. For sustainable agriculture, there is dire need to maintain a balance between profitability and input cost. To meet the steady growing demands of the farming community, researchers are utilizing all available resources to identify nutrient use efficient germplasm, but with very little success. Therefore, it is essential to understand the underlying genetic mechanism controlling nutrients efficiency, with the nitrogen use efficiency (NUE) being the most important trait. Information regarding genetic factors controlling nitrogen (N) transporters, assimilators, and remobilizers can help to identify candidate germplasms via high-throughput technologies. Large-scale field trials have provided morphological, physiological, and biochemical trait data for the detection of genomic regions controlling NUE. The functional aspects of these attributes are time-consuming, costly, labor-intensive, and less accurate. Therefore, the application of novel plant breeding techniques (NPBTs) with context to genome engineering has opened new avenues of research for crop improvement programs. Most recently, genome editing technologies (GETs) have undergone enormous development with various versions from Cas9, Cpf1, base, and prime editing. These GETs have been vigorously adapted in plant sciences for novel trait development to insure food quantity and quality. Base editing has been successfully applied to improve NUE in rice, demonstrating the potential of GETs to develop germplasms with improved resource use efficiency. NPBTs continue to face regulatory setbacks in some countries due to genome editing being categorized in the same category as genetically modified (GM) crops. Therefore, it is essential to involve all stakeholders in a detailed discussion on NPBTs and to formulate uniform policies tackling biosafety, social, ethical, and environmental concerns. In the current review, we have discussed the genetic mechanism of NUE and NPBTs for crop improvement programs with proof of concepts, transgenic and GET application for the development of NUE germplasms, and regulatory aspects of genome edited crops with future directions considering NUE.
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http://dx.doi.org/10.1080/21645698.2021.1921545DOI Listing
May 2021

COVID-19 and Nanoscience in the Developing World: Rapid Detection and Remediation in Wastewater.

Nanomaterials (Basel) 2021 Apr 12;11(4). Epub 2021 Apr 12.

Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.

Given the known presence of SARS-Cov-2 in wastewater, stemming disease spread in global regions where untreated effluent in the environment is common will experience additional pressure. Though development and preliminary trials of a vaccine against SARS-CoV-2 have been launched in several countries, rapid and effective alternative tools for the timely detection and remediation of SARS-CoV-2 in wastewater, especially in the developing countries, is of paramount importance. Here, we propose a promising, non-invasive technique for early prediction and targeted detection of SARS-CoV-2 to prevent current and future outbreaks. Thus, a combination of nanotechnology with wastewater-based epidemiology and artificial intelligence could be deployed for community-level wastewater virus detection and remediation.
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http://dx.doi.org/10.3390/nano11040991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8069490PMC
April 2021

Identification, methylation profiling, and expression analysis of stress-responsive cytochrome P450 genes in rice under abiotic and phytohormones stresses.

GM Crops Food 2021 Apr 20:1-13. Epub 2021 Apr 20.

College of Economics and Management, Kunming University, Kunming China.

The cytochrome P450 (CYP) is a large and complex eukaryotic gene superfamily with enzymatic activities involved in several physiological and regulatory processes. As an objective, an genome-wide DNA methylation (5mC) analysis was performed in rice ( cv. Zhonghua11), and the epigenetic role of CYPs in two abiotic stresses was observed. Being a stable representative mark, DNA-methylation alters the gene expression under stressful environmental conditions. Rice plants under salinity and drought stresses were analyzed through MeDIP-chip hybridization, and 14 unique genes of the CYP family were identified in the rice genome with varying degrees of methylation. The gene structure, promoter sequences, and phylogenetic analysis were performed. Furthermore, the responses of CYPs to various abiotic stresses, including salinity, drought, and cold were revealed. Similarly, the expression profile of potential CYPs was also investigated under various phytohormone stresses, which revealed the potential involvement of CYPs to hormone regulations. Overall, the current study provides evidence for CYP's stress regulation and fundamental for further characterization and understanding their epigenetic roles in gene expression regulation and environmental stress regulation in higher plants.
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http://dx.doi.org/10.1080/21645698.2021.1908813DOI Listing
April 2021

Haplotype- and SNP-Based GWAS for Growth and Wood Quality Traits in Trees under Arid Conditions.

Plants (Basel) 2021 Jan 13;10(1). Epub 2021 Jan 13.

Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile.

The agricultural and forestry productivity of Mediterranean ecosystems is strongly threatened by the adverse effects of climate change, including an increase in severe droughts and changes in rainfall distribution. In the present study, we performed a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) and haplotype blocks associated with the growth and wood quality of , a tree species suitable for low-rainfall sites. The study was conducted in a progeny-provenance trial established in an arid site with Mediterranean patterns located in the southern Atacama Desert, Chile. A total of 87 SNPs and 3 haplotype blocks were significantly associated with the 6 traits under study (tree height, diameter at breast height, slenderness coefficient, first bifurcation height, stem straightness, and pilodyn penetration). In addition, 11 loci were identified as pleiotropic through Bayesian multivariate regression and were mainly associated with wood hardness, height, and diameter. In general, the GWAS revealed associations with genes related to primary metabolism and biosynthesis of cell wall components. Additionally, associations coinciding with stress response genes, such as and , were detected. The findings of this study provide valuable information regarding genetic control of morphological traits related to adaptation to arid environments.
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http://dx.doi.org/10.3390/plants10010148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7828368PMC
January 2021

Apomixis and strategies to induce apomixis to preserve hybrid vigor for multiple generations.

GM Crops Food 2021 Jan;12(1):57-70

Department of Agricultural Engineering, Khawaja Fareed University of Engineering and Information Technology , Rahim Yar Khan, Pakistan.

Hybrid seeds of several important crops with supreme qualities including yield, biotic and abiotic stress tolerance have been cultivated for decades. Thus far, a major challenge with hybrid seeds is that they do not have the ability to produce plants with the same qualities over subsequent generations. Apomixis, an asexual mode of reproduction by avoiding meiosis, exists naturally in flowering plants, and ultimately leads to seed production. Apomixis has the potential to preserve hybrid vigor for multiple generations in economically important plant genotypes. The evolution and genetics of asexual seed production are unclear, and much more effort will be required to determine the genetic architecture of this phenomenon. To fix hybrid vigor, synthetic apomixis has been suggested. The development of (mitosis instead of meiosis) genotypes has been utilized for clonal gamete production. However, the identification and parental origin of genes responsible for synthetic apomixis are little known and need further clarification. Genome modifications utilizing genome editing technologies (GETs), such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (cas), a reverse genetics tool, have paved the way toward the utilization of emerging technologies in plant molecular biology. Over the last decade, several genes in important crops have been successfully edited. The vast availability of GETs has made functional genomics studies easy to conduct in crops important for food security. Disruption in the expression of genes specific to egg cell () through the CRISPR/Cas genome editing system promotes the induction of haploid seed, whereas triple knockout of the () genes , and cause embryo arrest and abortion, which can be fully rescued by male-transmitted . The establishment of synthetic apomixis by engineering the genotype by genome editing of expression or disruption of leads to clonal seed production and heritability for multiple generations. In the present review, we discuss current developments related to the use of CRISPR/Cas technology in plants and the possibility of promoting apomixis in crops to preserve hybrid vigor. In addition, genetics, evolution, epigenetic modifications, and strategies for genotype development are discussed in detail.
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http://dx.doi.org/10.1080/21645698.2020.1808423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7553744PMC
January 2021

Population genomics of honey bees reveals a selection signature indispensable for royal jelly production.

Mol Cell Probes 2020 08 24;52:101542. Epub 2020 Feb 24.

College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China. Electronic address:

In order to interpret the molecular mechanisms that modulating the organism variations and selection signatures to drive adaptive evolutionary changes are indispensable goals in the new evolutionary ecological genetics. Here, we identified the gene locus associated to royal jelly production through whole-genome sequencing of the DNA from eight populations of honeybees. The analysis of the samples was composed of 120 individuals and each pointed extremely opposite trait values for a given phenotype. We identified functional single nucleotide polymorphisms (SNPs) candidate that might be essential in regulating the phenotypic traits of honeybee populations. Moreover, selection signatures were investigated using pooling sequencing of eight distinct honeybee populations, and the results provided the evidence of signatures of recent selection among populations under different selection objectives. Furthermore, gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that selected genes were potentially involved in several biological processes and molecular functioning, which could directly or indirectly influence the production of royal jelly. Our findings can be used to understand the genomic signatures, as well as implicate a profound glance on genomic regions that control the production trait of royal jelly in honey bees.
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http://dx.doi.org/10.1016/j.mcp.2020.101542DOI Listing
August 2020

Generation of a new thermo-sensitive genic male sterile rice line by targeted mutagenesis of TMS5 gene through CRISPR/Cas9 system.

BMC Plant Biol 2019 Mar 20;19(1):109. Epub 2019 Mar 20.

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.

Background: Two-line hybrid rice with high yield potential is increasingly popular and the photo- and temperature-sensitive male sterile line is one of the basic components for two-line hybrid rice breeding. The development of male sterile lines through conventional breeding is a lengthy and laborious process, whereas developing thermo-sensitive genic male sterile (TGMS) lines for two-line hybrid breeding by editing a temperature-sensitivity gene by CRISPR/Cas9 is efficient and convenient.

Results: Here, thermo-sensitive genic male sterility (TGMS) was induced by employing the CRISPR/Cas9 gene editing technology to modify the gene TMS5. Two TGMS mutants, tms5-1 and tms5-2, both lacking any residual T-DNA, were generated in the indica rice cultivar Zhongjiazao17 (cv. YK17) background. When grown at a sub-optimal temperature (22 °C), both mutants produced viable pollen and successfully produced grain through self-fertilization, but at temperatures 24 and 26 °C, their pollen was sterile and no grain was set. F hybrids derived from the crosses between YK17S (tms5-1) and three different restorer lines outperformed both parental lines with respect to grain yield and related traits.

Conclusion: The YK17S generated by CRISPR/Cas9 system was proved to be a new TGMS line with superior yield potential and can be widely utilized in two-line hybrid breeding of indica rice.
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http://dx.doi.org/10.1186/s12870-019-1715-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425558PMC
March 2019

Applications of the CRISPR/Cas9 System for Rice Grain Quality Improvement: Perspectives and Opportunities.

Int J Mol Sci 2019 Feb 19;20(4). Epub 2019 Feb 19.

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.

Grain quality improvement is a key target for rice breeders, along with yield. It is a multigenic trait that is simultaneously influenced by many factors. Over the past few decades, breeding for semi-dwarf cultivars and hybrids has significantly contributed to the attainment of high yield demands but reduced grain quality, which thus needs the attention of researchers. The availability of rice genome sequences has facilitated gene discovery, targeted mutagenesis, and revealed functional aspects of rice grain quality attributes. Some success has been achieved through the application of molecular markers to understand the genetic mechanisms for better rice grain quality; however, researchers have opted for novel strategies. Genomic alteration employing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) for reverse genetics has opened new avenues of research in the life sciences, including for rice grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting. Over the past few years many genes that are related to various aspects of rice grain quality have been successfully edited via CRISPR/Cas9 technology. Interestingly, studies on functional genomics at larger scales have become possible because of the availability of GETs. In this review, we discuss the progress made in rice by employing the CRISPR/Cas9 editing system and its eminent applications. We also elaborate possible future avenues of research with this system, and our understanding regarding the biological mechanism of rice grain quality improvement.
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http://dx.doi.org/10.3390/ijms20040888DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6412304PMC
February 2019
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