Publications by authors named "Sunny Ahmar"

21 Publications

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Extracts of Euphorbia nivulia Buch.-Ham. showed both phytotoxic and insecticidal capacities against Lemna minor L. and Oxycarenus hyalinipennis Costa.

PLoS One 2021 30;16(4):e0250118. Epub 2021 Apr 30.

Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia.

Many phytochemicals can affect the growth and development of plants and insects which can be used as biological control agents. In this study, different concentrations of crude, hexane, chloroform, butanol, and aqueous extracts of Euphorbia nivulia Buch.-Ham., an endemic plant of the Cholistan desert in South Punjab of Pakistan, were analysed for their chemical constituents. Their various concentrations were also tested for their phytotoxic and insecticidal potential against duckweed, Lemna minor L., and the dusky cotton bug, Oxycarenus hyalinipennis Costa. various polyphenols, i.e., quercetin, gallic acid, caffeic acid, syringic acid, coumaric acid, ferulic acid, and cinnamic acid were detected in different concentrations with different solvents during the phytochemical screening of E. nivulia. In the phytotoxicity test, except for 100 μg/mL of the butanol extract gave 4.5% growth regulation, no phytotoxic lethality could be found at 10 and 100 μg/mL of all the extracts. The highest concentration, 1000 μg/mL, of the chloroform, crude, and butanol extracts showed 100, 63.1, and 27.1% of growth inhibition in duckweed, respectively. In the insecticidal bioassay, the highest O. hyalinipennis mortalities (87 and 75%) were recorded at 15% concentration of the chloroform and butanol extracts of E. nivulia. In contrast, the lower concentrations of the E. nivulia extracts caused the lower mortalities. Altogether, these findings revealed that E. nivulia chloroform extracts showed significant phytotoxicity while all the extracts showed insecticidal potential. This potential can be, further, refined to be developed for bio-control agents.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0250118PLOS
April 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

Jasmonates and Plant Salt Stress: Molecular Players, Physiological Effects, and Improving Tolerance by Using Genome-Associated Tools.

Int J Mol Sci 2021 Mar 17;22(6). Epub 2021 Mar 17.

Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca 3465548, Chile.

Soil salinity is one of the most limiting stresses for crop productivity and quality worldwide. In this sense, jasmonates (JAs) have emerged as phytohormones that play essential roles in mediating plant response to abiotic stresses, including salt stress. Here, we reviewed the mechanisms underlying the activation and response of the JA-biosynthesis and JA-signaling pathways under saline conditions in and several crops. In this sense, molecular components of JA-signaling such as MYC2 transcription factor and JASMONATE ZIM-DOMAIN (JAZ) repressors are key players for the JA-associated response. Moreover, we review the antagonist and synergistic effects between JA and other hormones such as abscisic acid (ABA). From an applied point of view, several reports have shown that exogenous JA applications increase the antioxidant response in plants to alleviate salt stress. Finally, we discuss the latest advances in genomic techniques for the improvement of crop tolerance to salt stress with a focus on jasmonates.
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http://dx.doi.org/10.3390/ijms22063082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8002660PMC
March 2021

Genome-wide association study of cyanogenic glycosides, proline, sugars, and pigments in Eucalyptus cladocalyx after 18 consecutive dry summers.

Physiol Plant 2021 Jan 28. Epub 2021 Jan 28.

Department of Food Biofunctionality, Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany.

Natural variation of cyanogenic glycosides, soluble sugars, proline, and nondestructive optical sensing of pigments (chlorophyll, flavonols, and anthocyanins) was examined in ex situ natural populations of Eucalyptus cladocalyx F. Muell. grown under dry environmental conditions in the southern Atacama Desert, Chile. After 18 consecutive dry seasons, considerable plant-to-plant phenotypic variation for all the traits was observed in the field. For example, leaf hydrogen cyanide (HCN) concentrations varied from 0 (two acyanogenic individuals) to 1.54 mg cyanide g DW. Subsequent genome-wide association study revealed associations with several genes with a known function in plants. HCN content was associated robustly with genes encoding Cytochrome P450 proteins, and with genes involved in the detoxification mechanism of HCN in cells (β-cyanoalanine synthase and cyanoalanine nitrilase). Another important finding was that sugars, proline, and pigment content were linked to genes involved in transport, biosynthesis, and/or catabolism. Estimates of genomic heritability (based on haplotypes) ranged between 0.46 and 0.84 (HCN and proline content, respectively). Proline and soluble sugars had the highest predictive ability of genomic prediction models (PA = 0.65 and PA = 0.71, respectively). PA values for HCN content and flavonols were relatively moderate, with estimates ranging from 0.44 to 0.50. These findings provide new understanding on the genetic architecture of cyanogenic capacity, and other key complex traits in cyanogenic E. cladocalyx.
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http://dx.doi.org/10.1111/ppl.13349DOI Listing
January 2021

Research advances and applications of biosensing technology for the diagnosis of pathogens in sustainable agriculture.

Environ Sci Pollut Res Int 2021 Feb 19;28(8):9002-9019. Epub 2021 Jan 19.

Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, 38000, Pakistan.

Plant diseases significantly impact the global economy, and plant pathogenic microorganisms such as nematodes, viruses, bacteria, fungi, and viroids may be the etiology for most infectious diseases. In agriculture, the development of disease-free plants is an important strategy for the determination of the survival and productivity of plants in the field. This article reviews biosensor methods of disease detection that have been used effectively in other fields, and these methods could possibly transform the production methods of the agricultural industry. The precise identification of plant pathogens assists in the assessment of effective management steps for minimization of production loss. The new plant pathogen detection methods include evaluation of signs of disease, detection of cultured organisms, or direct examination of contaminated tissues through molecular and serological techniques. Laboratory-based approaches are costly and time-consuming and require specialized skills. The conclusions of this review also indicate that there is an urgent need for the establishment of a reliable, fast, accurate, responsive, and cost-effective testing method for the detection of field plants at early stages of growth. We also summarized new emerging biosensor technologies, including isothermal amplification, detection of nanomaterials, paper-based techniques, robotics, and lab-on-a-chip analytical devices. However, these constitute novelty in the research and development of approaches for the early diagnosis of pathogens in sustainable agriculture.
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http://dx.doi.org/10.1007/s11356-021-12419-6DOI Listing
February 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

Genome-Wide Prediction of Complex Traits in Two Outcrossing Plant Species Through Deep Learning and Bayesian Regularized Neural Network.

Front Plant Sci 2020 27;11:593897. Epub 2020 Nov 27.

Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil.

Genomic selection models were investigated to predict several complex traits in breeding populations of L. and Labill. For this, the following methods of Machine Learning (ML) were implemented: (i) Deep Learning (DL) and (ii) Bayesian Regularized Neural Network (BRNN) both in combination with different hyperparameters. These ML methods were also compared with Genomic Best Linear Unbiased Prediction (GBLUP) and different Bayesian regression models [Bayes A, Bayes B, Bayes Cπ, Bayesian Ridge Regression, Bayesian LASSO, and Reproducing Kernel Hilbert Space (RKHS)]. DL models, using Rectified Linear Units (as the activation function), had higher predictive ability values, which varied from 0.27 (pilodyn penetration of 6 years old eucalypt trees) to 0.78 (flowering-related traits of maize). Moreover, the larger mini-batch size (100%) had a significantly higher predictive ability for wood-related traits than the smaller mini-batch size (10%). On the other hand, in the BRNN method, the architectures of one and two layers that used only the pureline function showed better results of prediction, with values ranging from 0.21 (pilodyn penetration) to 0.71 (flowering traits). A significant increase in the prediction ability was observed for DL in comparison with other methods of genomic prediction (Bayesian alphabet models, GBLUP, RKHS, and BRNN). Another important finding was the usefulness of DL models (through an iterative algorithm) as an SNP detection strategy for genome-wide association studies. The results of this study confirm the importance of DL for genome-wide analyses and crop/tree improvement strategies, which holds promise for accelerating breeding progress.
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http://dx.doi.org/10.3389/fpls.2020.593897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7728740PMC
November 2020

Plant-growth-promoting Bacillus and Paenibacillus species improve the nutritional status of Triticum aestivum L.

PLoS One 2020 1;15(12):e0241130. Epub 2020 Dec 1.

Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia.

Wheat is one of the best-domesticated cereal crops and one of the vital sources of nutrition for humans. An investigation was undertaken to reveal the potential of novel bio-inoculants enriching micronutrients in shoot and grains of wheat crop to eliminate the hazards of malnutrition. Sole as well as consortia inoculation of bio-inoculants significantly enhanced mineral nutrients including zinc (Zn) and iron (Fe) concentrations in shoot and grains of wheat. Various treatments of bio-inoculants increase Zn and Fe content up to 1-15% and 3-13%, respectively. Sole inoculation of Bacillus aryabhattai (S10) impressively improves the nutritious of wheat. However, the maximum increase in minerals contents of wheat was recorded by consortia inoculation of Paenibacillus polymyxa ZM27, Bacillus subtilis ZM63 and Bacillus aryabhattai S10. This treatment also showed a maximum bacterial population (18 × 104 cfu mL-1) in the rhizosphere. The consortium application of these strains showed up to a 17% increase in yield. It is evident from the results that the consortium application was more effective than sole and co-inoculation. A healthy positive correlation was found between growth, yield, and the accessibility of micronutrients to wheat crops at the harvesting stage. The present investigations revealed the significance of novel bacterial strains in improving the nutritional status of wheat crops. These strains could be used as bio-inoculants for the biofortification of wheat to combat hidden hunger in developing countries.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241130PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7707572PMC
January 2021

Genome-wide diversity analysis of TCP transcription factors revealed cases of selection from wild to cultivated barley.

Funct Integr Genomics 2021 Jan 9;21(1):31-42. Epub 2020 Nov 9.

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Plant-specific TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORS 1/2 (TCP) transcription factors have known roles in inflorescence architecture. In barley, there are two family members INTERMEDIUM-C (INT-c/HvTB1-1) and COMPOSITUM 1 (COM1/HvTCP24) which are involved in the manipulation of spike architecture, whereas the participation of TCP family genes in selection from wild (Hordeum vulgare subsp. spontaneum, Hs) to cultivated barley (Hordeum vulgare subsp. vulgare, Hv) remains poorly investigated. Here, by conducting a genome-wide survey for TCP-like sequences in publicly-released datasets, 22 HsTCP and 20 HvTCP genes encoded for mature proteins were identified and assigned into two classes (I and II) based on their functional domains and the phylogenetic analysis. Each counterpart of the orthologous gene in wild and cultivated barley usually represented a similarity on the transcriptional profile across the tissues. The diversity analysis of TCPs in 90 wild barley accessions and 137 landraces with geographically-referenced passport information revealed the detectable selection at three loci including INT-c/HvTB1-1, HvPCF2, and HvPCF8. Especially, the HvPCF8 haplotypes in cultivated barley were found correlating with their geographical collection sites. There was no difference observed in either transactivation activity in yeast or subcellular localization in Nicotiana benthamiana among these haplotypes. Nevertheless, the genome-wide diversity analysis of barley TCP genes in wild and cultivated populations provided insight for future functional characterization in plant development such as spike architecture.
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http://dx.doi.org/10.1007/s10142-020-00759-4DOI Listing
January 2021

Phytomelatonin: An overview of the importance and mediating functions of melatonin against environmental stresses.

Physiol Plant 2020 Nov 6. Epub 2020 Nov 6.

Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan.

Recently, melatonin has gained significant importance in plant research. The presence of melatonin in the plant kingdom has been known since 1995. It is a molecule that is conserved in a wide array of evolutionary distant organisms. Its functions and characteristics have been found to be similar in both plants and animals. The review focuses on the role of melatonin pertaining to physiological functions in higher plants. Melatonin regulates physiological functions regarding auxin activity, root, shoot, and explant growth, activates germination of seeds, promotes rhizogenesis (growth of adventitious and lateral roots), and holds up impelled leaf senescence. Melatonin is a natural bio-stimulant that creates resistance in field crops against various abiotic stress, including heat, chemical pollutants, cold, drought, salinity, and harmful ultra-violet radiation. The full potential of melatonin in regulating physiological functions in higher plants still needs to be explored by further research.
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http://dx.doi.org/10.1111/ppl.13262DOI Listing
November 2020

Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa.

J Genet Eng Biotechnol 2020 Oct 19;18(1):62. Epub 2020 Oct 19.

Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran.

Background: Ethylene is a gaseous plant hormone that acts as a requisite role in many aspects of the plant life cycle, and it is also a regulator of plant responses to abiotic and biotic stresses. In this study, we attempt to provide comprehensive information through analyses of existing data using bioinformatics tools to compare the identified ethylene biosynthesis genes between Arabidopsis (as dicotyledonous) and rice (as monocotyledonous).

Results: The results exposed that the Arabidopsis proteins of the ethylene biosynthesis pathway had more potential glycosylation sites than rice, and 1-aminocyclopropane-1-carboxylate oxidase proteins were less phosphorylated than 1-aminocyclopropane-1-carboxylate synthase and S-adenosylmethionine proteins. According to the gene expression patterns, S-adenosylmethionine genes were more involved in the rice-ripening stage while in Arabidopsis, ACS2, and 1-aminocyclopropane-1-carboxylate oxidase genes were contributed to seed maturity. Furthermore, the result of miRNA targeting the transcript sequences showed that ath-miR843 and osa-miR1858 play a key role to regulate the post-transcription modification of S-adenosylmethionine genes in Arabidopsis and rice, respectively. The discovered cis- motifs in the promoter site of all the ethylene biosynthesis genes of A. thaliana genes were engaged to light-induced response in the cotyledon and root genes, sulfur-responsive element, dehydration, cell cycle phase-independent activation, and salicylic acid. The ACS4 protein prediction demonstrated strong protein-protein interaction in Arabidopsis, as well as, SAM2, Os04T0578000, Os01T0192900, and Os03T0727600 predicted strong protein-protein interactions in rice.

Conclusion: In the current study, the complex between miRNAs with transcript sequences of ethylene biosynthesis genes in A. thaliana and O. sativa were identified, which could be helpful to understand the gene expression regulation after the transcription process. The binding sites of common transcription factors such as MYB, WRKY, and ABRE that control target genes in abiotic and biotic stresses were generally distributed in promoter sites of ethylene biosynthesis genes of A. thaliana. This was the first time to wide explore the ethylene biosynthesis pathway using bioinformatics tools that markedly showed the capability of the in silico study to integrate existing data and knowledge and furnish novel insights into the understanding of underlying ethylene biosynthesis pathway genes that will be helpful for more dissection.
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http://dx.doi.org/10.1186/s43141-020-00083-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7572930PMC
October 2020

Incredible Role of Osmotic Adjustment in Grain Yield Sustainability under Water Scarcity Conditions in Wheat ( L.).

Plants (Basel) 2020 Sep 15;9(9). Epub 2020 Sep 15.

Institute of Biological Sciences, University of Talca, Talca 3460000, Chile.

Interrogations of local germplasm and landraces can offer a foundation and genetic basis for drought tolerance in wheat. Potential of drought tolerance in a panel of 30 wheat genotypes including varieties, local landraces, and wild crosses were explored under drought stress (DS) and well-watered (WW) conditions. Considerable variation for an osmotic adjustment (OA) and yield components, coupled with genotype and environment interaction was observed, which indicates the differential potential of wheat genotypes under both conditions. Reduction in yield per plant (YP), thousand kernel weight (TKW), and induction of OA was detected. Correlation analysis revealed a strong positive association of YP with directly contributing yield components under both environments, indicating the impotence of these traits as a selection-criteria for the screening of drought-tolerant genotypes for drylands worldwide. Subsequently, the association of OA with TKW which contributes directly to YP, indicates that wheat attains OA to extract more water from the soil under low water-potential. Genotypes including WC-4, WC-8 and LLR-29 showed more TKW under both conditions, among them; LLR-29 also has maximum OA and batter yield comparatively. Result provides insight into the role of OA in plant yield sustainability under DS. In this study, we figure out the concept of OA and its incredible role in sustainable plant yield in wheat.
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http://dx.doi.org/10.3390/plants9091208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7569908PMC
September 2020

Comprehensive study and multipurpose role of the CLV3/ESR-related (CLE) genes family in plant growth and development.

J Cell Physiol 2021 Apr 31;236(4):2298-2317. Epub 2020 Aug 31.

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

The CLAVATA3/endosperm surrounding region-related (CLE) is one of the most important signaling peptides families in plants. These peptides signaling are common in the cell to cell communication and control various physiological and developmental processes, that is cell differentiation and proliferation, self-incompatibility, and the defense response. The CLE signaling systems are conserved across the plant kingdom but have a diverse mode of action in various developmental processes in different species. In this review, we concise various methods of peptides identification, structure, and molecular identity of the CLE family, the developmental role of CLE genes/peptides in plants, environmental stimuli, and CLE family and some other novel progress in CLE genes/peptides in various crops, and so forth. According to previous literature, about 1,628 CLE genes were identified in land plants, which deeply explained the tale of plant development. Nevertheless, some important queries need to be addressed to get clear insights into the CLE gene family in other organisms and their role in various physiological and developmental processes. Furthermore, we summarized the power of the CLE family around the environment as well as bifunctional activity and the crystal structure recognition mechanism of CLE peptides by their receptors and CLE clusters functions. We strongly believed that the discovery of the CLE family in other organisms would provide a significant breakthrough for future revolutionary and functional studies.
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http://dx.doi.org/10.1002/jcp.30021DOI Listing
April 2021

Targeted mutagenesis of EOD3 gene in Brassica napus L. regulates seed production.

J Cell Physiol 2021 Mar 25;236(3):1996-2007. Epub 2020 Aug 25.

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

Seed size and number are central to the evolutionary fitness of plants and are also crucial for seed production of crops. However, the molecular mechanisms of seed production control are poorly understood in Brassica crops. Here, we report the gene cloning, expression analysis, and functional characterization of the EOD3/CYP78A6 gene in rapeseed. BnaEOD3 has four copies located in two subgenomes, which exhibited a steady higher expression during seed development with differential expression among copies. The targeted mutations of BnaEOD3 gene were efficiently generated by stable transformation of the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat) vector. These mutations were stably transmitted to T and T generations and a large collection of homozygous mutants with combined loss-of-function alleles across four BnaEOD3 copies were created for phenotyping. All mutant T lines had shorter siliques, smaller seeds, and an increased number of seeds per silique, in which the quadrable mutants showed the most significant changes in these traits. Consequently, the seed weight per plant in the quadrable mutants increased by 13.9% on average compared with that of wild type, indicating that these BnaEOD3 copies have redundant functions in seed development in rapeseed. The phenotypes of the different allelic combinations of BnaEOD3 copies also revealed gene functional differentiation among the two subgenomes. Cytological observations indicated that the BnaEOD3 could act maternally to promote cotyledon cell expansion and proliferation to regulate seed growth in rapeseed. Collectively, our findings reveal the quantitative involvement of the different BnaEOD3 copies function in seed development, but also provided valuable resources for rapeseed breeding programs.
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http://dx.doi.org/10.1002/jcp.29986DOI Listing
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.
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http://dx.doi.org/10.3390/ijms21165665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461041PMC
August 2020

Cytological and Gene Profile Expression Analysis Reveals Modification in Metabolic Pathways and Catalytic Activities Induce Resistance in Against Iprodione Isolated From Tomato.

Int J Mol Sci 2020 Jul 9;21(14). Epub 2020 Jul 9.

Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, Agricultural College of Guangxi University, Nanning 530004, Guangxi, China.

Grey mold is one of the most serious and catastrophic diseases, causing significant yield losses in fruits and vegetables worldwide. Iprodione is a broad spectrum agrochemical used as a foliar application as well as a seed protectant against many fungal and nematode diseases of fruits and vegetables from the last thirty years. The extensive use of agrochemicals produces resistance in plant pathogens and is the most devastating issue in food and agriculture. However, the molecular mechanism (whole transcriptomic analysis) of a resistant mutant of against iprodione is still unknown. In the present study, mycelial growth, sporulation, virulence, osmotic potential, cell membrane permeability, enzymatic activity, and whole transcriptomic analysis of UV (ultraviolet) mutagenic mutant and its wild type were performed to compare the fitness. The EC (half maximal effective concentration that inhibits the growth of mycelium) value of iprodione for 112 isolates of ranged from 0.07 to 0.87 µg/mL with an average (0.47 µg/mL) collected from tomato field of Guangxi Province China. Results also revealed that, among iprodione sensitive strains, only B67 strain induced two mutants, M0 and M1 after UV application. The EC of these induced mutants were 1025.74 μg/mL and 674.48 μg/mL, respectively, as compared to its wild type 1.12 μg/mL. Furthermore, mutant M0 showed higher mycelial growth sclerotia formation, virulence, and enzymatic activity than wild type W0 and M1 on potato dextrose agar (PDA) medium. The gene in the mutant M0 replaced TTC and GAT codon at position 593 and 599 by TTA and GAA, resulting in replacement of phenyl alanine into leucine (transversion C/A) and aspartic acid into glutamic acid (transversion T/C) respectively. In contrast, in gene, GAT codon at position 646 is replaced by AAT and aspartic acid converted into asparagine (transition G/A). RNA sequencing of the mutant and its wild type was performed without (M0, W0) and with iprodione treatment (M-ipro, W-ipro). The differential gene expression (DEG) identified 720 unigenes in mutant M-ipro than W-ipro after iprodione treatment (FDR ≤ 0.05 and log2FC ≥ 1). Seven DEGs were randomly selected for quantitative real time polymerase chain reaction to validate the RNA sequencing genes expression (log fold 2 value). The gene ontology (GO) enrichment and Kyoto encyclopedia genes and genomes (KEGG) pathway functional analyses indicated that DEG's mainly associated with lysophopholipase, carbohydrate metabolism, amino acid metabolism, catalytic activity, multifunctional genes (MFO), glutathione-S transferase (GST), drug sensitivity, and cytochrome P450 related genes are upregulated in mutant type (M0, M-ipro) as compared to its wild type (W0, W-ipro), may be related to induce resistant in mutants of against iprodione.
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http://dx.doi.org/10.3390/ijms21144865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402349PMC
July 2020

Identification of QTLs Containing Resistance Genes for Sclerotinia Stem Rot in Using Comparative Transcriptomic Studies.

Front Plant Sci 2020 10;11:776. Epub 2020 Jun 10.

National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.

Sclerotinia stem rot is a major disease in that causes yield losses of 10-20% and reaching 80% in severely infected fields. SSR not only causes yield reduction but also causes low oil quality by reducing fatty acid content. There is a need to identify resistant genetic sources with functional significance for the breeding of SSR-resistant cultivars. In this study, we identified 17 QTLs involved in SSR resistance in three different seasons using SNP markers and disease lesion development after artificial inoculation. There were no common QTLs in all 3 years, but there were three QTLs that appeared in two seasons covering all seasons with a shared QTL. The QTLs identified in the 2 years were , and with phenotypic effect variances of 14.75 and 11.57% for , 7.49 and 10.38% for and 7.73 and 6.81% for in their 2 years, respectively. The flowering time was also found to have a negative correlation with disease resistance, i.e., early-maturing lines were more susceptible to disease. The stem width has shown a notably weak effect on disease development, causing researchers to ignore its effect. Given that flowering time is an important factor in disease resistance, we used comparative RNA-sequencing analysis of resistant and susceptible lines with consistent performance in 3 years with almost the same flowering time to identify the resistance genes directly involved in resistance within the QTL regions. Overall, there were more genes differentially expressed in resistant lines 19,970 than in susceptible lines 3936 compared to their mock-inoculated lines, demonstrating their tendency to cope with disease. We identified 36 putative candidate genes from the resistant lines that were upregulated in resistant lines compared to resistant mock and susceptible lines that might be involved in resistance to SSR.
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http://dx.doi.org/10.3389/fpls.2020.00776DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325899PMC
June 2020

Conventional and Molecular Techniques from Simple Breeding to Speed Breeding in Crop Plants: Recent Advances and Future Outlook.

Int J Mol Sci 2020 Apr 8;21(7). Epub 2020 Apr 8.

Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.

In most crop breeding programs, the rate of yield increment is insufficient to cope with the increased food demand caused by a rapidly expanding global population. In plant breeding, the development of improved crop varieties is limited by the very long crop duration. Given the many phases of crossing, selection, and testing involved in the production of new plant varieties, it can take one or two decades to create a new cultivar. One possible way of alleviating food scarcity problems and increasing food security is to develop improved plant varieties rapidly. Traditional farming methods practiced since quite some time have decreased the genetic variability of crops. To improve agronomic traits associated with yield, quality, and resistance to biotic and abiotic stresses in crop plants, several conventional and molecular approaches have been used, including genetic selection, mutagenic breeding, somaclonal variations, whole-genome sequence-based approaches, physical maps, and functional genomic tools. However, recent advances in genome editing technology using programmable nucleases, clustered regularly interspaced short palindromic repeats (CRISPR), and CRISPR-associated (Cas) proteins have opened the door to a new plant breeding era. Therefore, to increase the efficiency of crop breeding, plant breeders and researchers around the world are using novel strategies such as speed breeding, genome editing tools, and high-throughput phenotyping. In this review, we summarize recent findings on several aspects of crop breeding to describe the evolution of plant breeding practices, from traditional to modern speed breeding combined with genome editing tools, which aim to produce crop generations with desired traits annually.
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http://dx.doi.org/10.3390/ijms21072590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7177917PMC
April 2020

An Overview of Hazardous Impacts of Soil Salinity in Crops, Tolerance Mechanisms, and Amelioration through Selenium Supplementation.

Int J Mol Sci 2019 Dec 24;21(1). Epub 2019 Dec 24.

Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan.

Soil salinization is one of the major environmental stressors hampering the growth and yield of crops all over the world. A wide spectrum of physiological and biochemical alterations of plants are induced by salinity, which causes lowered water potential in the soil solution, ionic disequilibrium, specific ion effects, and a higher accumulation of reactive oxygen species (ROS). For many years, numerous investigations have been made into salinity stresses and attempts to minimize the losses of plant productivity, including the effects of phytohormones, osmoprotectants, antioxidants, polyamines, and trace elements. One of the protectants, selenium (Se), has been found to be effective in improving growth and inducing tolerance against excessive soil salinity. However, the in-depth mechanisms of Se-induced salinity tolerance are still unclear. This review refines the knowledge involved in Se-mediated improvements of plant growth when subjected to salinity and suggests future perspectives as well as several research limitations in this field.
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http://dx.doi.org/10.3390/ijms21010148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981449PMC
December 2019

Appraising growth, oxidative stress and copper phytoextraction potential of flax (Linum usitatissimum L.) grown in soil differentially spiked with copper.

J Environ Manage 2020 Mar 19;257:109994. Epub 2019 Dec 19.

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

Flax (Linum usitatissimum L.) is one of the oldest predominant industrial crops grown for seed, oil and fiber. The present study was executed to evaluate the morpho-physiological traits, biochemical responses, gas exchange parameters and phytoextraction potential of flax raised in differentially copper (Cu) spiked soil viz (0, 200, 400 and 600 mg Cu kg soil) under greenhouse pot experiment. The results revealed that flax plants were able to grow up to 400 mg kg Cu level without showing significant growth inhabitation while, further inference of Cu (600 mg kg) in the soil prominently inhibited flax growth and biomass accumulation. Compared to the control, contents of proline and malondialdehyde (MDA) were increased by 160.0% and 754.1% accordingly, at 600 mg Cu kg soil level. The Cu-induced oxidative stress was minimized by the enhanced activities of superoxide dismutase (SOD) by 189.2% and guaiacol peroxidase (POD) by 300.8% in the leaves of flax at 600 mg Cu kg soil level, compared to the untreated control. The plant Cu concentration was determined at 35, 70, 105 and 140 days after sowing (DAS) and results depicted that 16.9 times higher Cu concentration was accumulated in flax roots while little (14.9 times) was transported to the shoots at early stage of growth, i.e. 35 DAS. While at 140 DAS, Cu was highly (21.7 times) transported to the shoots while, only 12.3 times Cu was accumulated in the roots at 600 mg Cu kg soil level, compared to control. Meanwhile, Cu uptake by flax was boosted up to 253 mg kg from the soil and thereby extracted 43%, 39% and 41% of Cu at 200, 400 and 600 mg Cu kg soil level, compared to initial Cu concentration. Therefore, study concluded that flax has a great potential to accumulate high concentration of Cu in its shoots and can be utilized as phytoremediation material when grown in Cu contaminated soils.
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http://dx.doi.org/10.1016/j.jenvman.2019.109994DOI Listing
March 2020

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