Epigenetic variation as a new plant breeding tool : A review

Publisher Copyright: © 2022 The Author(s)Epigenetic variations are inherited or uninherited effects that occur beyond the DNA sequence of an individual. However, DNA sequence has a critical role in shaping epigenetic variation. The great diversity of epigenetic markers confers an advantage of various uses without interrupting its highly environmental independence. The epigenetic effects are highlighted by many vital events, especially the regulation of gene expression in hybrid vigor and inbreeding depression, even in the absence of genetic diversity. However, various stress genes can include many repeats that undergo alternately methylation and demethylation states to regulate gene expression positively or negatively. After all the arguments raised on the genetic basis of hybrid vigor in its both traditional and molecular aspects, the term ``epigenome" strongly emerged as one of the main causes of performance deviation among offspring. These include both histone and DNA biochemical modifications, which play a key role during successive stages of development and differentiation in addition to the regulation of gene expression in response to biotic and abiotic stresses. Evidence has shown a correlation between unique DNA methylation and heterosis in many plant species as well as between inbreeding and the sharp decline in fitness of most naturally crosspollinated species. Although detailed molecular mechanisms laying behind many of these plant breeding aspects remain little understood, epigenetics has provided some explanations. (c) 2022 The Author(s). Published by Elsevier B.V. on behalf of King Saud University.Peer reviewe

Investigation and Expression Analysis of R2R3-MYBs and Anthocyanin Biosynthesis-Related Genes during Seed Color Development of Common Bean (Phaseolus vulgaris)

Anthocyanins are responsible for the coloration of common bean seeds, and their accumulation is positively correlated with the expression level of anthocyanin biosynthetic genes. The MBW (MYB-bHLH-WD40) complex is thought to regulate the expression of these genes, and MYB proteins, which are a key factor in activating anthocyanin pathway genes, have been identified in several plants. This study demonstrated gene structures, chromosomal placements, gene duplications of R2R3-MYBs, miRNAs associated with R2R3-MYBs, and the interaction of these genes with other flavonoid regulatory genes. qRT-PCR was used to investigate the role of specific R2R3-MYBs and flavonoid genes in common bean seed color development. As a result of a comprehensive analysis with the help of in silico tools, we identified 160 R2R3-MYB genes in the common bean genome. We divided these genes into 16 classes on the basis of their intron-exon and motif structures. Except for three, the rest of the common bean R2R3-MYB members were distributed to all chromosomes with different densities, primarily located on chromosomes 3 and 8. We identified a total of 44 duplicated gene pairs dispersed across 11 chromosomes and evolved under purifying selection (Ka/Ks  <  1), 19 of which were derived from a whole-genome duplication. Our research uncovered 25 putative repressor PvMYB proteins that contain the EAR motif. Additionally, fifty different cis-regulatory elements regulated by light, stress, and hormone were identified. Within the genome of the common bean, we discovered a total of 36 microRNAs that target a total of 72 R2R3-MYB transcripts. The effect of 16 R2R3-MYB genes and 16 phenylpropanoid pathway genes, selected on the basis of their interaction in the protein-protein interaction map, playing role in the regulation of seed coat color development was evaluated using qRT-PCR in 5 different tissues at different developmental stages. The results revealed that these specific genes have different expression levels during different developmental periods, with higher levels in the pod filling and early pod stages than in the rest of the developmental periods. Furthermore, it was shown that PvTT8 (bHLH), PvTT2 (PvMYB42), PvMYB113, PvTTG1, and PvWD68 genes have effects on the regulation of seed coat color. The findings of this study, which is the first to use whole-genome analysis to identify and characterize the R2R3-MYB genes in common bean, may serve as a reference for future functional research in the legume

Investigation and Expression Analysis of R2R3-MYBs and Anthocyanin Biosynthesis-Related Genes during Seed Color Development of Common Bean (Phaseolus vulgaris)

Anthocyanins are responsible for the coloration of common bean seeds, and their accumulation is positively correlated with the expression level of anthocyanin biosynthetic genes. The MBW (MYB-bHLH-WD40) complex is thought to regulate the expression of these genes, and MYB proteins, which are a key factor in activating anthocyanin pathway genes, have been identified in several plants. This study demonstrated gene structures, chromosomal placements, gene duplications of R2R3-MYBs, miRNAs associated with R2R3-MYBs, and the interaction of these genes with other flavonoid regulatory genes. qRT-PCR was used to investigate the role of specific R2R3-MYBs and flavonoid genes in common bean seed color development. As a result of a comprehensive analysis with the help of in silico tools, we identified 160 R2R3-MYB genes in the common bean genome. We divided these genes into 16 classes on the basis of their intron-exon and motif structures. Except for three, the rest of the common bean R2R3-MYB members were distributed to all chromosomes with different densities, primarily located on chromosomes 3 and 8. We identified a total of 44 duplicated gene pairs dispersed across 11 chromosomes and evolved under purifying selection (Ka/Ks  <  1), 19 of which were derived from a whole-genome duplication. Our research uncovered 25 putative repressor PvMYB proteins that contain the EAR motif. Additionally, fifty different cis-regulatory elements regulated by light, stress, and hormone were identified. Within the genome of the common bean, we discovered a total of 36 microRNAs that target a total of 72 R2R3-MYB transcripts. The effect of 16 R2R3-MYB genes and 16 phenylpropanoid pathway genes, selected on the basis of their interaction in the protein-protein interaction map, playing role in the regulation of seed coat color development was evaluated using qRT-PCR in 5 different tissues at different developmental stages. The results revealed that these specific genes have different expression levels during different developmental periods, with higher levels in the pod filling and early pod stages than in the rest of the developmental periods. Furthermore, it was shown that PvTT8 (bHLH), PvTT2 (PvMYB42), PvMYB113, PvTTG1, and PvWD68 genes have effects on the regulation of seed coat color. The findings of this study, which is the first to use whole-genome analysis to identify and characterize the R2R3-MYB genes in common bean, may serve as a reference for future functional research in the legume

Green nanotechnology for plant bacterial diseases management in cereal crops: a review on metal-based nanoparticles

Cereals are an important source of nutrients for animals. Several diseases cause severe yield loss in cereal crops. Bacterial diseases result in varying yield losses across cereals: Wheat (5-40%), maize (15-98.9%), rice (20-70%), pearl millet (3-35%), and oats (15-49%). Diseases may be bacterial diseases, fungal or viral. Bacterial diseases are traditionally treated by pesticides. Chemically synthesized pesticides are toxic and hazardous to the environment. Nanotechnology is emerging and novel field for agriculture, especially in plant pathology as a strong antimicrobial agent. Nanoparticles have been synthesized in various ways i.e., biological, physical, and chemical methods. Chemical and physical methods of nanoparticles are costly and toxic to the environment. The biological method for the synthesis of nanoparticles is eco-friendly and economical. Microorganisms or plant extracts are used for metal nanoparticle synthesis. The application of nanoparticles in agriculture has a wide scope and it can bring nano-revolution. This review summarizes the antibacterial activity of biosynthesized metal nanoparticles and their role in bacterial disease management of cereals

Biochar a promising amendment to mitigate the drought stress in plants: review and future prospective

Drought stress (DS) is one of the most destructive abiotic stresses that negatively affects plant growth, and yield. The intensity of DS is continuously increasing due rapid of water sources, less rainfall, and an increase in global warming. The world’s population is increasing at an alarming rate which needs a substantial increase in crop production to meet global food needs. Therefore, in this context, we must have to increase crop production in the scenarios of rapid climate change and increasing intensity of abiotic stresses. Globally, different measures are used to mitigate the adverse impacts of DS, recently biochar (BC) has emerged as an excellent soil amendment to mitigate the toxic effects of DS and improve crop production. The application maintains membrane integrity, plant water relations, nutrient homeostasis, photosynthetic performance, hormonal balance and osmolytes accumulation, and gene expression thereby improving plant performance under DS. Moreover, BC application under DS also improves soil organic matter, water holding capacity, soil structure stability, and activity of beneficial microbes which can improve the plant performance under DS. In the present review different mechanisms through which BC mitigates the adverse impacts of DS on plants are discussed. This review provides new suggestions on the role of BC in mitigating the adverse impacts of DS

Drought stress-induced modification of morpho-anatomical and yield attributes of mung bean associated with the application of silicon and Moringa leaf extract

Mung bean (Vigna radiata) is the rich source of fiber and essential nutrients. They play a vital role in sustainable agriculture due to their ability to fix nitrogen in the soil and enhance soil fertility. Drought is characterized by limited water resources and severe arid climatic conditions, notably impair crop growth and yield. In the current experiment, two genotypes, Azri-M 2006 and NM-92, were studied against drought stress that was applied as 2 days and 4 days irrigation gap per week. Foliar application of magnesium-silicate (20 ppm and 30 ppm concentrations) and Moringa leaf extract (30% v/v solution) was applied as treatments. The results from the experiment morphology anatomical and yield components were recorded according to the prescribed methods. The result revealed that drought stress reduced the growth of plant. Foliar application of 30 ppm silicon against drought stress showed a highly significant (p&lt;0.001) result compared with control group. Morphology parameters, including shoot and root length, shoot and root fresh weight, root dry weight, leaf area, leaf number, the anatomical structure included (stem epidermis, cortex, and stem vascular bundles,) and also yield components (pod length, and seed numbers). In contrast, MLE (30%) showed a significant impact (p&lt;0.01) on leaf lamina thickness (Leaf anatomical parameters; midrib xylem and phloem, number of stomata on the adaxial and abaxial surface) and yield components included (100-grain weight, grains weight per plant, and numbers of pods,). The overall impact of 30 ppm Si was 39.9% more positive on Azri-M2006 than the NM-92 against the drought stress. The 30-ppm silicon and 30% MLE showed 90% similar results in all studied parameters. This study confirms that 30% MLE could be recommended to farmers to improve productivity under arid conditions than the silicon

Influence of 2iP and 2,4-D Concentrations on Accumulation of Biomass, Phenolics, Flavonoids and Radical Scavenging Activity in Date Palm (Phoenix dactylifera L.) Cell Suspension Culture

Plant hormones are chemical compounds that serve as crucial signal molecules. The growth and induction of bioactive compounds in plant suspension cultures depend on the exogenous application of auxins and cytokinins at different concentrations. In this study, date palm (Phoenix dactylifera L., cv. Shishi) cell suspension cultures initiated in Murashige and Skoog (MS) medium were treated with 2.5 and 5 mg/L 2-isopentenyladenine (2-iP) in combinations with 1, 2.5, 5 and 10 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D), and compared to the standard cell multiplication medium as the control, which contained 1.5 mg/L 2iP and 10 mg/L naphthaleneacetic acid (NAA). The optimum biomass accumulation, based on the packed cell volume and dry weight, was found in the cell suspension culture augmented with 1 mg/L 2,4-D + 5 mg/L 2iP followed by 5 mg/L 2,4-D + 2.5 mg/L 2-iP. In addition, the study assessed the total phenolic, flavonoid and radical scavenging activity, and high performance liquid chromatography (HPLC) was also used to determine the content of polyphenols (apigenin, caffeic acid, catechin and kaempferol) quantitatively. Cell suspension cultures containing 5 mg/L 2,4-D and 2.5 mg/L 2iP yielded the maximum accumulation of phenolics, flavonoids and radical scavenging activity (90.65%), and also a significantly higher content of caffeic acid (37.1 &micro;g/g DW). The present finding facilitates the scaling up and commercial production of polyphenols from date palm cell suspension culture

Synergistic Effects of Tragacanth and Anti-ethylene Treatments on Postharvest Quality Maintenance of Mango (<i>Mangifera indica</i> L.)

Mango (Mangifera indica L.) is one of the most popular tropical fruits grown in Egypt and several other countries, making it a potential export commodity. Excessive deterioration after harvest requires various treatments to maintain fruit quality. We evaluated the treatments effects of melatonin (MT) as an anti-ethylene agent and tragacanth gum (TRG) as an edible coating individually and together (MT–TRG) before storing mangoes at 12 °C for 32 days under 85–90% relative humidity. Compared with control, all treatments were significantly effective in preserving fruit quality. Fruits treated with MT–TRG showed significantly lower decay values, respiration rates, ethylene production, and weight loss than untreated fruits. MT–TRG treatment significantly enhanced fruit quality, thereby maintaining fruit appearance, flesh color, firmness, total soluble solids and phenolic contents, and pectin methyl esterase, polyphenol oxidase, and peroxidase activities during the storage period. We propose 200 µM MT + 1% TRG as a safe postharvest treatment to reduce the deterioration of mangoes and maintain fruit quality

Elicitor-Induced Production of Biomass and Pharmaceutical Phenolic Compounds in Cell Suspension Culture of Date Palm (Phoenix dactylifera L.)

Plants that synthesize bioactive compounds that have high antioxidant value and elicitation offer a reliable in vitro technique to produce important nutraceutical compounds. The objective of this study is to promote the biosynthesis of these phenolic compounds on a large scale using elicitors in date palm cell suspension culture. Elicitors such as pectin, yeast extract (YE), salicylic acid (SA), cadmium chloride (CdCl2), and silver nitrate (AgNO3) at 50, 100, and 200 mg/L concentrations are used. The effects of elicitors on cell culture were determined in terms of biomass [packed cell volume (PCV), fresh and dry weight], antioxidant activity, and phenolic compounds (catechin, caffeic acid, kaempferol, apigenin) were determined using high-performance liquid chromatography (HPLC). Results revealed that enhanced PCV (12.3%), total phenolic content [317.9 &plusmn; 28.7 mg gallic acid equivalents (GAE)/100 g of dry weight (DW)], and radical scavenging activity (86.0 &plusmn; 4.5%) were obtained in the 50 mg/L SA treated cell culture of Murashige and Skoog (MS) medium. The accumulation of optimum catechin (26.6 &plusmn; 1.3 &micro;g/g DW), caffeic acid (31.4 &plusmn; 3.8 &micro;g/g DW), and kaempferol (13.6 &plusmn; 1.6 &micro;g/g DW) was found in the 50 mg/L SA-treated culture when compared to the control. These outcomes could be of great importance in the nutraceutical and agronomic industries

Date palm micropropagation: Advances and applications

ABSTRACT Date palm (Phoenix dactylifera L.) is a fruit tree resilient to adverse climatic conditions predominating in hot arid regions of the Middle East and North Africa. The date fruit contains numerous chemical components that possess high nutritional and medicinal values. Traditional propagation by offshoots is inefficient to satisfy current demands for date palm trees. Alternatively, micropropagation provides an efficient means for large-scale propagation of date palm cultivars. Both somatic embryogenesis and organogenesis, either directly or indirectly though the callus phase, have been demonstrated in date palm in vitro regeneration. Culture initiation commonly utilizes shoot-tip explants isolated from young offshoots. Recently, the immature inflorescences of adult trees were utilized as an alternative nondestructive source of explants. In addition to the nature of the explant used, successful plant regeneration depends on the cultivar, composition of the culture medium and physical status. Challenges of date palm micropropagation include long in vitro cycle, latent contamination, browning, somaclonal variation as well as ex vitro acclimatization and transplanting. A remarkable amount of research investigating these factors has led to optimized protocols for the micropropagation of numerous commercially important cultivars. This has encouraged the development of several international commercial tissue culture laboratories. Molecular characterization provides an assurance of genetic conformity of regenerated plantlets, a key feature for commercial production. This article describes date palm micropropagation protocols and also discusses recent achievements with respect to somaclonal variation, molecular markers, cryopreservation and future prospects