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

Phytostimulatory Influence of Comamonas testosteroni and Silver Nanoparticles on Linum usitatissimum L. under Salinity Stress

They were shifting in land use increases salinity stress, significant abiotic stress affecting plant growth, limiting crop productivity. This work aimed to improve Linum usitatissimum L. (linseed) growth under salinity using Comamonas testosteroni and silver nanoparticles (AgNPs). AgNPs were fabricated exploiting Rosmarinus officinalis and monitored by U.V./Vis spectrophotometry scanning electron microscopy (SEM) and Fourier transforms infrared spectroscopy (FTIR). Photosynthetic pigments, enzymatic and nonenzymatic antioxidants of linseed were investigated under salt stress in treated and untreated plants with C. testosteroni alongside AgNPs. Our findings recorded the formation of AgNPs at 457 nm, which were globular and with a diameter of 75 nm. Notably, chlorophyll-a, b, and total chlorophyll reduction while enhanced carotenoids and anthocyanin contents were attained under salinity stress. Total dissoluble sugars, proline, and dissoluble proteins, H2O2, malondialdehyde, enzymatic and nonenzymatic antioxidants were significantly elevated in NaCl well. Combined AgNPs and C. testosteroni elevated photosynthetic pigments. Also, they led to the mounting of soluble sugars, proline, and soluble proteins. H2O2 and malondialdehyde decreased while enzymatic and nonenzymatic antioxidants increased in response to AgNPs, C. testosteroni, and their combination. Thus, AgNPs and C. testosteroni might bio-fertilizers to improve linseed crop productivity under salinity stress

Antioxidant Enzymatic Activities and Growth Response of Quinoa (Chenopodium quinoa Willd) to Exogenous Selenium Application

Selenium is a trace element essential to many organisms, including higher plants. At low concentrations, it enhances growth and development; however, it is toxic at high concentrations. The development of crops with proper levels of selenium will be worth for both nutrition and Se-based therapeutics. This study aimed to investigate the morphological, physiological, and biochemical responses of the quinoa plant to 0, 2.5, 5, 10, and 20 mg/L of Na2SeO3·5H2O. Selenium at low concentrations (2.5 and 5 mg/L), quinoa plant showed a significant increase of growth parameters, relative water content, photosynthetic pigments, proline, total soluble sugars, and antioxidant enzymes activities as (superoxide dismutase (SOD), catalase (CAT), peroxidase (POD, ascorbate peroxidase (APX), and glutathione reductase (GR)), and contents of malondialdehyde (MDA) and H2O2 were reduced. However, high concentrations (10 and 20) mg/L caused a decrease in plant growth parameters, relative water content, and photosynthetic pigments. In contrast, excess selenium increased the oxidative stress monitored by hydrogen peroxide and lipid peroxidation levels. The enzymatic antioxidant system responded to the selenium supply significantly increased. Osmolytes compounds, such as total sugars and proline, increased in selenium-treated plants. The increase in these osmolytes compounds may show a defense mechanism for the osmotic readjustment of quinoa plants to mitigate the toxicity caused by selenium. This study shows the morphological and physiological responses that must be considered for success in the sustainable cultivation of quinoa plants in environments containing excess selenium

Assessment of Morpho-Physiological and Biochemical Responses of Mercury-Stressed Trigonella foenum-gracum L. to Silver Nanoparticles and Sphingobacterium ginsenosidiumtans Applications

Heavy metals are primarily generated and deposited in the environment, causing phytotoxicity. This work evaluated fenugreek plants’ morpho-physiological and biochemical responses under mercury stress conditions toward Ag nanoparticles and Sphingobacterium ginsenosidiumtans applications. The fabrication of Ag nanoparticles by Thymus vulgaris was monitored and described by UV/Vis analysis, FTIR, and SEM. The effect of mercury on vegetative growth was determined by measuring the root and shoots length, the number and area of leaves, the relative water content, and the weight of the green and dried plants; appraisal of photosynthetic pigments, proline, hydrogen peroxide, and total phenols content were also performed. In addition, the manipulation of Ag nanoparticles, S. ginsenosidiumtans, and their combination were tested for mercury stress. Here, Ag nanoparticles were formed at 420 nm with a uniform cuboid form and size of 85 nm. Interestingly, the gradual suppression of vegetal growth and photosynthetic pigments by mercury, Ag nanoparticles, and S. ginsenosidiumtans were detected; however, carotenoids and anthocyanins were significantly increased. In addition, proline, hydrogen peroxide, and total phenols content were significantly increased because mercury and S. ginsenosidiumtans enhance this increase. Ag nanoparticles achieve higher levels by the combination. Thus, S. ginsenosidiumtans and Ag nanoparticles could have the plausible ability to relieve and combat mercury’s dangerous effects in fenugreek

Temporal Synchronization of Nitrogen and Sulfur Fertilization: Impacts on Nutrient Uptake, Use Efficiency, Productivity, and Relationships with Other Micronutrients in Soybean

Nitrogen (N) and sulfur (S) are essential nutrient elements, and their deficiency affects crop growth, productivity, and nutrient uptake due to their multifaceted role in plant metabolism, which has been well documented. Therefore, agricultural management strategies that can overcome these deficiencies are the need of the hour. In this context, a study was undertaken with the objective to assess the impacts of N and S applications, either basally or through split application (12.5, 25 and 50 kg ha−1), on the nutrient uptake, productivity, use efficiency, and micronutrient content status in soybean seeds, and also the change in soil nutrient zinc (Zn) and iron (Fe) content at different critical stages of soybean crop growth. The field trial was conducted utilizing a randomized complete-block design, and comprised fourteen treatments with varying N and S quantities. N and S were applied through basal and split applications in different combinations. The salient findings indicated that the highest seed, straw yield, N, and S uptake were obtained with the application of N25+25, S25+25, and did not significantly vary with N25+25, S12.5+12.5, N50, and N25+S50. The highest N use efficiency was recorded with the application of N25+S50, and S use efficiency with the application of N25+25, S25+25. The split application of N and S as N25+25, S25+25 significantly increased soil Zn and Fe content at R2 and R5 stages of soybean crop growth, as well as seed Zn and Fe uptake. It can be concluded that the basal and split application of N and S at the rate of 25 kg ha−1 can improve soybean productivity through increased mobilization and assimilation by plants. The findings indicated that applying N and S separately, with 25 kg ha−1 each basally and at the R2 stage resulted in the highest nutrient uptake, and seed and straw yields. The nutrient use efficiencies, along with Zn and Fe uptake by seeds, exhibited noticeable improvements with this split application approach compared to the control. Furthermore, the soil Zn and Fe contents also experienced enhancements due to the split application of both Nand S fertilizers. These results underscore the potential benefits of temporally adopting optimized fertilizer application strategies to maximize agricultural productivity while ensuring efficient nutrient utilization and soil health maintenance. Further research and field trials could provide deeper insights into the long-term impacts and scalability of this approach across different crop varieties and environmental conditions

Role of Temporal Zn Fertilization along with Zn Solubilizing Bacteria in Enhancing Zinc Content, Uptake, and Zinc Use Efficiency in Wheat Genotypes and Its Implications for Agronomic Biofortification

Wheat (Triticum aestivum L.) is a vital cereal crop for food security in Pakistan. In Zn-deficient soils, its productivity and quality suffer, affecting grain yield, Zn bioavailability, and nutrition, which can lead to malnutrition. Field experiments were conducted using factorial randomized block design at the Agricultural Research Institute (ARI) Tarnab, Peshawar, Pakistan to evaluate the impact of wheat genotypes (G1-TRB-72-311 synthetic hexaploid, G2-TRB-89-348 advanced line, and G3-Pirsabak-19-approved variety), Zn application methods (AM1: no Zn application, AM2: seed priming with 0.5% Zn, AM3: soil application of 10 kg ha−1 Zn, and AM4: foliar application of 0.5% Zn), and the experiment also explored the use of ZSB (BF1: with bacteria, BF0: without bacteria) to cope with Zn deficiency. The study revealed significant impacts on wheat’s Zn content, uptake, and nutrient efficiency, arising from genotypes variance, Zn application approaches, and ZSB. TRB-72-311 synthetic hexaploid genotype with 0.5% foliar Zn and ZSB excelled, enhancing grain (17.8%) and straw Zn (23.1%), increasing total Zn uptake (55.0%), reducing grain phytic acid (11.7%), and boosting Zn-related efficiencies in wheat. These results prompt further discussion regarding the potential implications for agricultural practices. In conclusion, utilizing the TRB-72-311 genotype with 0.5% foliar Zn application and ZSB enhances wheat’s Zn content, uptake, grain quality, and addresses malnutrition

Iron nanoparticles in combination with other conventional Fe sources remediate mercury toxicity-affected plants and soils by nutrient accumulation in bamboo species

The issue of mercury (Hg) toxicity has recently been identified as a significant environmental concern, with the potential to impede plant growth in forested and agricultural areas. Conversely, recent reports have indicated that Fe, may play a role in alleviating HM toxicity in plants. Therefore, this study's objective is to examine the potential of iron nanoparticles (Fe NPs) and various sources of Fe, particularly iron sulfate (Fe SO4 or Fe S) and iron-ethylene diamine tetra acetic acid (Fe - EDTA or Fe C), either individually or in combination, to mitigate the toxic effects of Hg on Pleioblastus pygmaeus. Involved mechanisms in the reduction of Hg toxicity in one-year bamboo species by Fe NPs, and by various Fe sources were introduced by a controlled greenhouse experiment. While 80 mg/L Hg significantly reduced plant growth and biomass (shoot dry weight (36%), root dry weight (31%), and shoot length (31%) and plant tolerance (34%) in comparison with control treatments, 60 mg/L Fe NPs and conventional sources of Fe increased proline accumulation (32%), antioxidant metabolism (21%), polyamines (114%), photosynthetic pigments (59%), as well as root dry weight (25%), and shoot dry weight (22%), and shoot length (22%). Fe NPs, Fe S, and Fe C in plant systems substantially enhanced tolerance to Hg toxicity (23%). This improvement was attributed to increased leaf-relative water content (39%), enhanced nutrient availability (50%), improved antioxidant capacity (34%), and reduced Hg translocation (6%) and accumulation (31%) in plant organs. Applying Fe NPs alone or in conjunction with a mixture of Fe C and Fe S can most efficiently improve bamboo plants' tolerance to Hg toxicity. The highest efficiency in increasing biochemical and physiological indexes under Hg, was related to the treatments of Fe NPs as well as Fe NPs + FeS + FeC. Thus, Fe NPs and other Fe sources might be effective options to remove toxicity from plants and soil. The future perspective may help establish mechanisms to regulate environmental toxicity and human health progressions

Seed germination ecology of Conyza sumatrensis populations stemming from different habitats and implications for management

Conyza sumatrensis (Retz.) E. H. Walker is an obnoxious weed, emerging as an invasive species globally. Seed germination biology of four populations of the species stemming from arid, semi-arid, temperate, and humid regions was determined in this study. Seed germination was recorded under six different environmental cues (i.e., light/dark periods, constant and alternating day and night temperatures, pH, salinity, and osmotic potential levels) in separate experiment for each cue. Populations were main factor, whereas levels of each environmental cue were considered as sub-factor. The impact of seed burial depths on seedling emergence was inferred in a greenhouse pot experiment. Seed germination was recorded daily and four germination indices, i.e., seed germination percentage, mean germination time, time to reach 50% germination, and mean daily germination were computed. Tested populations and levels of different environmental cues had significant impact on various seed germination indices. Overall, seeds stemming from arid and semi-arid regions had higher seed germination potential under stressful and benign environmental conditions compared to temperate and humid populations. Seed of all populations required a definite light period for germination and 12 hours alternating light and dark period resulted in the highest seed germination. Seed germination of all populations occurred under 5–30°C constant and all tested alternate day and night temperatures. However, the highest seed germination was recorded under 20°C. Seeds of arid and semi-arid populations exhibited higher germination under increased temperature, salinity and osmotic potential levels indicating that maternal environment strongly affected germination traits of the tested populations. The highest seed germination of the tested populations was noted under neutral pH, while higher and lower pH than neutral had negative impact on seed germination. Arid and semi-arid populations exhibited higher seed germination under increased pH compared to temperate and humid populations. Seed burial depth had a significant effect on the seedling emergence of all tested populations. An initial increase was noted in seedling emergence percentage with increasing soil depth. However, a steep decline was recorded after 2 cm seed burial depth. These results indicate that maternal environment strongly mediates germination traits of different populations. Lower emergence from >4 cm seed burial depth warrants that deep burial of seeds and subsequent zero or minimum soil disturbance could aid the management of the species in agricultural habitats. However, management strategies should be developed for other habitats to halt the spread of the species

Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton.

Segregation distortion (SD) is a genetic mechanism commonly found in segregating or stable populations. The principle behind this puzzles many researchers. The F2 generation developed from wild Gossypium darwinii and G. hirsutum CCRI12 species was used to investigate the possible transcription factors within the segregation distortion regions (SDRs). The 384 out of 2763 markers were distorted in 29 SDRs on 18 chromosomes. Good collinearity was observed among genetic and physical maps of G. hirsutum and G. barbadense syntenic blocks. Total 568 genes were identified from SDRs of 18 chromosomes. Out of these genes, 128 belonged to three top-ranked salt-tolerant gene families. The DUF597 contained 8 uncharacterized genes linked to Pkinase (PF00069) gene family in the phylogenetic tree, while 15 uncharacterized genes clustered with the zinc finger gene family. Two hundred thirty four miRNAs targeted numerous genes, including ghr-miR156, ghr-miR399 and ghr-miR482, while others targeted top-ranked stress-responsive transcription factors. Moreover, these genes were involved in the regulation of numerous stress-responsive cis-regulatory elements. The RNA sequence data of fifteen upregulated genes were verified through the RT-qPCR. The expression profiles of two highly upregulated genes (Gh_D01G2015 and Gh_A01G1773) in salt-tolerant G. darwinii showed antagonistic expression in G. hirsutum. The results indicated that salt-tolerant genes have been possibly transferred from the wild G. darwinii species. A detailed functional analysis of these genes can be carried out which might be helpful in the future for gene cloning, transformation, gene editing and the development of salt-resistant cotton varieties

Deep placement of nitrogen fertilizer improves yield, nitrogen use efficiency and economic returns of transplanted fine rice.

Rice (Oryza sativa L.) feeds to two-third of the global population by serving as staple food. It is the main export commodity of several countries; thus, contributes towards foreign exchange earnings. Unfortunately, average global rice yield is far below than its genetic potential. Low nitrogen (N) use efficiency (NUE) is among the major reasons for low average yield. Current study evaluated the impact of nitrogen fertilizer application methods (conventional and deep placement) on growth, yield-related traits, chlorophyll contents, photosynthesis rate, agronomic N-use efficiency (ANUE), partial factors productivity of applied N (PFP) and economic returns of two different transplanted rice varieties (Basmati-515 and Super-Basmati). Fertilizer application methods significantly affected allometry, yield-related traits, chlorophyll contents, photosynthesis rate, ANUE, PFP and economic returns. Deep placement of N-fertilizer (DPNF) observed better allometric traits, high chlorophyll contents, photosynthesis rate, ANUE, PFP, yield attributes and economic returns compared to conventional application of N-fertilizer (CANF). Similarly, Basmati-515 had better allometric and yield-related traits, chlorophyll contents, photosynthesis rate, ANUE, PFP and economic returns than Super-Basmati. Regarding interactions among N-fertilizer application methods and rice varieties, Basmati-515 with DPNF resulted in higher chlorophyll contents, photosynthesis rate, ANUE, PFP, allometric and yield related traits and economic returns than CANF. The lowest values of these traits were observed for Super-Basmati with no application of N-fertilizer. Both varieties had better yield and economic returns with DPNF compared to CANF. It is concluded that DPNF improved yield, ANUE and economic returns; therefore, should be opted to improve productivity of transplanted fine rice. Nonetheless, lower nitrogen doses need to be tested for DPNF to infer whether it could lower N use in rice crop