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

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

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

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

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

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