Epigenomics in stress tolerance of plants under the climate change.

BACKGROUND: Climate change has had a tremendous impact on the environment in general as well as agricultural crops grown in these situations as time passed. Agricultural production of crops is less suited and of lower quality due to disturbances in plant metabolism brought on by sensitivity to environmental stresses, which are brought on by climate change. Abiotic stressors that are specific to climate change, including as drought, extremes in temperature, increasing CO2, waterlogging from heavy rain, metal toxicity, and pH changes, are known to negatively affect an array of species. Plants adapt to these challenges by undergoing genome-wide epigenetic changes, which are frequently accompanied by differences in transcriptional gene expression. The sum of a cell's biochemical modifications to its nuclear DNA, post-translational modifications to histones, and variations in the synthesis of non-coding RNAs is called an epigenome. These modifications frequently lead to variations in gene expression that occur without any alteration in the underlying base sequence. EPIGENETIC MECHANISMS AND MARKS: The methylation of homologous loci by three different modifications-genomic (DNA methylation), chromatin (histone modifications), and RNA-directed DNA methylation (RdDM)-could be regarded as epigenetic mechanisms that control the regulation of differential gene expression. Stresses from the environment cause chromatin remodelling, which enables plant cells to adjust their expression patterns temporarily or permanently. EPIGENOMICS' CONSEQUENCES FOR GENOME STABILITY AND GENE EXPRESSION: DNA methylation affects gene expression in response to abiotic stressors by blocking or suppressing transcription. Environmental stimuli cause changes in DNA methylation levels, either upward in the case of hypermethylation or downward in the case of hypomethylation. The type of stress response that occurs as a result also affects the degree of DNA methylation alterations. Stress is also influenced by DRM2 and CMT3 methylating CNN, CNG, and CG. Both plant development and stress reactions depend on histone changes. Gene up-regulation is associated with histone tail phosphorylation, ubiquitination, and acetylation, while gene down-regulation is associated with de-acetylation and biotinylation. Plants undergo a variety of dynamic changes to histone tails in response to abiotic stressors. The relevance of these transcripts against stress is highlighted by the accumulation of numerous additional antisense transcripts, a source of siRNAs, caused by abiotic stresses. The study highlights the finding that plants can be protected from a range of abiotic stresses by epigenetic mechanisms such DNA methylation, histone modification, and RNA-directed DNA methylation. TRANSGENERATIONAL INHERITANCE AND SOURCES OF EPIGENETIC VARIATION: Stress results in the formation of epialleles, which are either transient or enduring epigenetic stress memory in plants. After the stress is gone, the stable memory is kept for the duration of the plant's remaining developmental cycles or passed on to the next generations, leading to plant evolution and adaptability. The bulk of epigenetic changes brought on by stress are temporary and return to normal after the stress has passed. Some of the modifications, however, might be long-lasting and transmitted across mitotic or even meiotic cell divisions. Epialleles often have genetic or non-genetic causes. Epialleles can arise spontaneously due to improper methylation state maintenance, short RNA off-target effects, or other non-genetic causes. Developmental or environmental variables that influence the stability of epigenetic states or direct chromatin modifications may also be non-genetic drivers of epigenetic variation. Transposon insertions that change local chromatin and structural rearrangements, such copy number changes that are genetically related or unrelated, are two genetic sources of epialleles. EPIGENOMICS IN CROP IMPROVEMENT: To include epigenetics into crop breeding, it is necessary to create epigenetic variation as well as to identify and evaluate epialleles. Epigenome editing or epi-genomic selection may be required for epiallele creation and identification. In order to combat the challenges given by changing environments, these epigenetic mechanisms have generated novel epialleles that can be exploited to develop new crop types that are more climate-resilient. Numerous techniques can be used to alter the epigenome generally or at specific target loci in order to induce the epigenetic alterations necessary for crop development. Technologies like CRISPR/Cas9 and dCas, which have recently advanced, have opened up new avenues for the study of epigenetics. Epialleles could be employed in epigenomics-assisted breeding in addition to sequence-based markers for crop breeding. CONCLUSIONS AND FUTURE PROSPECTUS: A few of the exciting questions that still need to be resolved in the area of heritable epigenetic variation include a better understanding of the epigenetic foundation of characteristics, the stability and heritability of epialleles, and the sources of epigenetic variation in crops. Investigating long intergenic non-coding RNAs (lincRNAs) as an epigenetic process might open up a new path to understanding crop plant's ability to withstand abiotic stress. For many of these technologies and approaches to be more applicable and deployable at a lower cost, technological breakthroughs will also be necessary. Breeders will probably need to pay closer attention to crop epialleles and how they can affect future responses to climate changes. The development of epialleles suitable for particular environmental circumstances may be made possible by creating targeted epigenetic changes in pertinent genes and by comprehending the molecular underpinnings of trans generational epigenetic inheritance. More research on a wider variety of plant species is required in order to fully comprehend the mechanisms that produce and stabilise epigenetic variation in crops. In addition to a collaborative and multidisciplinary effort by researchers in many fields of plant science, this will require a greater integration of the epigenomic data gathered in many crops. Before it may be applied generally, more study is required.

Evaluation of Indian ginseng [Withania somnifera (L.) Dunal] breeding lines and genotype-by-environment interaction across production environments in western India.

In order to find location-specific and broadly adapted genotypes for total root alkaloid content and dry root yield along with additive main effects and multiplicative interactions (AMMI) and genotype (G) main effects plus genotype × environment (E) interaction in Indian ginseng (Withania somnifera (L.) Dunal), (GGE) biplot analyses were used in the current study. Trials were carried out in a randomized complete block design (RCBD) over three succeeding years viz., 2016-2017, 2017-2018 and 2018-2019 at three different locations (S. K. Nagar, Bhiloda and Jagudan). Analysis of variance (ANOVA) for AMMI for dry root yield revealed that the environment, genotype, and GE interaction, respectively, accounted for significant sums of squares of 35.31%, 24.89%, and 32.96%. For total root alkaloid content, a significance of 27.59% of total sum of squares was justified by environment, 17.72% by genotype and 43.13% by GEI. Nine experimental trials in total were taken into consideration as contexts for the GEI analysis in 16 genotypes, including one check. AMMI analysis showed that genotypes, SKA-11, SKA-27, SKA-23 and SKA-10 were superior for mean dry root yield and SKA-11, SKA-27 and SKA-21 had better performance for total root alkaloid content across environment. The GGE biplot analysis showed genotypes SKA-11, SKA-27, SKA-10 desirable for dry root yield and SKA-26, SKA-27, SKA-11 for total root alkaloid content. As a result of the GGE and AMMI biplot techniques, SKA-11 and SKA-27 were determined to be the most desired genotypes for both total root alkaloid content and dry root yield. Further, simultaneous stability index or SSI statistics identified SKA-6, SKA-10, SKA-27, SKA-11 and AWS-1 for higher dry root yield, whilst SKA-25, SKA-6, SKA-11, SKA-12 and AWS-1 for total alkaloid content from root. Based on trait variation, GGE biplot analysis identified two mega-environments for dry root yield and a total of four for total root alkaloid content. Additionally, two representative and discriminating environments-one for dry root production and the other for total root alkaloid content were found. Location-specific and breeding for broad adaptation could be advocated for improvement and release of varieties for Indian ginseng.

Elucidation of genotype-environment interactions and genetic stability parameters for yield, quality and agromorphological traits in ashwagandha (Withania somnifera (L.) Dunal).

The present study was undertaken to delineate genotype-environment interactions and stability status of 16 genotypes of ashwagandha (Withania somnifera (L.) Dunal) in context to the 12 characters, namely plant height, number of primary branches, number of secondary branches, days to flowering, days to maturity, number of berries, number of seeds/berry, root length, root diameter, root branches, dry root yield and total alkaloid content (%). Experiment was carried out in a randomized complete block design with three replicationsover three different locations (S. K. Nagar, Jagudan and Bhiloda) in north Gujarat for three years (2016-17, 2017-18 and 2018-19). Pooled analysis of variance revealed that the mean squares due to genotypes and genotype 9 environment interaction along with linear and nonlinear components were highly significant (P<0.01) for most of the traits under study. Stability parameters for component traits through Eberhart and Russell model showed that genotypes that can be used directly in breeding programme are SKA-4 for early flowering, SKA-21 for early maturity and SKA-1, SKA-4, SKA-6 and SKA-17 for shorter plant height. Further, SKA-21 could be used for improving number of primary branches per plant, SKA-11 and SKA-17 for number of secondary branches per plant, SKA-19 for number of berries per plant, SKA-6, SKA-21, SKA-27 and AWS-1 for root branches and SKA-17 for root length as these genotypes were found to be moststable across the environments for mentioned traits. The result revealed that some reliable predictions about genotype 9 environment interaction and its unpredictable components were involved significantly in determining the stability of genotypes. Hence, the present investigation can be exploited for the identification of more productive genotypes in specific environments, leading to significant increase in root productivity of ashwagandha.

A case study of energy transfer mechanism from uranium to europium in ZnAl3O4 spinel host by photoluminescence spectroscopy.

Zinc aluminate (ZAO), a member of spinel class of inorganic compounds has been of much interest of late due to its wide range of use in catalysis, optical, electronic and ceramic industries. When doped with several lanthanides, this material has proved to be a potential host matrix for phosphors. As lanthanides suffer from poor (direct) excitation and emission cross sections, the use of a co-dopant ion can help to circumvent this and extract better emission from a lanthanide doped ZAO system. In this connection, energy transfer mechanism from uranium to europium in the ZAO host was investigated by photoluminescence spectroscopic technique. It was seen that uranium gets stabilized in the hexavalent state as UO6(6-) (octahedral uranate) where as the lanthanide ion, Eu is stabilized in its trivalent state in the ZAO host. In the co-doped system, an efficient energy transfer pathway from the uranate to europium ion was observed. Based upon emission and life time data a suitable mechanism was proposed for the energy transfer (quenching) process. It was proposed that after excitation by photons, the uranate ions transfer their energy to nearby (5)D1 level of Eu(3+) ions which non-radiatively de-excites to the corresponding lower levels of (5)D0. Further this (5)D0 level decays in a radiative mode to the (7)F manifold giving the characteristic emission profile of trivalent Eu. It was proposed that both static and dynamic types of energy transfer mechanism were responsible for this process.

Molecular analysis of soybean varying in water use efficiency using SSRs markers.

A set of 91 soybean germplasm lines, collected from different parts of the world, were screened for Water Use Efficiency (WUE) using Carbon Isotope Discrimination (CID) technique and were characterized for 10 quantitative traits. After screening under field condition, 44 soybean genotypes showed variations in WUE. Molecular diversity of these 44 diverse soybean lines was carried out with 26 Simple Sequence Repeats (SSRs) markers, of which 10 were polymorphic (38.47% polymorphism). 28 alleles were observed which were distributed over 10 loci, with an average of 2.8 alleles per locus. Polymorphism Information Content (PIC) value of 10 polymorphic markers ranged from 0.40 (locus Satt460) to 0.67 (locus satt260), with an average of 0.46. Pair-wise genetic similarity value, as calculated by simple matching coefficient, ranged from 0.99 to 0.40, with an average of 0.70. Genotypes were clustered using NTSYS-pc software employing unweighted paired group method using arithmetic averages to generate the dendrogram. Dendrogram exhibited 8 distinct clusters with a similarity coefficient of 0.69. Genotypes having low to medium and medium to high CID value were clustered in distant groups indicating usefulness of these polymorphic SSRs markers for differentiating genotypes on the basis of their CID value. The findings of this study indicate the need for broadening genetic base of the present Indian soybean cultivars through use of exotic sources of variation towards WUE. Thus, diverse genotypes identified in this study would be beneficial to soybean breeders to develop mapping population to identify QTLs for WUE.

Identification of simple sequence repeat markers associated with wilt resistance in pigeonpea.

The present study was carried out with the objective of identifying markers for Fusarium wilt resistance in pigeonpea using simple sequence repeat (SSR) and bulk segregant analysis (BSA). The wilt resistant (ICPL 87119) and wilt susceptible (T. Vishakha-1) genotypes were crossed and their F2 population was used for marker analysis. Although, the parents were surveyed with 76 SSR primers to identify the polymorphic markers, only 26 primers were found polymorphic between the parents under study. The polymorphic information content scores of SSR markers ranged between 0.077 to 0.333, with an average of 0.18 per marker. These 26 primers were selected for BSA, which indicated that five SSR primers (PFW 26, PFW 31, PFW 38, PFW 56, and PFW 70) were able to distinguish the resistant and susceptible bulks and parents for wilt resistance. Hence, these five SSR markers can be utilized further for identification of wilt resistant genotypes of pigeon pea and for development of new wilt resistant varieties of pigeonpea.

Photoluminescence and EPR studies on Fe³âº doped ZnAl2O4: an evidence for local site swapping of Fe³âº and formation of inverse and normal phase.

Considering that ZnAl2O4 spinel has two different sites (octahedral and tetrahedral) and its properties change with dopant ion distribution among these two sites; ZnAl2O4 doped with varied concentrations of Fe(3+) was synthesized by a low temperature sol-gel combustion method. Phase purity and structural investigations were carried out using Rietveld refined X-ray diffraction which shows a decrease in the value of cell parameters at higher doping levels. Photoluminescence (PL) and electron paramagnetic resonance (EPR) studies have shown that on doping, Fe(3+) ions were distributed in both tetrahedral and octahedral sites. At octahedral sites, Fe(3+) exhibited a broad red emission around 745 nm while at tetrahedral sites it exhibited well-defined vibronic sidebands at 665, 674, 684 and 693 nm along with a broad blue band with a maxima at 445 nm at room temperature. EPR studies have shown a broad spectrum at g ≈ 2.2 which corresponds to the Fe(3+) in octahedral sites, while the broad signal at g ≈ 4.2 belongs to Fe(3+) in tetrahedral sites. It was also inferred from these studies that Fe(3+) prefers to occupy octahedral sites at higher concentrations and at higher annealing temperatures. The PL decay behavior of Fe(3+) in ZnAl2O4 has also shown that two different types of Fe(3+) ions were present in this matrix. The first type was a long lived species (τ ≈ 170 µs) present at octahedral sites and the other was a short lived species (τ ≈ 40 µs) present at the tetrahedral sites; the fraction of the long lived species predominate at higher concentrations. Thus the present work is mainly focused on understanding the tuning of local site occupancy of the dopant ion among those sites with varying concentration and annealing temperature, using the dopant ion itself as a spectroscopic probe, which further helps in understanding the phase (inverse and normal) of the spinel.

Direct determination of metallic impurities in graphite by EDXRF.

Energy dispersive X-ray fluorescence (EDXRF) methods have been developed for the direct determination of 14 trace metallic impurities in graphite powder without any need for sample dissolution. Using synthetic standards, calibration curves were established for different elements after optimizing the spectrometer parameters. Two synthetic samples were analyzed to evaluate the performance of the developed analytical methods. The estimates for most of the analytes were in good agreement with the added amounts. Three graphite powder samples were analyzed by the present method as well as by D.C. arc emission spectrometric technique for comparison and the agreement between the analyte values determined, using both methods was good. Samples in pellet form were analyzed using a separate calibration with standards in pellet form. The present method is rapid, as it alleviates the need for any chemical treatment and gives good precision.