Pup1 QTL Regulates Gene Expression Through Epigenetic Modification of DNA Under Phosphate Starvation Stress in Rice

Physiological and molecular investigations on a high-yielding variety and near-isogenic line of rice under continuous phosphorus stress reveal major regulatory function of Pup1 QTL

Phosphorous (P) plays crucial roles in cellular functioning including respiration, photosynthesis, and membranes. P deficiency in the soil causes stunted growth, smaller/erect leaves, lesser tillers, and a considerable decrease in yield. To decipher the functions of Pup1 QTL and delineate the potential effects of continuous P stress on plant growth, yield/quality, physio-biochemical and molecular analyses of rice [Pusa-44 (P deficiency sensitive) and a near-isogenic line-23 (NIL-23), (harbouring Pup1 QTL, tolerant genotype)] were hydroponically grown under P continuous stress [deficiency (4 ppm) or extravagance (≥32 ppm)] till maturity. Decrease in the number of tillers and panicles under stress led to poor agronomic performance of rice. P concentration in roots, leaves, and seeds raised significantly with increasing concentration of P in hydroponic culture. Higher P concentration in the medium led to elevated phytate concentration in seeds; however, it was comparatively more in seeds of the tolerant (NIL-23) genotype. Comparative transcriptome analysis indicated differential expression of genes for P transporters and those implicated in P mobilization/homeostasis, carbohydrate/lipid metabolism, etc. on P deficiency. Moreover, the regulatory function of Pup1 in reprograming the gene expression involved in chromatin assembly, histone/DNA methylation, cell wall organization, etc. was detected in the panicle of tolerant genotype on P deficiency. This study confirms a major regulatory function of Pup1 and outlines the potential effects of excessive P on plant development, productivity, and quality of seeds. These findings would be useful in improving P uptake/use efficiency in rice and prudent/sustainable usage of phosphatic fertilizers.

Quantitative trait loci for grain mineral element accumulation in Vietnamese rice landraces

Rice (Oryza sativa L.) is a staple food for half of the world's population, and its biofortification is a key factor in fighting micronutrient malnutrition. However, harmful heavy metals tend to accumulate in rice grains due to soil and water contamination. Therefore, it is important to improve beneficial micronutrient contents and reduce the accumulation of undesirable metals in rice grain. To better characterize the genetic control of mineral accumulation in rice, we conducted association genetics on the ion contents of white and brown grains using a collection of 184 Vietnamese rice landraces. In total, 27 significant associations were identified and delimited into quantitative trait loci associated with macronutrients such as phosphorus, potassium or calcium; micronutrients such as iron or zinc; or toxic heavy metals such as arsenic and cadmium. Several genes related to ion homeostasis or ion transport were identified in the different quantitative trait loci. LOC_Os10g30610, present in qRAs10-1 associated with arsenic content in brown rice, encodes an ABC transporter (OsABCG25), which is involved in the silicon-induced formation of the Casparian strip in the rice exodermis and could act as a barrier restricting As diffusion within the root cortex. LOC_Os05g04330, present in qRP5-1 and associated with phosphorus content in brown rice, encodes a CHH methylation maintenance protein, and its expression is downregulated in roots in the presence of the phosphorus uptake 1 (Pup1), suggesting a role for epigenetics in the regulation of phosphorus uptake and accumulation in grain. These findings reveal novel quantitative trait loci associated with grain ion content and candidate genes that are potentially valuable for breeding programs aimed at rice grain biofortification and reducing toxic metal accumulation.

Dynamic DNA N 6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus

The formation of resting cysts commonly found in unicellular eukaryotes is a complex and highly regulated survival strategy against environmental stress that involves drastic physiological and biochemical changes. Although most studies have focused on the morphology and structure of cysts, little is known about the molecular mechanisms that control this process. Recent studies indicate that DNA N 6-adenine methylation (6mA) could be dynamically changing in response to external stimuli; however, its potential role in the regulation of cyst formation remains unknown. We used the ciliate Pseudocohnilembus persalinus, which can be easily induced to form cysts to investigate the dynamic pattern of 6mA in trophonts and cysts. Single-molecule real-time (SMRT) sequencing reveals high levels of 6mA in trophonts that decrease in cysts, along with a conversion of symmetric 6mA to asymmetric 6mA. Further analysis shows that 6mA, a mark of active transcription, is involved in altering the expression of encystment-related genes through changes in 6mA levels and 6mA symmetric-to-asymmetric conversion. Most importantly, we show that reducing 6mA levels by knocking down the DNA 6mA methyltransferase PpAMT1 accelerates cyst formation. Taken together, we characterize the genome-wide 6mA landscape in P. persalinus and provide insights into the role of 6mA in gene regulation under environmental stress in eukaryotes. We propose that 6mA acts as a mark of active transcription to regulate the encystment process along with symmetric-to-asymmetric conversion, providing important information for understanding the molecular response to environmental cues from the perspective of 6mA modification.

Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression

Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.

DNA methylome analysis provides insights into gene regulatory mechanism for better performance of rice under fluctuating environmental conditions: epigenomics of adaptive plasticity

MAIN CONCLUSION

Roots play an important role in adaptive plasticity of rice under dry/direct-sown conditions. However, hypomethylation of genes in leaves (resulting in up-regulated expression) complements the adaptive plasticity of Nagina-22 under DSR conditions. Rice is generally cultivated by transplanting which requires plenty of water for irrigation. Such a practice makes rice cultivation a challenging task under global climate change and reducing water availability. However, dry-seeded/direct-sown rice (DSR) has emerged as a resource-saving alternative to transplanted rice (TPR). Though some of the well-adapted local cultivars are used for DSR, only limited success has been achieved in developing DSR varieties mainly because of a limited knowledge of adaptability of rice under fluctuating environmental conditions. Based on better morpho-physiological and agronomic performance of Nagina-22 (N-22) under DSR conditions, N-22 and IR-64 were grown by transplanting and direct-sowing and used for whole genome methylome analysis to unravel the epigenetic basis of adaptive plasticity of rice. Comparative methylome and transcriptome analyses indicated a large number (4078) of genes regulated through DNA methylation/demethylation in N-22 under DSR conditions. Gene × environment interactions play important roles in adaptive plasticity of rice under direct-sown conditions. While genes for pectinesterase, LRK10, C2H2 zinc-finger protein, splicing factor, transposable elements, and some of the unannotated proteins were hypermethylated, the genes for regulation of transcription, protein phosphorylation, etc. were hypomethylated in CG context in the root of N-22, which played important roles in providing adaptive plasticity to N-22 under DSR conditions. Hypomethylation leading to up-regulation of gene expression in the leaf complements the adaptive plasticity of N-22 under DSR conditions. Moreover, differential post-translational modification of proteins and chromatin assembly/disassembly through DNA methylation in CHG context modulate adaptive plasticity of N-22. These findings would help developing DSR cultivars for increased water-productivity and ecological efficiency.

Comparative proteome analysis of phosphorus-responsive genotypes reveals the proteins differentially expressed under phosphorous starvation stress in rice

Phosphorus (P)-deficiency is one of the major nutrient constraints for global rice production. P-deficiency tolerance in rice involves complex regulatory mechanisms. To gain insights into the proteins involved in phosphorus acquisition and use efficiency in rice, proteome analysis of a high-yielding rice cultivar Pusa-44 and its near-isogenic line (NIL)-23 harboring a major phosphorous uptake (Pup1) QTL, grown under control and P-starvation stress, was performed. Comparative proteome profiling of shoot and root tissues from the plants grown hydroponically with P (16 ppm, +P) or without P (0 ppm, -P) resulted in the identification of 681 and 567 differentially expressed proteins (DEPs) in shoot of Pusa-44 and NIL-23, respectively. Similarly, 66 and 93 DEPs were identified in root of Pusa-44 and NIL-23, respectively. These P-starvation responsive DEPs were annotated to be involved in metabolic processes like photosynthesis, starch-, sucrose-, energy-metabolism, transcription factors (mainly ARF, ZFP, HD-ZIP, MYB), and phytohormone signaling. Comparative analysis of the expression patterns observed by proteome analysis with that reported at the transcriptome level indicated the Pup1 QTL-mediated post-transcriptional regulation plays an important role under -P stress. Thus, the present study describes the molecular aspect of the regulatory functions of Pup1 QTL under P-starvation stress in rice, which might help develop an efficient rice cultivar with enhanced P acquisition and assimilation for better performance in P-deficient soil.

Prospects of microgreens as budding living functional food: Breeding and biofortification through OMICS and other approaches for nutritional security

Nutrient deficiency has resulted in impaired growth and development of the population globally. Microgreens are considered immature greens (required light for photosynthesis and growing medium) and developed from the seeds of vegetables, legumes, herbs, and cereals. These are considered "living superfood/functional food" due to the presence of chlorophyll, beta carotene, lutein, and minerals like magnesium (Mg), Potassium (K), Phosphorus (P), and Calcium (Ca). Microgreens are rich at the nutritional level and contain several phytoactive compounds (carotenoids, phenols, glucosinolates, polysterols) that are helpful for human health on Earth and in space due to their anti-microbial, anti-inflammatory, antioxidant, and anti-carcinogenic properties. Microgreens can be used as plant-based nutritive vegetarian foods that will be fruitful as a nourishing constituent in the food industryfor garnish purposes, complement flavor, texture, and color to salads, soups, flat-breads, pizzas, and sandwiches (substitute to lettuce in tacos, sandwich, burger). Good handling practices may enhance microgreens'stability, storage, and shelf-life under appropriate conditions, including light, temperature, nutrients, humidity, and substrate. Moreover, the substrate may be a nutritive liquid solution (hydroponic system) or solid medium (coco peat, coconut fiber, coir dust and husks, sand, vermicompost, sugarcane filter cake, etc.) based on a variety of microgreens. However integrated multiomics approaches alongwith nutriomics and foodomics may be explored and utilized to identify and breed most potential microgreen genotypes, biofortify including increasing the nutritional content (macro-elements:K, Ca and Mg; oligo-elements: Fe and Zn and antioxidant activity) and microgreens related other traits viz., fast growth, good nutritional values, high germination percentage, and appropriate shelf-life through the implementation of integrated approaches includes genomics, transcriptomics, sequencing-based approaches, molecular breeding, machine learning, nanoparticles, and seed priming strategiesetc.

Molecular basis of genetic plasticity to varying environmental conditions on growing rice by dry/direct-sowing and exposure to drought stress: Insights for DSR varietal development

Rice requires plenty of water for its cultivation by transplanting. This poses several challenges to its cultivation due to erratic rainfall resulting in drought, flood, and other abiotic stresses of varying intensity. Dry/direct-sown rice (DSR) has emerged as a water-saving/climate-smart alternative to transplanted rice (TPR). The performance of a rice cultivar on growing by different methods of planting under varying environmental conditions varies considerably. However, the molecular basis of the observed phenotypic plasticity of rice to varying environmental conditions is still elusive. Resilience to various environmental fluctuations is important to ensure sustainable rice production in the present era of global climate change. Our observations on exclusively up-regulated genes in leaf of Nagina 22 (N 22) grown by dry/direct-sowing and subjected to drought stress at panicle initiation stage (compared to that in leaf of IR 64), and another set of genes exclusively down-regulated in leaf of N 22 (compared to that in leaf of IR 64) indicate important roles of leaf in stress resilience. A large number of genes down-regulated exclusively in root of N 22 on dry/direct-sowing subjected to drought stress indicates a major contribution of roots in stress tolerance. The genes for redox-homeostasis, transcription factors, stress signaling, carbohydrate metabolism, and epigenetic modifications play important roles in making N 22 better adapted to DSR conditions. More importantly, the involvement of genes in rendering genetic plasticity to N 22 under changing environmental conditions was confirmed by reversal of the method of planting. To the best of our knowledge, this is the first report on decoding the molecular basis of genetic plasticity of rice grown by two different methods of planting subjected to drought stress at the reproductive stage of plant growth. This might help in DSR varietal development program to enhance water-productivity, conserve natural resources, and minimize the emission of greenhouse gases, thus achieving the objectives of negative-emission agriculture.

Integrated methylome and transcriptome analysis unravel the cold tolerance mechanism in winter rapeseed(Brassica napus L.)

BACKGROUND

Cytosine methylation, the main type of DNA methylation, regulates gene expression in plant response to environmental stress. The winter rapeseed has high economic and ecological value in China's Northwest, but the DNA methylation pattern of winter rapeseed during freezing stress remains unclear.

RESULT

This study integrated the methylome and transcriptome to explore the genome-scale DNA methylation pattern and its regulated pathway of winter rapeseed, using freezing-sensitive (NF) and freezing-resistant (NS) cultivars.The average methylation level decreased under freezing stress, and the decline in NF was stronger than NS after freezing stress. The CG methylation level was the highest among the three contexts of CG, CHG, and CHH. At the same time, the CHH proportion was high, and the methylation levels were highest 2 kb up/downstream, followed by the intron region. The C sub-genomes methylation level was higher than the A sub-genomes. The methylation levels of chloroplast and mitochondrial DNA were much lower than the B. napus nuclear DNA, the SINE methylation level was highest among four types of transposable elements (TEs), and the preferred sequence of DNA methylation did not change after freezing stress. A total of 1732 differentially expressed genes associated with differentially methylated genes (DMEGs) were identified in two cultivars under 12 h and 24 h in three contexts by combining whole-genome bisulfite sequencing( and RNA-Seq data. Function enrichment analysis showed that most DMEGs participated in linoleic acid metabolism, alpha-linolenic acid metabolism, carbon fixation in photosynthetic organisms, flavonoid biosynthesis, and plant hormone signal transduction pathways. Meanwhile, some DMEGs encode core transcription factors in plant response to stress.

CONCLUSION

Based on the findings of DNA methylation, the freezing tolerance of winter rapeseed is achieved by enhanced signal transduction, lower lipid peroxidation, stronger cell stability, increased osmolytes, and greater reactive oxygen species (ROS) scavenging. These results provide novel insights into better knowledge of the methylation regulation of tolerance mechanism in winter rapeseed under freezing stress.