High-density rice planting reduces light quality within the canopy, especially the red to far-red (R: FR) ratio, triggering a physiological shift that enhances elongation growth at the expense of weakened defence mechanisms. This is not a passive consequence but a coordinated regulation controlled by the Phytochrome B (PhyB)-Phytochrome Interacting Factor (PIF) signalling module. Under low R: FR, PhyB becomes inactive, stabilising key PIFs such as OsPIL13 and OsPIF4. These transcription factors promote shade-avoidance growth by enhancing auxin and gibberellin biosynthesis, which in turn suppresses salicylic acid (SA) and jasmonic acid (JA) signalling. They also directly repress the expression of core defence genes. Together, these changes lower immune readiness in shaded rice plants. Here, we propose a rice-specific model in which low R: FR light signals directly suppress immunity through PIF-mediated transcriptional repression, highlighting a monocot-specific mechanism that integrates light perception with immune downregulation.

Photosynthesis is a key determinant for plant productivity, understanding its genetic basis will aid its improvement. The photosynthesis trait is primarily measured in terms of carbon and light utilization, using gas exchange and chlorophyll fluorescence methods. We report in this study, the extent of variability for photosynthetic trait in wild rice relatives, comprising a total of 26 taxa (22 wild species), using an infrared gas analyzer. The scale of measures used were, PN (net photosynthetic rate), E (transpiration), gs (stomatal conductance), Ci (intercellular CO2), Ci/Ca (ratio of intercellular to ambient CO2), WUE (water use efficiency), CE (carboxylation efficiency), Fv′/Fm′ (ratio of variable to maximum fluorescence, photosynthesis efficiency), qP (photochemical quenching), qN (non-photochemical quenching), ΦPSII (quantum yield of photosystemII), and ETR (electron transport rate). These were subjected to variability (ANOVA and PCA) and association (correlation matrices and path analysis) studies. The maximum PN was observed in Oryza australiensis, followed by Oryza officinalis and Oryza barthii. Maximum qP was observed in Oryza latifolia which was at par with O. australiensis, and Oryza alta. Highest CE was observed in O. australiensis. The CE values for O. barthii, Oryza grandiglumis and O. latifolia were at par with O. australiensis. Transcriptomic analysis for flag leaf between APO, the high efficient photosynthetic genotype with indica rice cultivar BAM4234 revealed key candidate genes underlying photosynthesis traits. These findings underscore the value of wild species and their alleles in expanding the photosynthetic capacity of rice potentially using classical breeding approaches.

This review provides a comprehensive mechanistic framework for rice adaptation to low-light stress, integrating morpho-physiological adjustments and biochemical plasticity with the phytochrome-PIF signalling network to guide molecular breeding of light-resilient cultivars. Low-light stress (LLS), defined as photosynthetically active radiation below 600 μmol m−2 s−1, is an increasingly important constraint on rice productivity in monsoon-dominated agroecosystems, where persistent cloud cover, dense planting, and atmospheric pollution markedly reduce light availability. Under natural field conditions, pollution-derived seasonal LLS causes yield losses of 10–20

Low light intensity is a major abiotic stress that severely affects rice yields, particularly in India and Southeast Asia, causing yield reductions of 35–40% during the wet season compared to the dry season. Tolerant rice genotypes exhibit adaptive changes at anatomical, physiological, biochemical, and molecular levels under low-light stress, enabling higher yields compared to susceptible varieties. Our study identified 20 novel QTLs associated with grain yields and nine related traits under low-light and control (normal)-light conditions, using a recombinant inbred line (RIL) population derived from the cross between the low-light-tolerant variety Swarnaprabha and the low-light-susceptible variety IR8. Across the Kharif seasons of 2019 and 2021, 33 stable QTLs were identified, with 11, 13, and 9 QTLs specific to low-light, normal-light, and both conditions, respectively. Of these, Swarnaprabha contributed 28 QTLs, while five were contributed by IR8. Notably, the study identified 11 and 9 novel QTLs under low-light and both conditions, respectively. Three hotspot regions on chromosomes 1, 4, and 8 were identified. These regions harbored 10 novel QTLs and revealed twenty candidate genes, out of which three key hub genes, OsAUX1, OsSBDCP1, and OsNPF5.16, were identified. These hub genes are involved in hormone signaling, starch metabolism, and nitrogen metabolism, respectively. A comprehensive expression analysis of these genes indicated that they are linked to low-light tolerance, offering deeper insights into the genetic and molecular mechanisms underlying low-light resilience. These findings provide valuable genomic resources and potential markers for breeding programs for improving rice productivity under low-light conditions.

Light has a significant impact on rice growth and development. It is essential for photosynthesis and plays a central role in coordinating photoperiodism, plant architecture, and yield. Countries with the highest rice yields are typically those receiving the most solar radiation. However, long stretches of the monsoonal wet season in South and Southeast Asia including India—particularly eastern and northeastern regions—as well as China, hamper rice productivity. During this period, rice crops receive only 800–900 h of bright sunshine, compared to the required 1,500 h, resulting in 30–60

Low-light (LL) stress imposes a major constraint on rice yield in densely planted and monsoonal environments, yet the mechanistic basis of shade tolerance remains insufficiently resolved. We investigated four rice genotypes under simulated LL conditions, including two LL-tolerant varieties (Purnendu and Swarnaprabha) and two LL-susceptible varieties (IR64 and IR8). Responses were systematically analysed from the flag leaf to the fourth leaf. Comprehensive evaluation included measurements of light interception, chlorophyll fluorescence, gas exchange, carbohydrate content, chloroplast ultrastructure, and the expression of fourteen photosynthesis-related genes. Our findings demonstrate that LL tolerance in rice cannot be explained by adaptation of a single leaf; rather, it results from a coordinated strategy involving integrated changes at morphological, physiological, biochemical, and gene expression levels throughout the entire canopy. Tolerant genotypes exhibited only 30-35% loss in photons from the flag leaf to the fourth leaf, whereas susceptible genotypes lost up to 75%. Architectural traits such as plant height, leaf area plasticity, and leaf angle accounted for 84% of the variation in radiation use efficiency, while tolerant genotypes sustained higher photosynthetic efficiency, carbohydrate reserves, and robust gene expression across all layers. These insights identify concrete trait targets for breeding LL-resilient rice varieties, supporting stable yield in dense and light-limited environments.

The CRISPR-Cas genome editing tools are revolutionizing agriculture and basic biology with their simplicity and precision ability to modify target genomic loci. Software-predicted guide RNAs (gRNAs) often fail to induce efficient cleavage at target loci. Many target loci are inaccessible due to complex chromatin structure. Currently, there is no suitable tool available to predict the architecture of genomic target sites and their accessibility. Hence, significant time and resources are spent on performing editing experiments with inefficient guides. Although in vitro-cleavage assay could provide a rough assessment of gRNA efficiency, it largely excludes the interference of native genomic context. Transient in-vivo testing gives a proper assessment of the cleavage ability of editing reagents in a native genomic context. Here, we developed a modified protocol that offers highly efficient protoplast isolation from rice, Arabidopsis, and chickpea, using a sucrose gradient, transfection using PEG (polyethylene glycol), and validation of single guide RNAs (sgRNAs) cleavage efficiency of CRISPR-Cas9. We have optimized various parameters for PEG-mediated protoplast transfection and achieved high transfection efficiency using our protocol in both monocots and dicots. We introduced plasmid vectors containing Cas9 and sgRNAs targeting genes in rice, Arabidopsis, and chickpea protoplasts. Using dual sgRNAs, our CRISPR-deletion strategy offers straightforward detection of genome editing success by simple agarose gel electrophoresis. Sanger sequencing of PCR products confirmed the editing efficiency of specific sgRNAs. Notably, we demonstrated that isolated protoplasts can be stored for up to 24/48 h with little loss of viability, allowing a pause between isolation and transfection. This high-efficiency protocol for protoplast isolation and transfection enables rapid (less than 7 days) validation of sgRNA cleavage efficiency before proceeding with stable transformation. The isolation and transfection method can also be utilized for rapid validation of editing strategies, evaluating diverse editing reagents, regenerating plants from transfected protoplasts, gene expression studies, protein localization and functional analysis, and other applications.

Pearl millet [Cenchrus americanus (L.) Morrone; also known as Pennisetum glaucum], originated 4900 years ago, is a C4 crop with high photosynthetic efficiency and fulfills the food and fodder needs of resource-poor farmers of sub-Saharan Africa, Southeast Asia, and the Indian subcontinent. Pearl millet is a climate-ready crop and grows well in poor and low-fertility soil. It is profoundly nutritious, fiber-rich, and non-glutinous. Based on transcriptome and bioinformatics studies, it is estimated that 1.79 Gb of the pearl millet genome consists of 38,579 genes. Unfortunately, functional genomics and genotype-phenotype association in pearl millet are poorly explored areas. Pearl millet suffers from low yield for many reasons. There is an urgent need to validate the functions of important genes to improve the crop and better utilize it for future agriculture in a changing climate scenario. In recent years, genome editing, especially CRISPR-Cas, has come under the spotlight for improving crop varieties. In this chapter, we discuss how the available genome editing tools can play a significant role in deciphering the functions of pearl millet genomic regions and crop improvement. We also highlight major bottlenecks to using genome editing in pearl millet and discuss possible ways to overcome those constraints.

Drought stress is a significant abiotic stress challenging crop production globally and future food security. The morphological, physiological, and biochemical traits of rice (Oryza sativa L.) are adversely impacted by drought stress, severely affecting its production. In this study, we aim to recognize the best genotypes among four rice genotypes with a combination of adaptive traits under drought stress by investigating the impact of drought stress on morpho-physiological and biochemical traits at the vegetative stage associated with drought tolerance. We conducted a pot experiment during the dry season of 2021 to explore the variations in accumulation and degradation activities of different traits of four rice genotypes at regular stress intervals. Drought stress decreased relative water content by 32.86

The most devastating abiotic stress on plant growth and development is drought. Abscisic acid plays a critical role in the physiological, biochemical, and molecular changes that plants initiate to counteract the negative effects of drought. The present investigation aims to study the impact of exogenously applied ABA in mitigating drought stress in rice varieties. Six rice genotypes were exposed to four types of treatments such as control (C), osmotic stress (2

A long tracrRNA (tracr-L), which naturally act as single guide RNA, and its truncated version, Δtracr-L, from S. pyogenes, efficiently induce Cas9-mediated double-strand breaks (DSBs) in plant genomic loci, as demonstrated by in vitro cleavage assay and protoplast transfection. CRISPR-Cas system provides a form of immune memory in prokaryotes and archaea, protecting them against viruses and foreign genetic elements. In Streptococcus pyogenes, this system includes the pre-crRNA along with another non-coding RNA, tracrRNA, which aids in CRISPR-based immunity. In S. pyogenes, two distinct tracrRNAs are produced: a long form (tracr-L) and a short form (tracr-S). The tracr-S regulates crRNA biogenesis and Cas9 cleavage, while tracr-L suppresses CRISPR-Cas expression by targeting the Cas9 promoter to prevent autoimmunity. Deleting 79 nucleotides from tracr-L results in Δtracr-L, which retains similar functionality in gene repression. This study investigates, for the first time, the effectiveness of tracr-L, and Δtracr-L in genome editing within plant systems. In vitro cleavage assays using purified Cas9 and synthesized sgRNAs targeting the Cas9 gene, OsPDS, and the OsSWEET11 promoter revealed that across all target sites, tracr-S demonstrated the highest cleavage efficiency compared to tracr-L and Δtracr-L. For in vivo genome editing, we transfected rice protoplasts with tracr-L, Δtracr-L, and tracr-S, targeting three rice genes: OsPDS, OsSPL14, and the promoter of OsSWEET14. Amplicon deep sequencing revealed various types of indels at the target regions across all three tracrRNA versions, indicating comparable levels of efficiency. This study establishes the utility of both the long-form tracrRNA (tracr-L) and its truncated variant (Δtracr-L) in eukaryote genome editing. These two new forms of tracrRNA provide proof of concept and expand the CRISPR-Cas toolkit for plant genome editing applications, and for eukaryotes more broadly.

The growth and development of plants are significantly affected by abiotic stress, ultimately influencing their quality and yield. Further, the effects of global warming and alterations in rainfall patterns are leading to substantial losses in crop productivity. The detrimental effects of such stress include the disruption of cellular redox homeostasis, the generation of reactive oxygen species (ROS), and oxidative stress in different cellular compartments, leading to their accumulation in various regions of the plant. This accumulation ultimately causes deleterious effects on proteins, lipids, carbohydrates, and DNA, which can result in membrane impairment and cell death. To counter these stressors and maintain essential balance, plants employ various mechanisms. Notably, the study of gasotransmitters in plants has garnered substantial attention, particularly in the context of abiotic stress. Gasotransmitters, a class of signaling molecules, play a crucial role in the functioning of plants under stress conditions. Examples of gasotransmitters include carbon monoxide, nitric oxide, and hydrogen sulfide. Furthermore, when plants experience combined stress, these gasotransmitters modulate cellular activities by interacting with other components of signal transduction. These gasotransmitters, in turn, boost the activity of several antioxidant enzymes, mitigate ROS harm, and enhance plant tolerance to diverse stress conditions. Therefore, the primary goal of this article is to familiarize readers with the production of gasotransmitters in plants, triggered by abiotic stress. Additionally, the interaction of gasotransmitters in plants under abiotic stress is discussed. Hence, understanding the specific and multifactorial stress conditions in which gasotransmitters are produced and exploring the crosstalk between various gasotransmitters can help elucidate how plants withstand multiple abiotic stresses effectively. Thus, due to their promising potential in agriculture, gasotransmitters are expected to find widespread adoption in the near future to enhance agriculture production through developing climate-smart cultivars, especially in the context of changing climate scenarios.

Abstract Identifying and engineering RNA-guided genome editing nucleases for size reduction is a highly coveted pursuit aimed at overcoming various bottlenecks. The size reduction not only facilitates effective delivery but also contributes to the generation of fusion proteins, enabling versatile applications in genome engineering. In this study, we demonstrate high-efficiency genome editing in both monocots and dicots, with average editing rates ranging from 0.63% to 33.58% and reaching up to 69%, using a 408-amino acid-long transposon-associated TnpB. Furthermore, we repurpose a catalytically dead TnpB system for transcriptional activation and base editing. This miniature TnpB, approximately one-third the size of canonical Cas9/Cas12a, emerges as a highly valuable tool for diverse applications in plant genome engineering and gene regulation.

Developing C4 rice is one of the global research challenges for yield improvement. In the optimal environment, the key difference between C3 and C4 plants with reference to biomass accumulation is photorespiration. Photorespiration is important for a plant’s survival. In spite of the high energy cost and carbon loss, diversion of a significant part of carbon from photorespiration to enrich CO2 concentration (preventing carbon loss) was opted for. Installation of photorespiratory bypasses was reported to improve biomass and yield in C3 plants. The contribution of non-foliar photosynthesis to yield improvement was well documented. However, its underlying genetic differences, when compared to foliar photosynthesis, are a research gap. In three rice genotypes (APO, BAM4234, and CROSSA), we compared the expression levels (for genes associated with photosynthesis and photorespiration) between the photosynthetic non-foliar (3–5-day old developing grains and peduncle) and foliar (flag leaf) organs to understand their differential expression pattern using an RNA-seq approach. Significant downregulation of the genes of photorespiration was observed in non-foliar photosynthetic tissue (3–5 dpa old developing grains) when compared to the flag leaves. Simultaneously, our study also revealed significant upregulation of the chloroplastic pyruvate dehydrogenase (cpPDC, BGIOSGA015796) gene in developing grains, when compared to the flag leaf, in all three genotypes. The occurrence of an in planta photorespiratory bypass in the photosynthetic tissues of the developing grains in rice is proposed. Enhanced expression levels for the cpPdc gene in the foliar tissues will potentially install a photorespiratory bypass for enhanced biomass accumulation and thereby yield.

Rice grains are the major source of nutrition for more than half of the world's population. With increased frequencies of cyclones in the last decade during grain maturation stage of rice crop, most of the rice cultivars in lowland ecologies are getting affected by pre harvest sprouting due to flash flooding and incessant rains. Significant economic loss is incurred in the global food grain industry of cereals due to pre-harvest sprouting (PHS). It is very important to develop climate resilient varieties with PHS resistant traits introgressed in them. Well characterized PHS resistant rice genotypes with optimal dormancy that can serve as donors are need of the hour. We conducted an experiment to identify PHS resistant genotypes, and also determine to their physiological and biochemical characteristics. 96 diverse rice genotypes were evaluated for PHS resistance from 20 to 40 days after flowering (DAF). Based on their response, 16 contrasting genotypes were identified from 96 genotypes to further study the underlying mechanism of PHS resistance. The results revealed that, susceptible genotypes (8) exhibited very high germination percentage (4 to 87.5

Pigeon pea, vital for farmers in semi-arid regions, suffers yield losses from Fusarium wilt caused by Fusarium udum. This study demonstrates that introducing the rice oxalate oxidase 4 (Osoxo4) gene significantly boosts wilt resistance. Enhanced resistance in transgenic lines was confirmed through gene expression analysis, enzyme activity assays, biochemical assessments, histochemical staining and in vitro and in vivo bioassays, including spore germination tests. We performed proteomics and metabolomics analyses to investigate mechanisms of enhanced resistance. LC-MS/MS-based label-free proteomics of wilt-infected transgenic and wild-type pigeon pea leaves identified 2386 proteins, with 1048 showing significant abundance changes-738 upregulated and 310 downregulated-in transgenic plants. Notably, proteins such as HMG1/2-like protein, Putative nucleosome assembly protein C364.06, DEAD-box ATP-dependent RNA helicase 3, Lipoxygenase 1, Annexin D1 and Annexin-like protein RJ4 were significantly upregulated, indicating their potential role in developing wilt-resistant cultivars. Metabolomic analysis showed elevated levels of amino acids, sugars, oxalic acid, sugar alcohols and myo-inositol in transgenic pigeon pea, with upregulated pathways in Sugar and Starch Metabolism and Inositol Phosphate Metabolism, indicating enhanced resilience to wilt stress. This study highlights unique regulatory proteins and metabolites, offering insights into stress adaptation and guiding genetic interventions for breeding disease-resistant pigeon pea varieties.

Rice is the major staple food crop for more than 50% of the world's total population, and its production is of immense importance for global food security. As a photophilic plant, its yield is governed by the quality and duration of light. Like all photosynthesizing plants, rice perceives the changes in the intensity of environmental light using phytochromes as photoreceptors, and it initiates a morphological response that is termed as the shade-avoidance response (SAR). Phytochromes (PHYs) are the most important photoreceptor family, and they are primarily responsible for the absorption of the red (R) and far-red (FR) spectra of light. In our endeavor, we identified the morphological differences between two contrasting cultivars of rice: IR-64 (low-light susceptible) and Swarnaprabha (low-light tolerant), and we observed the phenological differences in their growth in response to the reduced light conditions. In order to create genomic resources for low-light tolerant rice, we constructed a subgenomic library of Swarnaprabha that expedited our efforts to isolate light-responsive photoreceptors. The titer of the library was found to be 3.22 × 105 cfu/mL, and the constructed library comprised clones of 4-9 kb in length. The library was found to be highly efficient as per the number of recombinant clones. The subgenomic library will serve as a genomic resource for the Gramineae community to isolate photoreceptors and other genes from rice.

With the establishment of human civilization, wild plant species were domesticated and cultivated at their centres of origin and further disseminated in different parts of the world. While being grown in the wild and on farms, innumerable mutations occurred over years creating new variations in their genome. Today's improved crop plants are the result of years of artificial selection for a few of those mutations, many times coupled with deliberate selection for desirable recombinants that originated in nature or developed through targeted breeding. Artificial phenotypic selection leaves footprints in the genome of crop species. Over the last three decades, researchers have identified numerous genes and causal mutations associated with domestication events, leading to a better understanding of how our forefathers and foremothers tinkered with plant development to meet their food and fodder needs. Our ability to script complex genetic information through efficient genome editing tools has enabled us to take a great leap forward to accelerate crop domestication. In this review, we have discussed how genome editing tools facilitate the domestication of wild and semi-domesticated species, the prerequisites for performing editing in wild genomes, and the potential future target loci for installing domestication syndrome rapidly in wild plant species. Genome editing technologies could help us bring wild and partially domesticated crop plants to mainstream agriculture to sustainably meet our current and future needs.

In cereals, pre-harvest sprouting (PHS) or vivipary is a key physiological and agronomic trait that causes huge economic loss. PHS triggered by typhoons, cyclones, and high relative humidity at the late seed maturation stage is becoming a major threat to rice production in India. To explore the mechanism of PHS in rice, we evaluated 96 rice genotypes for PHS resistance and discovered 12 PHS resistant genotypes. These genotypes were classified into two groups susceptible and resistant, based on their phenotype. From the 96 genotypes, 16 contrasting genotypes were chosen, to unravel the underlying mechanism associated with PHS resistance. The results revealed that resistant genotypes had 0% germination at all the flowering stages (20 to 40 DAF), while susceptible genotypes had 4 to 87.5% germination from 20 to 40 DAF. In terms of pericarp color, 7 out of 8 resistant genotypes had red/pigmented pericarp color while the susceptible genotypes had white/non-pigmented pericarp color. The carotenoid content of leaves and seeds from 20 to 40 DAF was also measured and found to be significantly higher in resistant genotypes than susceptible genotypes. Carotenoids have been demonstrated to increase resistance by assisting in the synthesis of ABA and thereby seed dormancy. The 12 resistant genotypes were examined for germination to decide the duration of dormancy. The duration of dormancy varied in these 12 resistant genotypes varying from 10 days up to 40 days after harvest. These findings suggest that these novel PHS resistant genotypes (PB-68, HT-81, PB-50(1), HT-86, HT-20, Mahulata, PB-285, PB-47, NHN-279, PB-65, PB-259 and Budidhan) may be exploited as donors in the crop improvement programmes to generate PHS resistant genotypes.