Background: Rice (Oryza sativa L.) is the major source of daily caloric intake for more than 30% of the human population. However, the sustained productivity of this staple food crop is continuously threatened by various pathogens and herbivores. Breeding has been successful in utilizing various mechanisms of defense by gene pyramiding in elite cultivars, but the continuous resurgence of highly resistant races of pathogens and herbivores often overcomes the inherent capacity of host plant immunity. MicroRNAs (miRNAs) are endogenous, short, single-stranded, non-coding RNA molecules that regulate gene expression by sequence-specific cleavage of target mRNA or suppressing target mRNA translation. While miRNAs function as upstream regulators of plant growth, development, and host immunity, their direct effects on growth and development in the context of balancing defenses with agronomic potential have not been extensively discussed and explored as a more viable strategy in breeding for disease and pest resistant cultivars of rice with optimal agronomic potentials. Results: Using the available knowledge in rice and other model plants, this review examines the important roles of miRNAs in regulating host responses to various fungal, bacterial, and viral pathogens, and insect pests, in the context of gains and trade-offs to crop yield. Gains from R-gene-mediated resistance deployed in modern rice cultivars are often undermined by the rapid breakdown of resistance, negative pleiotropic effects, and linkage drags with undesirable traits. In stark contrast, several classes of miRNAs are known to efficiently balance the positive gains from host immunity without significant costs in terms of losses in agronomic potentials (i.e., yield penalty) in rice. Defense-related miRNAs such as Osa-miR156, Osa-miR159, Osa-miR162, Osa-miR396, Osa-530, Osa-miR1432, Osa-miR1871, and Osa-miR1873 are critical in fine-tuning and integrating immune responses with physiological processes that are necessary to the maintenance of grain yield. Recent research has shown that many defense-related miRNAs regulate complex and agronomically important traits. Conclusions: Identification of novel immune-responsive miRNAs that orchestrate physiological processes critical to the full expression of agronomic potential will facilitate the stacking of optimal combinations of miRNA-encoding genes to develop high-yielding cultivars with durable resistance to disease and insect pests with minimal penalties to yield.

Crop domestication has a tremendous impact on socio-economic conditions and human civilization. Modern cultivars were domesticated from their wild progenitors, thousands of years ago by the selection of natural variation by humans. New cultivars are being developed by crossing two or more compatible individuals. But the limited genetic diversity in the cultivars severely affects the yield and renders the crop susceptible to many biotic and abiotic stresses. Crop wild relatives (CWRs) are the rich reservoir for many valuable agronomic traits. The incorporation of useful genes from CWR is one of the sustainable approaches for enriching the gene pool of cultivated crops. However, CWRs are not suited for urban and intensive cultivation because of several undesirable traits. Researchers have begun to study the domestication traits in the CWRs and modify them using genome editing tools to make them suitable for extensive cultivation. Growing evidence has shown that modification in these genes is not sufficient to bring the desired change in the neodomesticated crop. However, the other dynamic genetic factors such as microRNAs (miRNAs), transposable elements, cis-regulatory elements, and epigenetic changes have reshaped the domesticated crops. The creation of allelic series for many valuable domestication traits through genome editing holds great potential for the accelerated development of neodomesticated crops. The present review describes the current understanding of the genetics of domestication traits that are responsible for the agricultural revolution. The targeted mutagenesis in these domestication genes via CRISPR/Cas9 could be used for the rapid domestication of CWRs.

Sheath blight (ShB) is the most serious disease of rice (Oryza sativa L.), caused by the soil-borne fungus Rhizoctonia solani Kühn (R. solani). It poses a significant threat to global rice productivity, resulting in approximately 50% annual yield loss. Managing ShB is particularly challenging due to the broad host range of the pathogen, its necrotrophic nature, the emergence of new races, and the limited availability of highly resistant germplasm. In this study, we conducted QTL mapping using an F₂ population derived from a cross between a partially resistant accession (IRGC81941A) of Oryza nivara and the susceptible rice cultivar Punjab rice 121 (PR121). Our analysis identified 29 QTLs for ShB resistance, collectively explaining a phenotypic variance ranging from 4.70 to 48.05%. Notably, a cluster of four QTLs (qRLH1.1, qRLH1.2, qRLH1.5, and qRLH1.8) on chromosome 1 consistently exhibit a resistant response against R. solani. These QTLs span from 0.096 to 420.1 Kb on the rice reference genome and contain several important genes, including Ser/Thr protein kinase, auxin-responsive protein, protease inhibitor/seed storage/LTP family protein, MLO domain-containing protein, disease-responsive protein, thaumatin-like protein, Avr9/Cf9-eliciting protein, and various transcription factors. Additionally, simple sequence repeats (SSR) markers RM212 and RM246 linked to these QTLs effectively distinguish resistant and susceptible rice cultivars, showing great promise for marker-assisted selection programs. Furthermore, our study identified pre-breeding lines in the advanced backcrossed population that exhibited superior agronomic traits and sheath blight resistance compared to the recurrent parent. These promising lines hold significant potential for enhancing the sheath blight resistance in elite cultivars through targeted improvement efforts.

Rice (Oryza sativa L.) is continuously challenged by various biotic stresses including fungal, bacterial, viral, parasites, and insect pests. These stresses threaten global rice productivity each year. Numerous resistance (R) genes have been identified, but only a few of them have been deployed in rice improvement programs due to the rapid breakdown of resistance, pleiotropic effects, and negative associations with important agronomic traits. Modern varieties are being developed by pyramiding multiple R-genes from diverse germplasm. However, unregulated expression of R-genes often comes with unexpected yield trade-offs and poor plant fitness. MicroRNAs (miRNAs) are endogenous, short, single-stranded, non-coding RNA molecules that function as master regulators for balancing immunity and yield. Defense-related miRNAs such as Osa-miR156, Osa-miR162, Osa-miR396, and Osa-miR1873 have been identified in rice that fine-tunes immunity and yield under various biotic stresses. Recent advances showed that many immune-responsive miRNAs also regulate many complex traits of agronomic importance. This allows researchers to assemble the appropriate combinations of agriculturally important traits to be targeted using genetic engineering approaches that involved miRNAs.

Ashwagandha ( Withania somnifera L. Dunal) is a medicinally important plant with high demand in Ayurveda and other indigenous medicinal systems. Conventional propagation through seeds is inadequate to meet pharmaceutical demand due to poor germination, pathogen susceptibility, and genetic heterogeneity. Micropropagation provides a reliable alternative to overcome these limitations. In the present study, efficient protocols were developed for both direct and indirect regeneration. Shoot tip explants regenerated directly on MS medium supplemented with 5.0 mg/L BAP, while callus cultures induced with 0.5 mg/L 2,4-D supported indirect regeneration. Complete plantlets were established on MS medium containing 2.0 mg/L kinetin (KIN) and 0.1 mg/L IAA. Prolonged in vitro culture induced morphological, biochemical, and genetic variations among regenerants. Total protein and flavonoid contents were elevated during early subcultures, whereas H₂O₂ levels progressively declined with successive passages. Activities of ROS-scavenging enzymes such as superoxide dismutase (SOD) and ascorbate peroxidase (APX) increased significantly. Regenerated plants exhibited distinct morphological leaf variations, further supported by genetic fidelity analysis, which confirmed divergence from greenhouse-grown counterparts. To evaluate stress responses, transcript levels of oxidative and abiotic stress-related genes (SOD, CAT, MYB, and HSP70) were quantified. Among these, HSP70 showed a pronounced upregulation (6.93-fold) in regenerants. Moreover, withanolide A accumulation under heat stress was significantly enhanced, highlighting tissue culture-induced metabolic shifts. Overall, this study establishes tissue culture-induced biochemical reprogramming, stress-gene upregulation, and secondary metabolite enhancement. These findings emphasize the need for monitoring physiological and genetic stability during in vitro culture of medicinal plants.