Search Results (544)

Direct seeded rice, being less water- and labor-intensive, can be an alternative approach to conventional rice planting methods. However, uneven and poor stand establishment caused by deep sowing in the field is one of the major hurdles in the adoption of direct seeding technology. Varieties with the potential to emerge from deeper layers of soil may have a positive impact on crop establishment. To evaluate the behavior of ten rice cultivars against their potential to emerge from different soil depths (0, 2.5, and 5.0 cm), a pot experiment was conducted under semi-controlled conditions at the PARC Rice Programme, Kala Shah Kaku, Lahore. Data on different seedling parameters were collected. The results showed that the highest mean seedling emergence percentage (95%) was achieved by the tested genotypes at a 2.5 cm seeding depth, while surface sowing and placement of seeds at a 5 cm depth demonstrated a similar mean emergence percentage (89%). Seeding depth, genotypes, and their interactions significantly affected mean emergence time, mesocotyl and coleoptile lengths, and root and shoot lengths. Sowing seeds at a 5 cm depth increased mean emergence time by 28%. However, increasing sowing depth increased the coleoptile length, mesocotyl length, first leaf sheath length, and shoot length of rice seedlings. Mesocotyls and coleoptile lengths showed a linear relationship with mean emergence time. Mesocotyl and coleoptile are key structures of the apical–basal axis in grasses that elongate to facilitate the emergence of germinating seeds under deep sowing. The longest coleoptiles (1.47 cm) and mesocotyls (3.27 cm) were measured from seedlings sown at a depth of 5 cm. Among genotypes, PK-1121 exhibited maximum coleoptile elongation (2.10 cm) under deep sowing (5 cm), while the longest mesocotyls were recorded from deep-sown (5 cm) seedlings of Chenab Basmati. Root length was found to be inversely proportional to sowing depth. PK-1121 aromatic, Kisan Basmati, Punjab Basmati, and Chenab Basmati produced longer shoots (22.61, 23.37, 23.32, and 21.05 cm, respectively) and took a relatively short time for emergence when sown deep. These varieties may have better potential to emerge from deeper soil layers, which may have a positive impact on even germination and better crop stand establishment. Full article

This systematic review synthesizes evidence on upland rice (Oryza sativa L.) genotypes resistant to neck blast disease caused by Magnaporthe oryzae, focusing on resistant lines, screening methods, and genetic factors underlying resistance. Empirical studies published in English between 1980 and 2025 were identified through searches of PubMed, ScienceDirect, Google Scholar, and grey literature, with final searches completed on 31 October 2025. Eligible studies evaluated upland rice under upland or rainfed conditions. The risk of bias was assessed using a customized framework adapted from the ROBINS-I tool, and findings were synthesized narratively due to substantial methodological heterogeneity. Six studies from Asia and Africa, encompassing 248 genotypes, met the inclusion criteria. Twenty genotypes—including Kahei, Barkhe 1032, Barkhe 1035, Barkhe 2014, several NERICA lines, and BC1F4 backcross derivatives—demonstrated moderate to high resistance based on the IRRI 0–9 Standard Evaluation System. Two studies reported quantitative trait loci (qBFR4-1, qBl1, and qBl2) associated with durable resistance, highlighting the potential of QTL-based breeding. Despite limitations related to small sample sizes, heterogeneous methodologies, and limited molecular characterization, particularly for neck blast-specific resistance, this review underscores the promise of marker-assisted selection. Future research should prioritize neck blast-focused QTL validation, expanded genomic screening, harmonized screening protocols, and multi-location field trials to confirm resistance durability and agronomic performance across diverse upland environments. Full article

Accurate genotyping of small insertions and deletions (InDels; <5 bp) remains technically challenging in routine molecular breeding, largely due to the limited resolution of agarose gel electrophoresis and the labor-intensive nature of polyacrylamide-based assays. Here, we present the Tri-Primer Amplification Refractory Mutation System (TP-ARMS), a simple and cost-effective PCR-based strategy that enables high-resolution genotyping of small InDels using standard agarose gels. The TP-ARMS employs a universal reverse primer in combination with two allele-specific forward primers targeting insertion and deletion alleles, respectively. This design allows clear discrimination of homozygous and heterozygous genotypes using a two-tube PCR workflow. The method showed complete concordance with Sanger sequencing in detecting 1–5 bp InDels across multiple crop species, including rice (Oryza sativa) and quinoa (Chenopodium quinoa). In addition, using a TP-ARMS reduced experimental time by approximately 90% compared with PAGE-based approaches and avoided the high equipment and DNA quality requirements of fluorescence-based assays. The practical applicability of the TP-ARMS was demonstrated in breeding populations, including efficient genotyping of a 3-bp InDel in OsNRAMP5 associated with cadmium accumulation and a 6-bp promoter InDel in OsSPL10 underlying natural variation in rice trichome density across 370 accessions. Collectively, the TP-ARMS provides a robust, scalable, and low-cost solution for precise small InDel genotyping, with broad applicability in marker-assisted breeding and functional genetic studies. Full article

Background: Rice is one of the world’s main staple crops , and improving its productivity and resilience is important to achieving food security under varying climatic conditions. Objectives: This systematic review synthesizes the existing evidence on the application, technical limitations, and potential of the development of genome editing technologies (CRISPR-Cas) in rice (Oryza sativa L.), as well as presents a novel approach called the CRISPR Trait Prioritization and Readiness Framework (CTPRF). Methods: Peer-reviewed articles that reported applications of genome editing based on the CRISPR-Cas system in the genome of rice for trait improvement or functional genomics were identified through searches fromPubMed, Scopus, Web of Science, and Google Scholar with studies published between 2012 and 2025. Studies were screened on predefined inclusion criteria related to experimental validation, reporting of editing efficiency, and clear phenotypic results. Data on CRISPR systems, target genes, methods of delivery, traits modified, and phenotypic results were extracted and synthesized by comparative analysis. Results: A wide variety of different CRISPR systems have been used in rice, and our results indicate that NHEJ-mediated knockouts are effective in average genotypes with editing efficiencies in the range of 70–90%, but HDR and prime editing are still under 10%. The CTPRF is being introduced as a strategic decision support tool to evaluate traits from four dimensions: technical feasibility, phenotypic predictability, impact potential, and regulatory pathway. We use this framework for case studies in pioneering countries (USA, Japan, China) and show how it can be useful for guiding research investment and policy. Conclusions: CRISPR-Cas technologies have transformed rice breeding, but their introduction requires overcoming genotype-dependent barriers to transformation and negotiating patchwork regulatory environments. The CTPRF offers a roadmap for the acceleration of the development of climate-resilient and nutritious rice varieties for the action plan. Full article

Efficient in vitro regeneration remains a major constraint in the genetic transformation, genome editing, and molecular breeding of wheat (Triticum aestivum L.), largely due to strong genotype-dependent recalcitrance and limited activation of developmental programs required for somatic embryogenesis. Plant regeneration relies on extensive transcriptional reprogramming and epigenetic remodeling orchestrated by morphogenic regulators that modulate meristem identity, as well as cellular pluri- and totipotency. In this review, we synthesize current molecular knowledge on key transcription factors (BBM, WUS/WUS2, GRF-GIF, WOX, LAX1, SERK, WIND1/ERF115) and signaling peptides (CLE/CLV-WUS module, phytosulfokine/PSK) that regulate embryogenic competence in monocot cereals, with emphasis on their orthologs and functional relevance in wheat. We highlight how controlled expression of these morphogenic genes, promoter engineering, and transient or excisable induction systems can significantly enhance regeneration capacity, reduce chimerism in CRISPR-Cas-edited plants, and facilitate genotype-independent transformation. We also discuss epigenetic and metabolic constraints underlying wheat recalcitrance and their potential modulation to improve culture responsiveness. By integrating evidence from wheat, rice, maize, and barley, we outline conserved gene-regulatory networks that reinitiate totipotency and propose strategies to accelerate doubled haploid production and speed-breeding pipelines. Collectively, morphogenic factors emerge as central molecular tools for overcoming regeneration bottlenecks and enabling next-generation wheat improvement. The objective of this review is to synthesize and critically evaluate current molecular knowledge on morphogenic regulators controlling in vitro regeneration in wheat (Triticum aestivum L.), with particular emphasis on their roles in genetic transformation and genome editing. Full article

Selenium (Se) biofortification in rice presents a promising strategy to address Se deficiency in populations relying on rice as a staple food. This study evaluated the impact of foliar Se application on Se accumulation, its distribution in unpolished and polished rice grains, grain yield, and antioxidant capacity across 21 rice genotypes. Foliar Se application significantly improved grain yield, with increases ranging from 5.7 to 67.5% compared to non-foliar Se application. Se concentrations in both unpolished and polished grains were notably enhanced by foliar application, reaching 41.1–543.9 µg kg⁻¹, whereas non-foliar treatments resulted in much lower concentrations (0–30.5 µg kg⁻¹). Foliar Se also altered Se partitioning, decreasing Se retention in unpolished grains (from 9.8–100% under non-foliar application to 19.7–66.1% with foliar Se application) and increasing its proportion in polished rice. Se loss during polishing was genotype-dependent and generally reduced by foliar Se application (9.4–72.3%). Antioxidant capacity was highest in unpolished rice and varied among genotypes, increasing further with foliar Se. A positive correlation between grain antioxidant capacity and Se concentration was observed in unpolished, but not polished rice. Overall, these findings demonstrate the effectiveness of foliar Se biofortification in enhancing Se content and antioxidant properties, emphasizing the importance of genotype selection such as RD16, RD79, KDML105, K2, KJ CMU 107, and HMD to maximize biofortification benefits. Full article

Rice blast and bacterial blight cause severe harm to rice production, and the breeding of resistant varieties guarantees the safety of rice production. Meanwhile, multigene pyramiding breeding based on molecular marker-assisted selection is a crucial approach for rice breeding to combat multiple diseases. This study aimed to develop accurate and efficient PARMS markers for rice blast resistance genes Pita, Pigm, and Pi2, and bacterial blight resistance gene Xa23. A systematic genotyping analysis of the resistant alleles of these 4 genes was performed on 384 major cultivated varieties in production. The results showed that only 5.21% of the varieties harbored more than two resistant alleles simultaneously. Using traditional breeding strategies in combination with the developed PARMS markers, the high-quality three-line male sterile line Ruanfeng A (pyramiding Pita and Pigm) and the strong restorer line Gui 610 (pyramiding Pi2 and Xa23) were bred. Crossing these lines produced a new hybrid rice variety, Ruanfengyou 610. Ruanfengyou 610 pyramids 4 resistance genes (Pita/Pigm/Pi2/Xa23), exhibits resistance to both rice blast and bacterial blight, has prominent heterosis and excellent grain quality, and has strong application potential, which is of great significance for ensuring the safety of rice production. Full article

Background/Objectives: Chemical methods for quantifying resistant starch (RS) in rice are labor-intensive, costly, and lack high repeatability, creating a bottleneck in breeding. This study aimed to develop specific, codominant molecular markers for the Wx gene to enable rapid and accurate genotype screening for RS content, thereby accelerating the development of high-RS rice varieties. Methods: Based on sequence alignment of the Wx gene in rice varieties with divergent RS content, a key single-nucleotide polymorphism was targeted. Two sets of tetra-primer amplification refractory mutation system polymerase chain reaction (ARMS-PCR) markers, T-Wx9-RS1 and T-Wx9-RS2, were designed. These markers were used to genotype diverse rice varieties and F₄ segregating populations, with results validated against standard chemical assays. Results: Sequence analysis identified a critical T → C base mutation at position 202 of the ninth exon in high-RS varieties. The developed ARMS-PCR markers successfully and consistently distinguished all three possible genotypes (homozygous mutant, homozygous wild-type, and heterozygous). The genotyping results showed complete concordance with the phenotypes determined by chemical methods. Conclusions: The developed molecular markers, T-Wx9-RS1 and T-Wx9-RS2, provide a rapid, reliable, and cost-effective tool for marker-assisted selection of high resistant starch content in rice. Their implementation can significantly enhance screening efficiency and expedite the breeding pipeline for novel, nutritionally improved rice cultivars. Full article

Soil salinity is a major abiotic stress that limits rice production, with severity varying among genotypes. It disrupts key physiological processes, particularly water uptake and membrane integrity. This study evaluated six rice genotypes to (i) determine the critical salinity threshold for seed germination and (ii) investigate the physiological mechanisms underlying genotypic variation. Seeds were exposed to saline solutions of up to 32 dS m⁻¹ under controlled conditions, and germination was recorded at 2, 5, 10, and 14 days after stress imposition. Additional assays at 0, 12, 18, and 24 dS m⁻¹ for 1, 3, and 5 days assessed water uptake, electrolyte leakage, and malondialdehyde (MDA) accumulation. The critical threshold for germination was consistent across genotypes (26.01–28.53 dS m⁻¹), except for Nona Bokra, which was more sensitive (20.5 dS m⁻¹). Salinity reduced seed water uptake and promoted membrane degradation, as evidenced by increased electrolyte leakage and MDA accumulation, with severity proportional to stress duration. Full article

Background: The coordinated improvement of yield, quality and resistance is a primary goal in rice breeding. Gene editing technology is a novel method for precise multiplex gene improvement. Methods: In this study, we constructed a multiplex CRISPR/Cas9 vector targeting yield-related genes (GS3, OsPIL15, Gn1a), fragrance gene (OsBADH2) and rice blast resistance gene (Pi21) to pyramid traits for enhanced yield, quality, and disease resistance in rice. A tRNA-assisted CRISPR/Cas9 multiplex gene editing vector, M601-OsPIL15/GS3/Gn1a/OsBADH2/Pi21-gRNA, was constructed. Genetic transformation was performed using the Agrobacterium-mediated method with the japonica rice variety Xin Dao 53 as the recipient. Mutation editing efficiency was detected in T₀ transgenic plants. Grain length, grain number per panicle, thousand-grain weight, 2-acetyl-1-pyrroline (2-AP) content, and rice blast resistance of homozygous lines were measured in the T₃ generations. Results: Effectively edited plants were obtained in the T₀ generation. The simultaneous editing efficiency for all five genes reached 9.38%. The individual gene editing efficiencies for Pi21, GS3, OsBADH2, Gn1a, and OsPIL15 were 78%, 63%, 56%, 54%, and 13%, respectively. Five five-gene homozygous edited lines with two genotypes were selected in the T₂ generation. In the T₃ generation, compared with the wild-type (WT), the edited homozygous lines showed increased grain number per panicle (14.60–25.61%), increased grain length (7.39–11.16%), increased grain length–width ratio (8.37–13.02%), increased thousand-grain weight (3.79–9.15%), a 42–64 folds increase in the fragrant substance 2-AP content, and significantly enhanced rice blast resistance. Meanwhile, there were no significant changes in other agronomic traits. Conclusions: CRISPR/Cas9-mediated multiplex gene editing technology enabled the simultaneous editing of genes related to rice yield, quality, and disease resistance. This provides an effective approach for obtaining new japonica rice germplasm with blast resistance, long grains, and fragrance. Full article

Egyptian rice landraces represent a unique genetic reservoir shaped by arid environments, yet their genomic and transcriptional response to salt stress remains largely unexplored. Here, we integrated genomic, transcriptomic, and population genetic analyses to systematically unravel the mechanisms of salt tolerance in this vital germplasm. Resequencing 56 Egyptian accessions uncovered a treasure trove of genetic variation, including 18,204 novel SNPs. An expanded GWAS on 258 accessions discovered 17 novel loci for salt tolerance. Parallel RNA-Seq analysis of a salt-tolerant-susceptible pair (Giza 176 vs. 9311) under stress delineated a defense network centered on phenylpropanoid and lipid metabolic pathways in the tolerant genotype. The power of our integrated approach was exemplified by the convergent identification of ONAC063, where GWAS loci, transcriptional responsiveness, and haplotype-phenotype association collectively validated its role. Furthermore, selection sweep analysis highlighted 62 candidate genes under divergent selection. Our study not only positions Egyptian rice as a key resource for allele mining but also establishes a robust multi-omics pipeline for bridging genetic diversity with complex traits, accelerating the discovery of functional genes for breeding climate-resilient crops. Full article

Yellow Mosaic Disease (YMD) caused by mungbean yellow mosaic virus (MYMV, begomovirus) is one of the main causes of low mungbean (Vigna radiata L.) productivity, primarily in South Asia. Agroinoculation screening for MYMV resistance in mungbean cultivar VGGRU 1, an interspecific derivative of mungbean × rice bean and VRM (Gg)1 across replications, revealed VGGRU1 as highly resistant to MYMV infection. Gas chromatography mass spectrometry analysis was performed on the methanolic leaf extracts of susceptible and resistant genotypes, along with necessary controls. The metabolite profiling of the susceptible and resistant genotypes, along with controls, identified 121 discriminant metabolites belonging to 24 different classes of metabolites. A maximum number of 27 metabolites were accumulated in agroinoculated VGGRU1 alone. Metabolite profiles of VGGRU1 and VRM1 were clustered hierarchically and revealed substantial variations between the genotypes. Fold change revealed the upregulation of amino acids and phenol in the resistant genotype. The resistant genotype, VGGRU1, showed significantly higher levels of key defense-related metabolites, such as amino acids and phenolics. In this study, 18 significant VIP metabolites were identified, differentiating the resistant VGGRU1 and susceptible VRM (Gg)1 genotypes. Full article

Cold stress impairs crop productivity through cascading inhibition of root growth, nitrogen (N) metabolism, and photosynthesis, yet the systematic linkages among these physiological disruptions remain poorly understood. It is crucial to elucidate the mechanisms by which cold-tolerant varieties maintain root growth and N-metabolizing enzyme homeostasis. This two-year field study investigated how cold duration at the tillering stage impacted root traits, N metabolism, photosynthesis, and their relationships with the yield of two japonica rice varieties differing in cold tolerance. A cold-tolerant (Dongnong 428) and a cold-sensitive variety (Songjing 10) were grown in a paddy field for two consecutive growing seasons in 2021 and 2022. Cold water (15 °C) was irrigated for 0 (denoted as D0), 5 (D5), 10 (D10), and 15 days (D15) during the tillering stage. Compared to D0, cold-water treatments significantly reduced root traits and total dry weight of both varieties. Cold stress significantly impaired N metabolism and photosynthesis, leading to significant reductions in N efficiency. The magnitude of these changes turned to greater with cold-water treatment duration. Dongnong 428 showed stronger cold tolerance, attributed to its maintenance of superior root traits and photosynthetic performance, as well as higher activities of enzymes in the roots, which sustained N assimilation and utilization. These factors primarily contributed to Dongnong 428 achieving 11.6–20.9% higher yields compared to Songjing 10. Cold stress during the tillering stage disrupts root growth and photosynthesis, impairs plant N acquisition ability, resulting in substantial yield loss. Cold-tolerant varieties maintain superior root morphology/functionality and photosynthetic performance. Full article

The System of Rice Intensification which promotes agro-ecological practices like alternate wetting and drying (AWD) to enhance root growth and resource efficiency, relies on the genotypic capacity of rice varieties to undergo physiological adaptation. This study elucidates the molecular basis of such adaptation by investigating the transcriptomic profile of four rice varieties to continuous flooding (CF) and AWD at 50 days after transplanting. Our analysis revealed distinct, organ-specific acclimation strategies. Roots underwent extensive transcriptional reprogramming, underscoring their role as the primary site of plasticity. Under CF, a conserved response involving cell wall reinforcement was accompanied by variety-specific strategies, ranging from sustained growth to enhanced anaerobic metabolism. Under AWD, roots shifted toward water stress management, with varieties employing distinct defensive (e.g., diterpenoid biosynthesis) and metabolic programs. Associated transcription factors (TFs) enriched under CF included Dof and MYB, whereas bZIP, HSF, and WRKY factors predominated under AWD. In leaves, acclimation to AWD involved more targeted adjustments, including modulation of nitric oxide signaling and photoprotective pathways, regulated by TFs such as WRKY, NAC, and HSF. Varieties with robust TF responses, such as IR64 and Hitachi hatamochi, showed comprehensive regulatory shifts, while others exhibited more constrained profiles. Overall, this study provides a molecular framework for understanding variety-specific adaptation to SRI-relevant water management practices and identifies key TFs as promising candidates for breeding climate-resilient rice. Full article

Nitrogen (N) is an essential nutrient for the growth and development of rice. However, excessive N fertiliser application and low N Use Efficiency (NUE) have led to serious environmental problems and threatened agricultural sustainability. In this study, we compared the physiological and transcriptomic profiles of roots of two cultivars exposed to normal nitrogen (NN) and low nitrogen (LN). The results showed that the LN treatment suppressed root growth and severely affected enzymatic activities in the roots of both rice cultivars compared to the NN treatment. Moreover, HJ753 exhibited significantly higher activities of NITRATE REDUCTASE (NR) and GLUTAMINE SYNTHETASE (GS) in its roots than DJ8 under both LN and NN conditions. Transcriptomic analysis identified 23,205 genes across all samples, with more than 5000 differentially expressed genes (DEGs) detected in response to LN stress in both cultivars. The KEGG analysis revealed that the DEGs were primarily involved in DNA replication, tryptophan metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and N metabolism. Under LN stress, most genes associated with tryptophan metabolism and phenylpropanoid biosynthesis pathways remained stable or were upregulated in both cultivars. In contrast, genes related to auxin signalling transduction, N metabolism, and N utilisation exhibited significant genotype-specific expression patterns between HJ753 and DJ8. In conclusion, this study elucidated the genotypic differences in root development and N response mechanisms under LN stress at the molecular level, providing new insights into the regulatory mechanisms of N efficiency that may be used to develop and support the breeding of N-efficient rice cultivars. Full article