Rice Varieties Research Articles

Morphological and Physiological Responses of Two Tropical Rice (Oryza sativa) Varieties to High-Temperature Stress

Morphological and Physiological Responses of Two Tropical Rice (Oryza sativa) Varieties to High-Temperature Stress

Impact of field drying at different initial leaf ages on growth and yield formation of direct seeding rice in Chengdu plain

AbstractTo determine the optimal drying period for direct seeding rice, we conducted experiments using two rice cultivars: hybrid indica (Shuyou 217) and conventional indica (Huang Huazhan). The experiments explored the influence of varying initial leaf development stages on tillering dynamics, leaf area, dry matter production, yield, and yield components in direct seeding rice. The results indicated a significant correlation between the initial leaf development stage and the yield of direct seeding rice. As the initial leaf development stage progressed, the number of effective panicles increased, while key traits affecting panicle yield, such as grain/spikelet? Number per panicle, seed setting rate, and 1000-grain weight, decreased. Additionally, varietal differences in tillering reduction were observed across different leaf development stages. Shuyou 217 exhibited a decrease in heading rate with increasing leaf development stage, whereas Huang Huazhan showed no significant difference. With delayed seeding planting age, both cultivars demonstrated an increasing trend in the leaf area index, initially leading to a rise in effective leaf area proportion, followed by a decline. At the full heading and maturity stages, the dry weight of the stem sheath and panicles per plant decreased as the leaf development stage was delayed. However, the output and transport rates of stem sheath assimilated first increased and then decreased. From a practical perspective, field drying management should be aligned with varietal characteristics to reduce ineffective tillering, ensure sufficient dry matter accumulation during the full heading stage, and optimize post-heading dry matter export and transport. This strategy promotes the coordination between the “source” and “sink” dynamics in rice, ultimately maximizing yield in direct-seeded rice systems.

Genome-wide association study reveals novel QTLs and candidate genes for panicle number in rice

IntroductionPanicle number (PN) is one of the three key yield components in rice, maintaining stable tiller and PN is a crucial characteristic of an ideal plant architecture. Understanding the molecular mechanisms underlying PN is essential for breeders aiming to improve rice yield.MethodsTo dissect the genetic architecture of panicle number, a genome-wide association study (GWAS) was conducted in 411 japonica rice varieties. GWAS analysis was carried out with the mixed linear model using 743,678 high-quality SNPs.ResultsOver two experimental years, we detected a total of seven quantitative trait loci (QTLs), located on chromosomes 1, 4, 6, 8, 11, and 12; notably, qPN1.1 and qPN8 were detected consistently in both years. By combining haplotype and expression analyses, OsCKX11 was identified as the candidate gene for qPN8, while LOC_Os01g07870 and LOC_Os01g07950 were identified as candidate genes for qPN1.1. Significant differences were observed among the haplotypes of these candidate genes. Additionally, qRT-PCR results showed that LOC_Os01g07870 expression levels were significantly lower in accessions with high panicle numbers compared to those with low panicle numbers.DiscussionTo understand the natural biological function of these candidate genes, further research involving overexpression or silencing in rice is needed. Despite these challenges, our results will lay the foundation for further study of panicle development and provide valuable genetic resources for developing high-panicle-number rice cultivars using genetic engineering and molecular breeding.

Evaluation of Genotypes against Water Stress and Salinity in Rice (Oryza sativa L.)

Abiotic stresses pose significant challenges to growth, yield and productivity thus threatening food security. Hence, it is essential to develop climate resilient rice varieties that mitigate the impact of abiotic stress. A study on physiological characterization for water and salinity stress was conducted in twenty-eight rice genotypes during kharif 2023 at Regional Agricultural Research Station, Maruteru. Among all the treatments, root length, shoot length, root and shoot dry weight and chlorophyll content was maximum under control followed by 1% mannitol, 2% mannitol and salinity stress. Visual scoring for water stress at seedling stage revealed that under mild water stress (1% M) more than 90% of plants survived in genotypes viz., AC-35678, FL 478, Ravana, Rahaspunjar, AUS 63, AUS 73, Vandana, NICRA 16, NICRA 17, CR-3439-4-E-17-2-1-B-1-S-1, CR-4215-2-5-2-M-4-SUB-2-5-1. Under severe water stress (2% M) more than 70% of the seedlings survived in NICRA 16, CR-4215-2-5-2-M-4-SUB-2-5-1, CRAC-4423-3, IET -18727, IC-516 149, IET-18716, AC-35678, FL 478, AC 85, Rahaspunjar, AUS 100, NICRA 17, CR-3439-4-E-17-2-1-B-1-S-1. Under salinity stress the score 3 was recorded in FL 478, and 5 in Rahaspunjar, IET -18727, NICRA 16, Ravana, NICRA 17. For both combined stresses, FL 478, Rahaspunjar, NICRA 16 and NICRA 17 were identified as tolerant and can be identified as donors for development of rice varieties having climate resilience.

Genome Wide Association Analysis for Uniform Coleoptiles Emergence and Early Seedling Growth in Rice

Early seedling vigour (ESV) is a complex trait in rice. Detection of QTLs/genes controlling these traits can help us in enhancing the yield potential in rice varieties. Association mapping is a technique based on the principle of linkage disequilibrium that is used to find genes or quantitative trait loci (QTL) underlying the complex traits. In this study of haplotype breeding 281 rice genotypes were taken. ANOVA analysis showed P- value for traits and genotypes was found significant. Similarly, P-value for interaction between the traits and genotypes was also found to be highly significant (1.8663*10-208). Further, mean germination data positively correlated with mean shoot length, mean leaf number, mean culm diameter, mean shoot dry weight, and mean shoot area of 21st day among the 281 genotypes. Among the 281 number of genotypes, 111 genotypes are found to be in PCA1 and 170 genotypes are found to be in PCA2 based on the phenotypic analysis. PCA1 component constituted 29.93% and PCA2 constituted the 13.68% of total variation in the analysis. Besides, whole genome phylogenetic analysis showed three major groups of which Group 1 consists of 215 genotypes, group 2 consists of 38 genotypes and group 3 consists of 28 genotypes respectively. Especially, both the subgroups II and III comprised of the unique genotypes from the indica and aus subpopulations of rice. In this analysis, 16 significant associations (LOD Score >7) for different traits were identified using the three different models (MLM, farmCPU, and blink) for GWAS studies Especially, one major QTL was identified for the mean coleoptiles’ emergence for 10 DAS on 11th chromosome (18983591) which explained 49% of the phenotypic variance. Additionally, another major QTL contributing to the shoot length variation of 29.75% was identified in the Chr02 (32954393) for shoot length trait on 28 DAS. A candidate gene namely Os02g0778400 UMP/CMP kinase A/adenylate kinase (LOC_Os02g53790) was located in the significant SNP region of the GWAS analysis. Further characterization of this gene would assist in elucidation of the mechanism regulating the early seedling length in rice under direct seeded rice.

Molecular Confirmation for Gall Midge (Biotype 3) Resistance in Phenotypically Resistant Rice Genotypes Using Functional Markers

This study performed molecular screening of rice genotypes, which showed no gall infestation in field conditions at the Regional Agricultural Research Station (RARS), Jagtial, during rabi, 2021-22. using functional markers such as “gm3del3” for the gm3 gene, “LRR del” for the Gm4 gene, and “PRP” for the Gm8 gene, six genotypes were analyzed. WGL-1145 contained all three resistance genes (gm3, Gm4, and Gm8). Additionally, three genotypes namely WGL-1147, WGL-1127, and Kakai had the Gm4 and Gm8 genes, while RP-5332-54-11-8-2-13 had only Gm8 and IR72476-B-P-9-3-1-1 possessed only gm3. These findings contribute to developing new rice varieties with resistance to gall midge, which can improve crop yields and food security in affected regions. Some promising rice varieties may be used as donors in breeding programs aimed at creating pyramided lines with durable gall midge resistance.

Transgenic rice (Oryza sativa L.) varieties exhibit superior salt stress resilience: a comparative study of physiological and biochemical responses in transgenic and non-transgenic genotypes

Transgenic rice (Oryza sativa L.) varieties exhibit superior salt stress resilience: a comparative study of physiological and biochemical responses in transgenic and non-transgenic genotypes

Drought Stress Screening in Backcross Inbred Lines of Rice (Oryza sativa L.) at Germination and Seedling Stage

Drought is a key stress factor that limits rice production globally. The present study was carried out to identify drought tolerant rice lines at the germination and seedling stages using polyethylene glycol (PEG) induced stress. Twenty promising high yielding BC2F4 lines, stacked with drought yield QTLs qDTY₁⸳₁ and qDTY₁₂.₁, derived from the cross between Manu Ratna X Improved White Ponni, were subjected to drought stress. Drought was imposed during germination using three levels (0, 10 and 15%) of polyethylene glycol (PEG 6000) concentrations. The experiment was conducted in factorial completely randomized block design with three replications and the observations on number of seeds germinated, root length, shoot length, germination index, germination stress tolerance index, fresh weight stress tolerance index, dry weight stress tolerance index and seedling vigour index were evaluated after stress treatment. A significant difference was noted among lines for characters under drought stress. Among the lines, MIB-29-2-3-1, MIB-29-8-5-35, MIB-43-5-3-66 and MIB-119-5-7-33 were selected which showed higher germination percentage, root length, shoot length, germination stress tolerance index and and seeding vigour index. The selected lines can be further evaluated in the field to develop drought tolerant rice varieties.

Selenium Utilization, Distribution and Its Theoretical Biofortification Enhancement in Rice Granary of China

Selenium, as an essential trace element, is intricately linked to the onset and progression of numerous diseases due to deficiencies in selenium intake. Selenium compounds exhibit tumor specificity and can efficiently inhibit the growth of tumor cells, making them potential candidates for cancer treatment. Nevertheless, given its status as one of the most widely consumed crops globally, increasing the selenium content in rice could prove advantageous in alleviating the prevailing issue of selenium intake deficiency, particularly in China. This review explored the regulatory role of selenium in rice growth, the regional distribution characteristics of soil selenium content in various rice-growing regions in China, and the impact of cultivation practices on selenium fortification in rice, aiming to suggest improved rice cultivation management strategies to enhance the capacity for rice selenium biofortification. The findings revealed that: (1) In Northeast and North China, characterized by alkaline soils and severe selenium deficiency, it is advisable to moderately decrease the duration of flooding, elevate the soil redox potential, and apply organic and nitrogen fertilizers in a judicious manner. (2) In Southwest China, which is characterized by acidic soils, alternating wet and dry irrigation should be employed, and the biofortification of selenium can be facilitated by applying lime and foliar spraying of selenium fertilizer. (3) In the south-central region of China, distinguished by acidic soils and double-cropped rice, it is recommended that intermittent or alternating wet and dry irrigation be employed, and the reasonable application of organic, silica, and selenium fertilizers is advocated. (4) In the northwest region, characterized by slightly alkaline soil and mild selenium deficiency, it is recommended to implement various water management practices, including shallow water during the seedling stage, deep water during the booting stage, and wet grain filling. Additionally, a rational application of nitrogen, phosphorus, and potassium fertilizers, along with foliar application of selenium fertilizer, should be employed. (5) Cultivating selenium-enriched, high-yielding, and high-quality rice varieties proves to be an effective strategy in addressing selenium deficiency. In conclusion, the unique characteristics of diverse rice-growing regions in China indicate that suitable water management, fertilization techniques, and varietal selection practices can effectively enhance the selenium content in rice, thereby maximizing the nutritional requirements for selenium.

Integrative Proteomic and Phosphoproteomic Profiling Reveals the Salt-Responsive Mechanisms in Two Rice Varieties (Oryza Sativa subsp. Japonica and Indica).

Salinity stress induces ionic and osmotic imbalances in rice plants that in turn negatively affect the photosynthesis rate, resulting in growth retardation and yield penalty. Efforts have, therefore, been carried out to understand the mechanism of salt tolerance, however, the complexity of biological processes at proteome levels remains a major challenge. Here, we performed a comparative proteome and phosphoproteome profiling of microsome enriched fractions of salt-tolerant (cv. IR73; indica) and salt-susceptible (cv. Dongjin/DJ; japonica) rice varieties. This approach led to the identification of 5856 proteins, of which 473 and 484 proteins showed differential modulation between DJ and IR73 sample sets, respectively. The phosphoproteome analysis led to the identification of a total of 10,873 phosphopeptides of which 2929 and 3049 phosphopeptides showed significant differences in DJ and IR73 sample sets, respectively. The integration of proteome and phosphoproteome data showed activation of ABA and Ca2+ signaling components exclusively in the salt-tolerant variety IR73 in response to salinity stress. Taken together, our results highlight the changes at proteome and phosphoproteome levels and provide a mechanistic understanding of salinity stress tolerance in rice.

Effects of Bacillus spp. inoculation on suggested shoot tolerance mechanisms in lowland rice (Oryza sativa L.) grown under iron toxicity

AbstractBackgroundIn areas of lowland rice production, high iron concentrations in the soil often lead to yield reductions. Local adapted varieties possess different adaptation mechanisms, which, however, are not fully understood. Previous studies have shown that endophytic bacteria can influence plant tolerance to abiotic stresses, including iron toxicity.AimThis study aims at analyzing the effects of different Bacillus isolates on distinct shoot tolerance mechanism in different rice cultivars grown under iron toxicity.MethodsThree lowland rice cultivars, varying in their tolerance against iron toxicity (IR31785‐58‐1‐2‐3‐3, Sahel 108, Suakoko 8), were inoculated with three Bacillus strains (two of B. pumilus and one of B. megaterium). One week after Bacillus inoculation plants were subjected to high iron levels (1000 ppm) for 7 days. Leaf symptom scoring was used to assess tolerance levels. Activities of ascorbate peroxidase (APX), glutathione reductase (GR), catalase (CAT), superoxide dismutase (SOD), and guaiacol peroxidase (PRX) were measured by spectrophotometric assays. Transcription of genes related to iron toxicity (OsFER, OsFRO1, OsNRAMP6) was determined by RT‐qPCR. Bacterial production of NO was evaluated by measuring nitrite levels in the culture supernatants.ResultsIn general, iron toxicity affected the activities of APX, GR, CAT, and PRX but not SOD activity. Only PRX activity in response to iron differed between cultivars with a significantly stronger increase in IR31785‐58‐1‐2‐3‐3. Inoculation with B. pumilus Ni9MO12 led to higher activity of CAT in the leaf sheaths of all cultivars and an increase in GR activity in the sheaths that was significantly higher in Suakoko 8. In the young leaf blades of IR31785‐58‐1‐2‐3‐3, transcription of OsFRO1 and OsNRAMP6 was not significantly affected by Bacillus inoculation, whereas accumulation of OsFER mRNA was significantly higher in iron‐stressed, B. pumilus Ni9MO12 inoculated plants compared to non‐inoculated, non‐iron‐stressed plants. Nitrite concentration as an indicator for NO production was increased in B. pumilus Ni9MO12 culture supernatants.ConclusionOur results show that in the sensitive cultivar IR31785‐58‐1‐2‐3‐3 tolerance to iron toxicity increases when inoculated with B. pumilus Ni9MO12, coinciding with higher levels of ferritin transcription. NO production by the Bacillus isolate might confer the promotion of OsFER gene transcription in the inoculated plants.

Rice Responses to the Stem Borer Diatraea saccharalis (Lepidoptera: Crambidae) by Infrared-Thermal Imaging: Implications for Field Management

Diatraea saccharalis (Fabricius) is a major pest of rice crops, and its early detection—before any visible plant damage occurs—is crucial to prevent yield losses and establish effective, rational control methods. This study aimed to model the infrared-thermal responses of rice cultivars to D. saccharalis infestation levels. Between 2019 and 2020, two experiments were conducted in a controlled environment using the cultivars IR 40 and BR IRGA 409, previously identified as having different resistance reactions. Rice plants grown in pots were manually infested with first-instar larvae of D. saccharalis, ranging from 0 to 10 caterpillars per plant, with the plants maintained in cages covered with voile fabric throughout the trial. After 30 days of infestation, the number of live and dead caterpillars, the number of damaged and healthy stems, and the dry mass of the aerial parts were evaluated. A generalized linear mixed model was applied to the data obtained from leaf temperature as a function of infestation level throughout the infestation period, using the F-test to detect significant differences between cultivars. Generalized Additive Models for Location, Scale, and Shape (GAMLSS) were fitted to the variables related to resistance. It was observed that leaf surface temperature is related to the level of infestation and could be used to detect susceptibility in IR 40. In both cultivars, leaf temperatures were higher within the first 15 days post-infestation.

Impact of Salinity Stress on Morpho-physiology of Four Rice (Oryza sativa L.) Varieties

Abiotic stress, especially salinity, is one of the major restraints for attaining self-sufficiency in the food grain production. The saline soils affect the crop growth both directly and indirectly by interfering with plant metabolism resulting in reduction in yield potential of various crops. Rice (Oryza sativa L.), the staple food of much of the world’s population, is categorized as a salt-susceptible crop. Improving the salt tolerance of rice would increase the potential of saline-alkali land and ensure food security. To investigate the effect of different levels of salinity on morpho-physiological characters and yield of four rice variety viz. Pokkali, Narendra Ushar Dhan 3, IR 28 and IR 29. A pot experiment was conducted during Kharif 2011 and 2012 at the Department of Crop Physiology, Narendra Deva University of Agriculture and Technology, Kumarganj, Faizabad (U.P.) under normal soil and saline conditions with EC 6.0 and EC 10.0 dS/m. Gradual increase on plant height as well as biomass with the advancement in the age of crop up to dough grain in all the varities under both normal and salinity treatment. Maximum grain yield recorded in tolerant varieties Narendra Usar Dhan 3 followed by Pokkali, whereas minimum in IR 28. Under saline conditions regarding sink potential, the tolerant varieties recorded less reduction in yield attributes like length of panicle (cm), number of panicle per plant, number grain panicle-1 and grain yield plant-1 as compared to normal condition. The salinity tolerance capacity of tolerance varieties was associated with increased the activity of catalase and superoxide dismutase enzyme batter accumulation of proline and total carbohydrate as compared to normal condition.

Diversity of Pleosporalean Fungi Isolated from Rice (Oryza sativa L.) in Northern Thailand and Descriptions of Five New Species

Pleosporales represents the largest order within the class Dothideomycetes (Fungi), comprising phytopathogenic, saprobic, and endophytic taxa with a widespread presence in terrestrial and aquatic environments. Rice (Oryza sativa) is a primary economic crop in numerous tropical countries, particularly in Thailand. Studying fungal species associated with rice holds the potential to enhance our understanding of fungal diversity, lifestyles, and biology of rice, offering valuable insights for future research aimed at disease management and yield improvement. Thirty-nine pleosporalean isolates were obtained from various parts of rice plants collected across diverse regions in Chiang Rai Province, Thailand. Species identification involved a combination of morphology and molecular phylogeny, utilizing multi-locus sequence analyses of the ITS, LSU, SSU, gapdh, rpb2, tef1, and tub2 genes. The isolates were identified in 18 taxa distributed across five families and ten genera, including five new species (Bipolaris chiangraiensis, Ophiosphaerella oryzae, Paraphaeosphaeria oryzae, Pyrenochaetopsis oryzicola, and Setophoma oryzicola). Additionally, six new host records and two new geographical records are documented. Photoplates, detailed morphological descriptions, and phylogenetic trees are provided to elucidate the placement of both known and novel taxa.

Morpho-molecular Genetic Diversity Analysis of Basmati and Non-basmati Rice (Oryza sativa L.) Germplasm

This study evaluated genetic variability and relatedness among 34 rice genotypes, encompassing basmati and non-basmati varieties using morphological and molecular data. The findings revealed significant variability across all traits assessed. High phenotypic and genotypic coefficients of variation (PCV and GCV) were observed for traits such as days to 50% flowering, days to maturity, biological yield, grain yield, test weight, flag leaf length, and number of effective tillers. Notably, high heritability and genetic advance indicated that these traits are likely influenced by additive gene effects, making them suitable for selection in breeding programs. D2 analysis confirmed substantial genetic diversity among the genotypes and five clusters were formed based on the morphological data. Molecular analysis using 13 SSR primers, out of 13 primers 11 primers are showed the banding pattern, with the highest polymorphism information content (PIC) value recorded at 0.79 for marker HvSSR04-46. Clustering based on Jaccard’s dissimilarity coefficient revealed two distinct clusters. Based on the dendrogram pattern molecular data is divided into two clusters, cluster I and Cluster II, cluster I is subdivided into Cluster Ia and Cluster Ib. This research was conducted at Sardar Vallabhbhai Patel University of Agricultural & Technology, Modipuram, Meerut, Uttar Pradesh, highlights the potential for selecting diverse rice genotypes to enhance breeding programs.

Rapid identification of fragrant rice using starch flavor compound via NIR spectroscopy coupled with GC–MS and Badh2 genotyping

The identification of fragrant rice varieties using near-infrared reflectance spectroscopy (NIRS) models has attracted extensive attention from regulatory authorities worldwide. In this study, 138 fragrant and 54 nonfragrant rice varieties were planted in the same region and distinguished using sensory evaluation, gas chromatography–mass spectrometry analysis, and betaine aldehyde dehydrogenase 2 (Badh2) genotyping. Then, the 2-acetyl−1-pyrroline (2-AP) content was assessed based on partial least-squares discriminant (PLS-DA) models generated after 2nd individually or combined with SNV/MSC/smoothing preprocessing successfully classified fragrant rice both in the calibration and predictive sets. Moreover, design of experiments (DoE)-based preprocessing selection was employed as an effective strategy to optimize the calibration models compared with the one variable at a time (OVAT) method. Further, Badh2 genotype sample screening assisted with identifying authentic fragrant rice and guaranteed the NIRS model's prediction accuracy in identifying fragrant rice. In conclusion, the high throughput PLS-DA multivariate method coupled with NIRS data was applied to identify fragrant rice varieties in routine monitoring and was effective, accurate, and rapid.

Using Marker-Assisted Selection to Develop a Drought-Tolerant Rice Line with Enhanced Resistance to Blast and Brown Planthopper

Rice is a major global staple crop, but rising temperatures and freshwater shortages have made drought one of the most severe abiotic stresses affecting agriculture. Additionally, rice blast disease and brown planthopper infestations significantly impact yields. Therefore, developing water-saving, drought-resistant, high-yielding, and disease-resistant rice varieties is critical for sustainable rice production. The new water-saving and drought-resistant (WDR) rice ‘Huhan 1516’, bred using marker-assisted selection (MAS) and marker-assisted backcrossing (MABC) techniques, addresses these challenges. This variety is highly adaptable to drought-prone and water-scarce regions such as the Yangtze and Huai River basins. With its high yield, drought tolerance, and broad-spectrum resistance to rice blast (conferred by the Pi2 gene) and brown planthopper (BPH), ‘Huhan 1516’ is suitable for various farming systems and environments. Field trials show that this variety outperforms control varieties by 2.2% in yield and exhibits moderate resistance to both rice blast and brown planthopper. ‘Huhan 1516’ has been recognized as a new water-saving and drought-resistant rice variety by the state, and as a released cultivar, it has great potential for market promotion and application.

Morphological, physiological, and biochemical responses of rice (Oryza sativa L.) varieties to drought stress via regulating respiration and ROS metabolism during germination

Morphological, physiological, and biochemical responses of rice (Oryza sativa L.) varieties to drought stress via regulating respiration and ROS metabolism during germination

Optimization of Milling Degree for Maximizing Nutrient Retention and Yield in Milled Rice: A Study on Six Common Bangladeshi Rice Cultivars

Optimization of Milling Degree for Maximizing Nutrient Retention and Yield in Milled Rice: A Study on Six Common Bangladeshi Rice Cultivars

Starch digestion and physiochemical properties of a newly developed rice variety with low glycemic index

Starch digestion and physiochemical properties of a newly developed rice variety with low glycemic index