Oryza Sativa Research Articles

Isolation and Molecular Characterization of Rice Brown Spot Disease in Major Cauvery Delta Regions

Rice (Oryza sativa L.) is the second most important staple food among agricultural cereal crops, with over half of the world's population dependent on rice. 165.59 million hectares of land is used for rice production worldwide, yielding 518.1 million tonnes and a productivity of 4.68 t/ha (FAOSTAT 2022 - 2023). In India, the rice production is about 132 million tonnes which is produced in about 47 million hectares of land with a productivity of about 4.21 t/ha (Ministry of Agriculture & Farmers welfare, Government of India 2023). In Tamil Nadu, the rice production is about 6.8 million metric tonnes which is produced in about 2.21 million hectares of land with a productivity of about 3.76 t/ha (Department of Economics and Statistics, Government of Tamil Nadu 2022-23). One of the biotic stresses that accounts for about 15.6% of losses each year is rice disease. Of them, Bipolaris oryzae (Breda de haan) causing brown spots of rice is the most destructive disease which causes about 90% of yield loss. Ten isolates of brown spot pathogen were collected from the Cauvery delta regions and of them, the virulent isolate (Bo9) was characterized molecularly. All the isolates were studied based on their morphological characteristics. ITS primers were utilized to do the molecular characterization of the pathogen.

The Role of Net Assimilation Rate and Nitrogen Management in Optimizing Rice (Oryza sativa L.) Yield

Background: The net assimilation rate (NAR) is a physiological parameter related to leaf area and dry weight per unit of time. It is used to figure out how much grain a plant will produce. This study aims to explain the net assimilation rate of several types of rice at different doses and nitrogen application times. Methods: The research was conducted from December 2021 to April 2022. The experimental design was a split-plot design consisting of two treatment factors: the variety (main plot) and the time and dose of fertilization N (subplot). The variety factor consists of four varieties: IPB 3S (new type varieties), Inpari 33 (new high-yielding varieties), Hipa 21 (hybrids) and Mentik Wangi (local) at nitrogen 4 levels, namely 0 kg ha-1 (N0), 45 kg ha-1 applied when planting (N1), 90 kg ha-1 applied twice [45 kg at planting and 45 kg at panicle initiation (N2)] and 90 kg ha-1 applied three times, namely 45 kg at planting, 22.5 kg at the age of panicle initiation and 22.5 kg at heading (N3). Result: Results demonstrated that applying 90 kg ha-1 nitrogen fertilizer in three split applications (N3) improved agronomic performance by increasing tiller number, leaf area, dry matter accumulation, leaf nitrogen content and grain yield compared to other nitrogen regimes. Our findings newly highlight the vital influence of net assimilation rate (NAR) on panicle development, as NAR was positively correlated with panicle length. Uniquely, among all four varieties tested, the local cultivar Mentik Wangi recorded the highest NAR across N treatments.

Impact of Rhizospheric Microbiome on Rice Cultivation.

The rhizosphere niche is extremely important for the overall growth and development of plants. Evidently, it is necessary to understand the complete mechanism of plant microbe interactions of the rhizosphere for sustainable and low input productivity. To meet the increasing global food demand, rice (Oryza sativa L.) agriculture seeks optimal conditions. The unique oxic-anoxic interface of rice-growing soil has invited divergent microbes with dynamic biogeochemical cycles. This review provides the systematic analysis of microbes associated with the major biogeochemical cycles with the aim to generate better management strategies of rhizospheric microbiome in the field of rice agriculture. For instance, several methanogenic and methanotrophic bacteria in the rice rhizosphere make an equilibrium for methane concentration in the environment. The carbon sequestration in paddy soil is again done through many rhizospheric microorganisms that can directly assimilate CO2 with their photoautotrophic mode of nutrition. Also the phosphate solubilizing microbes remain to be the most important keys for the PGPR activity of the paddy ecosystem. In addition, rhizospheric microbiome remain crucial in degradation and solubilization of organo-sulfur and insoluble inorganic sulfides which can be taken by the plants. Further, this review elucidates on the advantages of using metagenomic and metaproteomic approaches as an alternative of traditional approaches to understand the overall metabolic pathways operational in paddy-field. These knowledges are expected to open new possibilities for designing the balanced microbiome used as inoculum for intensive farming and will eventually lead to exert positive impacts on rice cultivation.

Influence of establishment methods and seed coating techniques on the performance of direct seeded rice (Oryza sativa L.) under Periyar Vaigai command area of Tamil Nadu

Rice is a crucial staple crop cultivated extensively in command areas worldwide. In the command areas, the release of water varies due to the inadequate amount of rainfall in the source area and its proper supply. To combat such situations, direct seeding (DS) methods can be opted for; however, lacunae like excess seeds per drop, scattering of seeds, and intercultural operations like thinning, gap filling, and excess weed growth need a clear refinement to enhance the profitability of rice cultivation. Therefore, a research trial was conducted during 2022-24 at Central Farm, Agricultural College and Research Institute, Madurai, to evolve a suitable direct seeding method. The present investigation was laid out under a split-plot design comprising four main plot treatments and four subplot treatments replicated thrice. The main plot treatments comprised different seeding methods (S) and the subplot treatments comprised different seed coating techniques (P). Based on the experimental results, paper roll seeding and DS + Seed coating @ 2% KNO3 fb Bacillus sp. and Azospirillum (PR + P-KN) combination performed better on establishment with grain (6150 kg/ha) and straw yield (7824 kg/ha) respectively. Regarding the B:C ratio, OS-GP + P-KN resulted in higher with 2.64, closely followed by PR + P-KN with 2.61. The least effect was recorded in the combination of round slots in rice drum seeder and dry seeding (RS + DS). Investigating different techniques of direct seeding and seed coating is essential across various regions, particularly in regulated areas where water discharge remains unpredictable.

Enhancing the efficacy of biochar derived from crop residues on rice (Oryza sativa L.) dry matter, yield accumulation and soil organic carbon in Central Vietnam

Biochar from crop residues plays an important role in reclamation of degraded rice soil due to imbalance fertilizer application and soil carbon sequestration. The objective of this study aimed to evaluate the best type and rate of biochar application for rice dry matter and soil organic carbon improvement. Therefore, pot experiments were carried out in two seasons of spring and summer 2023 at the University of Agriculture and Forestry, Hue University. Twelve treatments including 2 types of biochar (rice husk and peanut shell) and 6 application rates (0, 1, 2, 3, 4, 5%) were used and arranged in a randomized block design with three replications. Research results showed that the shoot dry matter was higher 9.5 – 27.0% (spring season) and 19.1 – 26.9% (summer season) at a rate of 5% application in both types of biochar than control. Rice husk biochar application had higher shoot dry matter than peanut shell biochar application in the same application rate from 0.30 – 0.46 g/plant in both seasons. Similarly, organic carbon was found the highest content (2.15 - 2.21%) when the application of biochar from crop residues at a rate of 5%. Biochar from crop residues is considered as a good amendment for increasing crop dry matter and soil organic carbon.

Efficacy of broad-spectrum herbicide mixtures on weed flora in wet direct seeded rice (Oryza sativa L.) in the east coast plain region of India

Efficacy of broad-spectrum herbicide mixtures on weed flora in wet direct seeded rice (Oryza sativa L.) in the east coast plain region of India

Impact of rice straw biochar and reduced chemical fertilizer on the growth and yield of rice (Oryza sativa L.) in Central Vietnam

One way to effectively use rice straw without causing environmental pollution is to produce biochar and reuse it to improve rice yield and soil properties. Using rice straw biochar has increased rice productivity and can reduce chemical fertilizers. Therefore, this study aimed to evaluate the effects of rice straw biochar application with reduced chemical fertilizer on the growth and yield of rice at Quang Phu commune, Quang Dien district, Thua Thien Hue province, Vietnam with four treatments of the co-application of rice straw biochar doses of 5, 7.5 and 10 t/ha and chemical fertilizers of 75, 50 and 25% of the recommended dose. Growth parameters, yield components, yield of rice, and soil property were investigated. The results showed that the rice straw biochar had a positive effect on the growth, yield of rice, and soil properties. The co-application of rice straw biochar of the level of 10 t/ha and chemical fertilizer of 25% of the recommended dose was optimal levels produced the highest growth and yield (63 t/ ha). The co-application of rice straw biochar and chemical fertilizers increased organic matter, improved both soil physical and chemical properties, and reduced chemical fertilizer use. As a result, the rice straw biochar may be recommended to farmers to apply for rice production.

Optimizing bioherbicide application timing and plant spacing to manage weed growth in rice (Oryza sativa L.) cultivation

Weed management is crucial for successful rice cultivation. Bioherbicides derived from cogon grass extract offer a promising solution for weed control. Additionally, optimizing plant spacing has been recognized as an effective method to suppress weed growth. Thus, this study aims to investigate the impact of cogon grass extract application timing and plant spacing on weed growth in rice cultivation. The study was conducted from October 2022 to February 2023 in the Special Region of Yogyakarta, Indonesia. The study was 3 × 2 factorial and arranged in a randomized completely block design (RCBD). The first factor was the bioherbicide application timing: control (no application), three days before planting, and at the time of planting. The second factor was plant spacing: 15 × 15 and 25 × 25 cm. In total, there were six treatment combinations and three replications (replications as blocks). The research results indicated the application timing of bioherbicide did not significant effect on the growth of weed and rice, as well as the grain dry weight. Fimbristylis miliacea was obtained as the dominant weed species. Bioherbicide application at the time of planting could alter the composition of weed species compared to the control in plant spacing of 15 × 15 cm. Furthermore, the plant spacing of 25 × 25 cm resulted in higher grain and weed dry weight (19.40 g/clump and 45.00 g/0.25 m2) compared to 15 × 15 cm (12.92 g/clump and 23.04 g/0.25 m2). On the contrary, the grain dry weight per hectare was higher in 15 × 15 cm (5.74 t/ha) than in 25 × 25 cm (3.10 t/ha). The research findings indicate that closer plant spacing can suppress weed growth and increase the grain dry weight per hectare compared to wider plant spacing. We recommend that the use of cogon grass extract dosage needs to be increased above 50 L/ha.

Essential residues in diterpene synthases for biosynthesis of oryzalexins A-F in rice phytoalexin.

Cultivated rice (Oryza sativa) produces a variety of diterpenoid-type phytoalexins. Diterpene synthase genes that are responsible for the biosynthesis of momilactones, phytocassanes, and oryzalexins have been identified in O. sativa cv. Nipponbare. OsKSL10 (Os12t0491800 in RAP and LOC_Os12g30824 in MSU) was previously identified as an enzyme catalyzing the conversion of ent-copalyl diphosphate to ent-sandaracopimaradiene for the production of oryzalexins A to F. Our previous study on Oryza rufipogon, a wild progenitor of Asian cultivated rice, showed that both OrKSL10 and OrKSL10ind from O. rufipogon accessions W1943 and W0106, respectively, closely related to the japonica and indica subspecies, converted ent-copalyl diphosphate to ent-miltiradiene. Thus, the functional conversion of ent-miltiradiene synthase into ent-sandaracopimaradiene synthase is implied to have occurred through natural amino acid mutations, the details of which have not been elucidated. In this study, we show that introduction of A654G substitution into OrKSL10 significantly alters its function into more closely resembling that of OsKSL10. Moreover, double substitution V546I/A654G almost completely converts the function of OrKSL10 into that of OsKSL10. On the other hand, the reversed substitution I546V/G654A was insufficient to convert the function of OsKSL10 into OrKSL10, indicating the introduction of additional substitution S522I is required for the functionality of OsKSL10. Lastly, point mutations atthe 654A residue in OrKSL10 suggest that hydrophobic side chains atthis position have a negative influence on the production of ent-sandaracopimaradiene.

Genome-wide identification and expression-pattern analysis of sulfate transporter (SULTR) gene family in cotton under multiple abiotic stresses and fiber development.

Sulfate transporter (SULTR) proteins are in charge of the transport and absorption on sulfate substances, and have been reported to play vital roles in the biological processes of plant growth and stress response. However, there were few reports of genome-wide identification and expression-pattern analysis of SULTRs in Hibiscus mutabilis. Gossypium genus is a ideal model for studying the allopolyploidy, therefore two diploid species (G. raimondii and G. arboreum) and two tetraploid species (G. hirsutum and G. barbadense) were chosen in this study to perform bioinformatic analyses, identifying 18, 18, 35, and 35 SULTR members, respectively. All the 106 cotton SULTR genes were utilized to construct the phylogenetic tree together with 11 Arabidopsis thaliana, 13 Oryza sativa, and 8 Zea mays ones, which was divided into Group1-Group4. The clustering analyses of gene structures and 10 conserved motifs among the cotton SULTR genes showed the consistent evolutionary relationship with the phylogenetic tree, and the results of gene-duplication identification among the four representative Gossypium species indicated that genome-wide or segment duplication might make main contributions to the expansion of SULTR gene family in cotton. Having conducted the cis-regulatory element analysis in promoter region, we noticed that the existing salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) elements could have influences with expression levels of cotton SULTR genes. The expression patterns of GhSULTR genes were also investigated on the 7 different tissues or organs and the developing ovules and fibers, most of which were highly expressed in root, stem, sepal, receptacel, ovule at 10 DPA, and fiber at 20 and 25 DPA. In addition, more active regulatory were observed in GhSULTR genes responding to multiple abiotic stresses, and 12 highly expressed genes showed the similar expression patterns in the quantitative Real-time PCR experiments under cold, heat, salt, and drought treatments. These findings broaden our insight into the evolutionary relationships and expression patterns of the SULTR gene family in cotton, and provide the valuable information for further screening the vital candidate genes on trait improvement.

Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network.

Deciphering the targets of microRNAs (miRNAs) in plants is crucial for comprehending their function and the variation in phenotype that they cause. As the highly cell-specific nature of miRNA regulation, recent computational approaches usually utilize expression data to identify the most physiologically relevant targets. Although these methods are effective, they typically require a large sample size and high-depth sequencing to detect potential miRNA-target pairs, thereby limiting their applicability in improving plant breeding. In this study, we propose a novel miRNA-target prediction framework named kmerPMTF (k-mer-based prediction framework for plant miRNA-target). Our framework effectively extracts the latent semantic embeddings of sequences by utilizing k-mer splitting and a deep self-supervised neural network. We construct multiple similarity networks based on k-mer embeddings and employ graph convolutional networks to derive deep representations of miRNAs and targets and calculate the probabilities of potential associations. We evaluated the performance of kmerPMTF on four typical plant datasets: Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, and Prunus persica. The results demonstrate its ability to achieve AUPRC values of 84.9%, 91.0%, 80.1%, and 82.1% in 5-fold cross-validation, respectively. Compared with several state-of-the-art existing methods, our framework achieves better performance on threshold-independent evaluation metrics. Overall, our study provides an efficient and simplified methodology for identifying plant miRNA-target associations, which will contribute to a deeper comprehension of miRNA regulatory mechanisms in plants.

The Study Evaluated the Potential Viability of Seeds from Various Types of Rice (Oryza sativa L.)

Rice, a crucial staple crop for global food security, requires efficient production to meet the nutritional needs of an expanding population. Seed vigour is a crucial aspect of seed quality, and ANDUAT has introduced rice cultivars designed for the agricultural terrain of Acharya Narendra Deva University of Agriculture & Technology in India. This approach aims to improve seed vigour and quality in response to changing agro-climatic conditions. The study used a completely randomised design to assess seed vigour using various metrics such as electrical conductivity, field emergence, radicle emergence time, mean germination time, germination percentage, speed of emergence, shoot length, root length, days to first count, and days to final count. The study's findings revealed that rice types were categorized into three based on seed vigour. Eleven seeds showed varying levels of seed vigour potential, ranging from high to medium to low, NDR-359, IR-64, Damini, Sarjoo-52, Nagina-22, DRR-44, Barani Deep, Varalu, Lalat, NDR-2065 and NDR-2064. The study provides eleven categories for informed decision-making in seed management and cultivation, highlighting the suitability of high-vigor varieties for direct planting and improving agricultural yield.

In silico analysis identified bZIP transcription factors genes responsive to abiotic stress in Alfalfa (Medicago sativa L.)

BackgroundAlfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies including, but not limited to, differential gene expression to respond to environmental cues. Transcription factors control the expression of genes that contribute to or enable tolerance and survival during periods of stress. Basic-leucine zipper (bZIP) transcription factors have been demonstrated to play a critical role in regulating plant growth and development as well as mediate the responses to abiotic stress in several species, including Arabidopsis thaliana, Oryza sativa, Lotus japonicus and Medicago truncatula. However, there is little information about bZIP transcription factors in cultivated alfalfa.ResultIn the present study, 237 bZIP genes were identified in alfalfa from publicly available sequencing data. Multiple sequence alignments showed the presence of intact bZIP motifs in the identified sequences. Based on previous phylogenetic analyses in A. thaliana, alfalfa bZIPs were similarly divided and fell into 10 groups. The physico-chemical properties, motif analysis and phylogenetic study of the alfalfa bZIPs revealed high specificity within groups. The differential expression of alfalfa bZIPs in a suite of tissues indicates that bZIP genes are specifically expressed at different developmental stages in alfalfa. Similarly, expression analysis in response to ABA, cold, drought and salt stresses, indicates that a subset of bZIP genes are also differentially expressed and likely play a role in abiotic stress signaling and/or tolerance. RT-qPCR analysis on selected genes further verified these differential expression patterns.ConclusionsTaken together, this work provides a framework for the future study of bZIPs in alfalfa and presents candidate bZIPs involved in stress-response signaling.

Convolutional neural networks combined with conventional filtering to semantically segment plant roots in rapidly scanned X-ray computed tomography volumes with high noise levels

BackgroundX-ray computed tomography (CT) is a powerful tool for measuring plant root growth in soil. However, a rapid scan with larger pots, which is required for throughput-prioritized crop breeding, results in high noise levels, low resolution, and blurred root segments in the CT volumes. Moreover, while plant root segmentation is essential for root quantification, detailed conditional studies on segmenting noisy root segments are scarce. The present study aimed to investigate the effects of scanning time and deep learning-based restoration of image quality on semantic segmentation of blurry rice (Oryza sativa) root segments in CT volumes.ResultsVoxResNet, a convolutional neural network-based voxel-wise residual network, was used as the segmentation model. The training efficiency of the model was compared using CT volumes obtained at scan times of 33, 66, 150, 300, and 600 s. The learning efficiencies of the samples were similar, except for scan times of 33 and 66 s. In addition, The noise levels of predicted volumes differd among scanning conditions, indicating that the noise level of a scan time ≥ 150 s does not affect the model training efficiency. Conventional filtering methods, such as median filtering and edge detection, increased the training efficiency by approximately 10% under any conditions. However, the training efficiency of 33 and 66 s-scanned samples remained relatively low. We concluded that scan time must be at least 150 s to not affect segmentation. Finally, we constructed a semantic segmentation model for 150 s-scanned CT volumes, for which the Dice loss reached 0.093. This model could not predict the lateral roots, which were not included in the training data. This limitation will be addressed by preparing appropriate training data.ConclusionsA semantic segmentation model can be constructed even with rapidly scanned CT volumes with high noise levels. Given that scanning times ≥ 150 s did not affect the segmentation results, this technique holds promise for rapid and low-dose scanning. This study offers insights into images other than CT volumes with high noise levels that are challenging to determine when annotating.

Application and prospect of BSA method based on bibliometrics in crop breeding.

In order to understand the progress and frontier in the application of BSA(bulked segregant analysis) method in crop breeding and to reflect objectively the contribution of different countries, institutions and researchers in this field at home and abroad, this study analyzed 2111 items in the WOS (Web of Science) database from 2000 to 2023 and 446 items in the CNKI (China National through Knowledge Infrastructure) database from 2003 to 2023, regarding the researches of the application of BSA in crop breeding, basing on bibliometric analysis methods using CiteSpace software including keyword co-occurrence analysis, highlight word analysis, keyword clustering analysis, clustering timeline analysis and author co-citation. The results showed that there was an consistent increasing trend in the publication number of the application of BSA in crop breeding both in the domestic and foreign journals year by year. Ranking of the top countries according to the number of publications was China, the United States and India. The Huazhong Agricultural University displayed the highest number of publications in the CNKI database, while the Chinese Academy of Agricultural Sciences was found to have the highest number of publications in the WOS database. The published articles related to the application of BSA in crop breeding abroad mainly focused on the disciplines such as plant science, agronomy, horticulture and genetics, while those in China mainly concentrated on such disciplines as plant science, plant protection, horticulture and biology. The top three authors in terms of influence in the field of appling BSA in crop breeding were Michelmore RW, Kosambi DD and Li H, while Michelmore RW, Lander ES and Li H had closer cooperations with other authors. The top three crops relating to the studies of BSA were rice(Oryza sativa), soybean(Glycine max), corn(Zea mays L.) with the hot spot traits of disease resistance and plant height domestically. The top three crops involving the studies of BSA were rice, Arabidopsis thaliana and wheat(Triticum aestivum L.) with hot spot traits of disease resistance abroad. Up to now, BSA was mainly used to localize and functionally verify the candidate genes linking target traits and the mutated genes in crops in the domestical documents, while the foreign published studies based on BSA were mainly focused on the fine mapping and functional verification of target trait genes aiming at the revelation of genetic mechanisms in crops. Research frontier analysis indicated that rice, peanuts(Arachis hypogaea L.), upland cotton(Gossypium hirsutum L.) would be the main objects of studies concerning application of BSA in crop breeding with the hot topics of crop mutants and crop metabolites in the future.

Double-barreled defense: dual ent-miltiradiene synthases in most rice cultivars

AbstractRice (Oryza sativa) produces numerous diterpenoid phytoalexins that are important in defense against pathogens. Surprisingly, despite extensive previous investigations, a major group of such phytoalexins, the abietoryzins, were only recently reported. These aromatic abietanes are presumably derived from ent-miltiradiene, but such biosynthetic capacity has not yet been reported in O. sativa. While wild rice has been reported to contain such an enzyme, specifically ent-kaurene synthase-like 10 (KSL10), the only characterized ortholog from O. sativa (OsKSL10), specifically from the well-studied cultivar (cv.) Nipponbare, instead has been shown to make ent-sandaracopimaradiene, precursor to the oryzalexins. Notably, in many other cultivars, OsKSL10 is accompanied by a tandem duplicate, termed here OsKSL14. Biochemical characterization of OsKLS14 from cv. Kitaake demonstrates that this produces the expected abietoryzin precursor ent-miltiradiene. Strikingly, phylogenetic analysis of OsKSL10 across the rice pan-genome reveals that from cv. Nipponbare is an outlier, whereas the alleles from most other cultivars group with those from wild rice, suggesting that these also might produce ent-miltiradiene. Indeed, OsKSL10 from cv. Kitaake exhibits such activity as well, consistent with its production of abietoryzins but not oryzalexins. Similarly consistent with these results is the lack of abietoryzin production by cv. Nipponbare. Although their equivalent product outcome might suggest redundancy, OsKSL10 and OsKSL14 were observed to exhibit distinct expression patterns, indicating such differences may underlie retention of these duplicated genes. Regardless, the results reported here clarify abietoryzin biosynthesis and provide insight into the evolution of rice diterpenoid phytoalexins.

Effects of Bed Width and Crop Row Spacing on Barnyardgrass (Echinochloa crus-galli) Emergence and Seed Production in Furrow-Irrigated Rice

Abstract Furrow-irrigated rice (Oryza sativa L.) has become a popular option for rice production in Arkansas. Highly troublesome weeds like barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] are a major problem for producers in all rice production systems. Cultural tactics should become a priority to enhance crop growth and competitiveness. This research aimed to determine the effects of bed width (irrigation furrow spacing) and crop row spacing manipulation on E. crus-galli emergence and seed production in a furrow-irrigated rice system. Three bed widths (76-, 97-, and 152-cm) (whole plot factor) were used, and plots were drill-seeded in four crop row spacings (subplot factor) (13-, 19-, 25-, and 38-cm). The widest width of 152-cm had a slight increase in E. crus-galli density in the early rice life cycle but, by the end of the season, did not differ from the narrower bed widths. Conversely, a decrease in E. crus-galli seed production was observed as the bed width increased. Similar rice canopy coverage and yields occurred between all three bed widths. As for crop row spacing, as the width increased, E. crus-galli density also increased. The 13-cm crop row spacing had the lowest preflood E. crus-galli density, preharvest panicle count, and seed production. No effect of crop row spacing was observed on rice canopy coverage; however, the 13-cm crop row spacing produced the greatest rice yield. The 13-cm crop row spacing paired with the 152-cm bed width may be the optimum combination of ecological strategies in furrow-irrigated rice to reduce E. crus-galli seed production while maintaining rice growth and yield.

Identification and Expression Profile of NCED Genes in Arachis hypogaea L. during Drought Stress

Peanut (Arachis hypogaea L.) is an important crop that provides essential proteins and oils for human and animal consumption. 9-cis-epoxycarotenoid dioxygenase (NCED) have been found can play a vital role in abscisic acid (ABA) biosynthesis and may be a response to drought stress. Until now, in Arachis hypogaea, no information about the NCED gene family has been reported and the importance of NCED-related drought tolerance is unclear. In this study, eight NCED genes in Arachis hypogaea, referred to as AhNCEDs, are distributed across eight chromosomes, with duplication events in AhNCED1 and AhNCED2, AhNCED3 and AhNCED4, and AhNCED6 and AhNCED7. Comparative analysis revealed that NCED genes are highly conserved among plant species, including Pisum sativum, Phaseolus vulgaris, Glycine max, Arabidopsis thaliana, Gossypium hirsutum, and Oryza sativa. Further promoter analysis showed AhNCEDs have ABA-related and drought-inducible elements. The phenotyping of Arachis hypogaea cultivars NH5 and FH18 demonstrated that NH5 is drought-tolerant and FH18 is drought-sensitive. Transcriptome expression analysis revealed the differential regulation of AhNCEDs expression in both NH5 and FH18 cultivars under drought stress. Furthermore, compared to the Arachis hypogaea cultivar FH18, the NH5 exhibited a significant upregulation of AhNCED1/2 expression under drought. To sum up, this study provides an insight into the drought-related AhNCED genes, screened out the potential candidates to regulate drought tolerance and ABA biosynthesis in Arachis hypogaea.

Identification of Insertion/Deletion Markers for Photoperiod Sensitivity in Rice (Oryza sativa L.).

The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies.

Genome-Wide Identification and Expression Analysis of ent-kaurene synthase-like Gene Family Associated with Abiotic Stress in Rice.

Rice (Oryza sativa) is one of the most important crops for humans. The homologs of ent-kaurene synthase (KS) in rice, which are responsible for the biosynthesis of gibberellins and various phytoalexins, are identified by their distinct biochemical functions. However, the KS-Like (KSL) family's potential functions related to hormone and abiotic stress in rice remain uncertain. Here, we identified the KSL family of 19 species by domain analysis and grouped 97 KSL family proteins into three categories. Collinearity analysis of KSLs among Poaceae indicated that the KSL gene may independently evolve and OsKSL1 and OsKSL4 likely play a significant role in the evolutionary process. Tissue expression analysis showed that two-thirds of OsKSLs were expressed in various tissues, whereas OsKSL3 and OsKSL5 were specifically expressed in the root and OsKSL4 in the leaf. Based on the fact that OsKSL2 participates in the biosynthesis of gibberellins and promoter analysis, we detected the gene expression profiles of OsKSLs under hormone treatments (GA, PAC, and ABA) and abiotic stresses (darkness and submergence). The qRT-PCR results demonstrated that OsKSL1, OsKSL3, and OsKSL4 responded to all of the treatments, meaning that these three genes can be candidate genes for abiotic stress. Our results provide new insights into the function of the KSL family in rice growth and resistance to abiotic stress.