Rice Species Research Articles

Xanthomonas protegens sp. nov., a novel rice seed-associated bacterium, provides in vivo protection against X. oryzae pv. oryzae, the bacterial leaf blight pathogen.

Historically, Xanthomonas species are primarily known for their pathogenicity against plants, but recently, there have been more findings of non-pathogenic xanthomonads. In the present study, we report isolates from healthy rice seeds that belong to a new species, X. protegens, a protector of the rice plants against a serious pathogenic counterpart, i.e. X. oryzae pv. oryzae upon leaf clip co-inoculation. The new member species is non-pathogenic to rice and lacks a type III secretion system. The pangenome investigation revealed a large number of unique genes, including a novel lipopolysaccharide biosynthetic gene cluster, that might be important in its adaptation. The phylo-taxonogenomic analysis revealed that X. protegens is a taxonomic outlier species of X. sontii, a core, vertically transmitted rice seed endophyte with numerous probiotic properties. Interestingly, X. sontii is also reported as a keystone species of healthy rice seed microbiome. The findings and resources will help in the development of unique gene markers and evolutionary studies of X. sontii as a successful symbiont and X. oryzae as a serious pathogen. Here, we propose X. protegens sp. nov. as a novel species of the genus Xanthomonas with PPL118=MTCC 13396=CFBP 9164=ICMP 25181 as the type strain. PPL117, PPL124, PPL125 and PPL126 are other strains of the species.

Reexploring Rice Germplasm: Enlightening a New Path Towards Abiotic Stress-resilient Crop

Oryza sativa, the commonly cultivated rice, is one of the most important crops for human consumption, but is also a crop whose production system is increasingly threatened by the current climate changes. Due to its intensive water requirement rice faces a lot of challenges due to abiotic stresses like drought, heat stress, salinity, flooding etc. Drought is the major abiotic stress to rice grain production under unpredictable and changing environmental conditions. Traits supporting drought resistance are limited in cultivars, while wild rice species like O. glaberrima, O. longistaminata, O. rufipogon and O. meridonalis represent an important reservoir of useful genes for this trait which can be exploited to develop varieties tolerant to drought. Similarly O. australiensis, O. coarctata and O. rufipogon serve as an important sources for salinity-tolerant genes. O. rufipogon, O. meridonalis, O. australiensis comprise a collection of accessions that are reservoirs for heat-tolerant genes. Although many efforts have resulted in breeding rice varieties that are relatively tolerant to their local environments; climate change and population growth are expected to soon require a new, rapid generation of stress-tolerant rice germplasm. Diversity studies suggest that the current diversity within rice varieties may not be sufficient for generation of highly resistant or tolerant varieties for the unfavorable growing conditions. All the efforts to design an ideotype to increase production and productivity has been attempted previously, rice self-sufficiency can be attained only if high production and productivity is coupled with a high degree of tolerance and resistance to biotic and abiotic stress factors. Since it has been found that wild rice relatives serve as a hub for many desirable genes conferring tolerance or resistance to specific stresses, the present article is focused on provide an overview of different wild ancestors of rice which can be exploited to identify suitable donors for gene of interest, their ecological and genomic diversity and the variation observed in wild Oryza species for different stress tolerance traits. Such identified traits can be incorporated in modern day breeding programmes through marker assisted breeding to develop cultivable varieties with desired tolerance to abiotic stresses or transfer such traits to modern day cultivars through backcross breeding.

Evolutionary Systems Biology Identifies Genetic Trade-offs In Rice Defense Against Above- and Belowground Attackers.

Like other plants, wild and domesticated rice species (Oryza nivara, O. rufipogon, and O. sativa) evolve in environments with various biotic and abiotic stresses that fluctuate in intensity through space and time. Microbial pathogens and invertebrate herbivores such as plant-parasitic nematodes and caterpillars show geographical and temporal variation in activity patterns and may respond differently to certain plant defensive mechanisms. As such, plant interactions with multiple community members may result in conflicting selection pressures on genetic polymorphisms. Here, through assays with different above- and belowground herbivores, the fall armyworm (Spodoptera frugiperda) and the southern root-knot nematode (Meloidogyne incognita), respectively, and comparison with rice responses to microbial pathogens, we identify potential genetic trade-offs at the KSL8 and MG1 loci on chromosome 11. KSL8 encodes the first committed step towards biosynthesis of either stemarane- or stemodane-type diterpenoids through the japonica (KSL8-jap) or indica (KSL8-ind) allele. Knocking out KSL8-jap and CPS4, encoding an enzyme that acts upstream in diterpenoid synthesis, in japonica rice cultivars increased resistance to S. frugiperda and decreased resistance to M. incognita. Furthermore, MG1 resides in a haplotype that provided resistance to M. incognita, while alternative haplotypes are involved in mediating resistance to the rice blast fungus Magnaporthe oryzae and other pests and pathogens. Finally, KSL8 and MG1 alleles are located within trans-species haplotypes and may be evolving under long-term balancing selection. Our data are consistent with a hypothesis that polymorphisms at KSL8 and MG1 may be maintained through complex and diffuse community interactions.

A proposed plant classification framework for smart agricultural applications using UAV images and artificial intelligence techniques

Utilizing Wireless Sensor Networks (WSNs), Internet of Things (IoTs) sensors, and Unmanned Aerial Vehicles (UAVs), in conjunction with optimization techniques and machine learning algorithms, can present a novel approach to Precision Agricultural (PA) crops. Agriculture has transitioned from traditional legacy systems to incorporate advanced smart technologies. Several complex farming problems are utilized to promote a variety of UAV sensing and Artificial Intelligence (AI) algorithms in PA applications of smart agriculture, especially in developing countries. This paper proposes the design of a conceptual UAV sensing system for crop management using a novel classification framework. UAV-based image datasets can be implemented and expanded to various types of crops. In addition, it can classify various types of rice species and detect weed farms as it consists of a multistage process for identifying and monitoring different crops. The proposed classification framework is evaluated using three different real UAV image datasets compared with Naive Bayes, Decision Tree (DT), Bagging, and Random Forest (RF) techniques. The classification performance metrics obtained are as follows: i) the WeedNet dataset with 100 % F1-score, 100 % recall, 100 % precision, and 100 % accuracy; ii) the Rice Seedling dataset with 99.5 % F1-score, 99.5 % recall, 99.5 % precision, and 99.5 % accuracy; and iii) the Rice Varieties dataset with 97.99 % F1-score, 97.99 % recall, 98.14 % precision, and 97.99 % accuracy. The success rates achieved by the proposed classification framework outperform those of other recent state-of-the-art techniques, demonstrating its efficacy in crop management applications.

Recognition of Rice Species Based on Gas Chromatography-Ion Mobility Spectrometry and Deep Learning

To address the challenge of relying on complex biochemical methods for identifying rice species, a prediction model that combines gas chromatography-ion mobility spectroscopy (GC-IMS) with a convolutional neural network (CNN) was developed. The model utilizes the GC-IMS fingerprint data of each rice variety sample, and an improved CNN structure is employed to increase the recognition accuracy. First, an improved generative adversarial network based on the diffusion model (DGAN) is used for data enhancement to expand the dataset size. Then, on the basis of a residual network called ResNet50, a transfer learning method is introduced to improve the training effect of the model under the condition of a small sample. In addition, a new attention mechanism called Triplet is introduced to further highlight useful features and improve the feature extraction performance of the model. Finally, to reduce the number of model parameters and improve the efficiency of the model, a method called knowledge distillation is used to compress the model. The results of our experiments revealed that the recognition accuracy for identifying the 10 rice varieties was close to 96%; hence, the proposed model significantly outperformed traditional models such as principal component analysis and support vector machine. Furthermore, compared to the traditional CNN, our model reduced the number of parameters and number of computations by 53% and 55%, respectively, without compromising classification accuracy. The study also suggests that the combination of GC-IMS and our proposed deep learning method had better discrimination abilities for rice varieties than traditional chromatography and other spectral analysis methods and that it effectively identified rice varieties.

Tetraploid interspecific hybrids between Asian and African rice species restore fertility depending on killer-protector loci for hybrid sterility.

Interspecific F1 hybrids between Asian (Oryza sativa) and African rice (Oryza glaberrima) exhibit severe sterility caused by the accumulation of hybrid sterility genes/loci at 15 or more loci. The mechanisms underlying the hybrid sterility genes are largely unknown; however, a few genes associated with the killer-protector system, which is the system most frequently associated with hybrid sterility genes, have been identified. We previously produced fertile plants as tetraploids derived from diploid interspecific F1 hybrids through anther culture; therefore, it was suggested that hybrid sterility could be overcome following tetraploidization. We investigated whether tetraploid interspecific plants produced by crossing are fertile and tested the involvement of hybrid sterility genes in the process. Fertile tetraploid interspecific F1 hybrid plants were obtained by crossing 2 tetraploids of O. sativa and O. glaberrima. To elucidate the relationships between pollen fertility and the hybrid sterility loci in the tetraploid F1 microspores, we performed genetic analyses of the tetraploid F2 hybrids and diploid plants obtained from the microspores of tetraploid interspecific hybrids by anther culture. The result suggested that the tetraploid interspecific hybrids overcame pollen and seed infertility based on the proportion of loci with the killer-protector system present in the tetraploids. The heterozygous hybrid sterility loci with the killer-protector system in the tetraploid segregate the homozygous killed allele (16.7-21.4%), with more than three-quarters of the gametes surviving. We theoretically and experimentally demonstrated that fertile rice progenies can be grown from tetraploid interspecific hybrids.

Mechanism of betterment towards growth and induction of defense in rice (Oryza sativa L.) by biopriming with bacterial endophytes isolated from wild rice

Utilizing beneficial microorganisms associated with plants, particularly endophytes, is becoming more and more prevalent since it supports the physiological health and evolutionary adaption of the host. The range of enhanced endophytic bacteria found in wild rice makes it a promising resource for sustainable agriculture. Current study focused on bacterial endophytes the tissues of wild rice plants' roots, stems, and leaves for managing the health and development of rice (Oryza sativa L.) plants. Bacterial endophytes were characterized using 16S rRNA. Treatments with Priestia megaterium (NRRI EB 1) and Priestia aryabhattai (NRRI EB 2) outperformed the other isolates in rice growth enhancement activities significantly. The biocontrol efficacy of bacterial endophytes was tested against Xanthomonas oryzae pv. oryzae and Rhizoctonia solani and percentage of inhibition was the higher in NRRI EB 1 by 79.32-80.83% and in NRRI EB 2 by 79.69-80.45%. Bio-priming the seeds with specific endophytic bacterial strains led to a decrease in average germination time, an increase in seedling vigor, and total chlorophyll content. Additionally, they generated greater amounts of soluble phosphate (40.91-83.70 μg/mL) and indole acetic acid (28.10-60.18 μg/mL), which are in the midst of encouraging more plant development. Higher expressions of defense enzymes in comparison to the control, including catalase (>220% in root and shoot), peroxidase (>200% in shoot and root), and superoxide dismutase (> 150% in shoot and root) illustrates the rice crop's resilience to withstand stress. The activity of the mentioned enzymes was further validated through the activation of corresponding defense genes such as DEFENSIN (>2-fold), PAL (>3-fold), PR-3 (>2-fold), POX (>2-fold) and LOX (>1-fold) relative to the control's untreated plants. The possibility exists to extract advantageous endophytic bacteria from wild rice species, potentially rewilding the microbiome of farmed rice cultivators and fostering their development.

Wild rice: unlocking the future of rice breeding.

Germplasm resources serve as the foundations of advancements in breeding and are crucial for maintaining food security. Wild rice species of the genus Oryza include rich sources of genetic diversity and high adaptability, making them a substantial resource for rice breeding. The discovery of wild-type cytoplasmic male sterility resources enabled the achievement of the 'three lines' goal in hybrid rice, significantly increasing rice yields. The application of resistance alleles from wild rice enables rice production to withstand losses caused by stress. Reduced genetic diversity due to rice breeding poses a significant limitation to further advances and can be alleviated through a systematic use of wild genetic resources that integrate geographic, climatic and environmental data of the original habitat, along with extensive germplasm collection and identification using advanced methods. Leveraging technological advancements in plant genomics, the understanding of genetic mechanisms and the application of artificial intelligence and gene editing can further enhance the efficiency and accuracy of this process. These advancements facilitate rapid isolation and functional studies of genes, and precise genome manipulation. This review systematically summarizes the utilization of superior genes and germplasm resources derived from wild rice sources, while also exploring the collection, conservation, identification and utilization of further wild rice germplasm resources. A focus on genome sequencing and biotechnology developments is leading to new breeding and biotechnology opportunities. These new opportunities will not only promote the development of rice varieties that exhibit high yields, superior stress resistance and high quality but also expand the genetic diversity among rice cultivars.

Comparative Analysis of Peroxidase and Catalase Isoenzymes via Native-PAGE Electrophoresis and SDS-PAGE Profiling of Leaf Proteins in Rice Varieties under Infection Stress

Rice (Oryza sativa L.) is a staple food for over half of the world's population. However, rice productivity is significantly hindered by various diseases, including sheath blight caused by Rhizoctonia solani. This study aims to evaluate the resistance of different rice varieties and wild rice accessions to sheath blight and to analyze the biochemical responses, specifically peroxidase and catalase activities, under infection stress. The results revealed that Kalanamak and Pusa Basmati were highly susceptible, with high disease indices and visual ratings. Conversely, wild rice accessions such as O. rufipogon and O. australiensis exhibited lower disease indices, indicating moderate resistance. Peroxidase activity varied significantly among the rice leaves, ranging from 148.83 to 182.44 mg/g fresh weight/min. Dhanya 748 showed the highest peroxidase activity, followed by O. australiensis and O. rufipogon. Native-PAGE electrophoresis of peroxidase isoenzymes demonstrated high-intensity bands in O. rufipogon, BPT 5204, and Swarna Sub-1, while minimal or no bands were observed in other genotypes, indicating varying levels of peroxidase activity. Catalase activity also showed significant variation, ranging from 138.18 to 152.14 mg/g fresh weight/min. BPT-5204 exhibited the highest catalase activity, followed by O. australiensis and Pusa Basmati. Isoenzyme analysis via Native-PAGE revealed high-intensity catalase bands in O. australiensis, Dhanya 748, NDR 118, and Pusa Basmati, while no bands were observed in O. rufipogon, CSR 13, Arize 6444, and Swarna Sub-1. SDS-PAGE analysis of leaf proteins showed variability in banding patterns. Non-infected leaves of Swarna Sub-1, Arize 6444, Kalanamak, and Pusa Basmati had minimal bands, while O. australiensis and Dhanya 748 showed maximum bands. Infected leaves of CSR 13, NDR 118, Arize 6444, Kalanamak, Dhanya 748, and Pusa Basmati had minimal bands, whereas O. australiensis exhibited maximum bands. Overall, the study highlights the potential of wild rice species in enhancing disease resistance and provides insights into the biochemical responses of rice varieties under pathogen stress.

Development of a Reference Transcriptome and Identification of Differentially Expressed Genes Linked to Salt Stress in Salt Marsh Grass (Sporobolus alterniflorus) along Delaware Coastal Regions.

Salt marsh grass (Sporobolus alterniflorus) plays a crucial role in Delaware coastal regions by serving as a physical barrier between land and water along the inland bays and beaches. This vegetation helps to stabilize the shoreline and prevent erosion, protecting the land from the powerful forces of the waves and tides. In addition to providing a physical barrier, salt marsh grass is responsible for filtering nutrients in the water, offering an environment for aquatic species and presenting a focal point of study for high salt tolerance in plants. As seawater concentrations vary along the Delaware coast from low to medium to high salinity, our study seeks to identify the impact of salt tolerance in marsh grass and to identify genes associated with salt tolerance levels. We developed more than 211,000 next-generation-sequencing (Illumina) transcriptomic reads to create a reference transcriptome from low-, medium-, and high-salinity marsh grass leaf samples collected from the Delaware coastline. Contiguous sequences were annotated based on a homology search using BLASTX against rice (Oryza sativa), foxtail millet (Setaria italica), and non-redundant species within the Viridiplantae database. Additionally, we identified differentially expressed genes related to salinity stress as candidates for salt stress qPCR analysis. The data generated from this study may help to elucidate the genetic signatures and physiological responses of plants to salinity stress, thereby offering valuable insight into the use of innovative approaches for gene expression studies in crops that are less salt tolerant.

Cropping systems and production assessment in southern Myanmar: Informing strategic interventions

Abstract Cropland expansion into natural forests in the Kyunsu Township, southern Myanmar, has diminished the sustainability of natural resources in this area. Analyzing local cropping systems can help explore options for improving land productivity on the existing croplands. To achieve this, a study was conducted between June 2020 and June 2021, involving 301 farmers’ households within the township. The study focused on socioeconomic status, crop production characteristics, key soil properties, and production constraints. Hierarchical clustering on principal components was applied to identify the existing cropping systems. Subsequently, a comparative analysis of variables between identified cropping systems was performed. The findings revealed that in the plantation zone, the median gross value added (GVA) reached US$ 1,276 ha−1 year−1 for perennial monocropping and US$ 1,715 ha−1 year−1 for perennial-multiple cropping. These values were higher than the median GVAs of perennial monocropping (US$ 460 ha−1 year−1) and perennial-multiple cropping (US$ 474 ha−1 year−1) in the sea zone. In the lowland and sea zones, annual monocropping of rice had low median GVAs of 206 and US$ 165 ha−1 year−1, respectively. The combination of rice and perennial species in the lowland zone resulted in a higher median GVA (US$ 383 ha−1 year−1) compared to rice sole cropping in both the lowland and sea zones. Coupled with favorable soil properties, cropping systems that integrated perennial species, particularly multiple cropping with strategic input use, demonstrated enhanced land productivity. However, to optimize land productivity in these cropping systems, it is crucial to address major constraints, such as high input prices, poor soil quality, and scarcity of freshwater.

First Report of Pantoea ananatis causing leaf streak disease on wheat (Triticum aestivum) in the United States of America.

Wheat (Triticum aestivum) loses 21.5% yield to pests and diseases annually (Savary et al. 2019). Among the wheat diseases, bacterial leaf streak (BLS) is a growing problem, costing $78.5 million in losses (https://cropprotectionnetwork.org/). In July 2022, we sampled winter wheat leaf samples at Volga (44.30, -96.92), South Dakota, USA with an estimated disease incidence of 40% (n=100). The typical symptoms were water-soaking with large necrotic and chlorotic streaks extending the length of the leaves and were strikingly similar to BLS. To isolate the pathogen, leaves were cut lengthwise into 1 cm pieces and surface-sterilized using a 10% NaOCl solution for 3 min, followed by 70% ethanol for 3 min, and then rinsed with sterile distilled water and placed in 500 ul of sterile distilled water for 5 min and using a sterile loop the water was streaked over a plate of Nutrient Agar (NA). Following Duveiller et al. (1997), the streaked plate was incubated in the dark at 28℃ for 48 h. Observed single colonies were sub-cultured thrice onto fresh NA plates to obtain a pure culture. We named the culture SD101. Bacteria were found to be gram-negative with a colony morphology initially raised, smooth, and white that later turned yellow. DNA was extracted using the Wizard HMW DNA Extraction Kit (Promega, Madison, WI) following the manufacturer's protocol, and sequenced using Nanopore MinION R9.4 (Oxford Nanopore Technology). We used the Rapid Annotation Using Subsystems Technology approach (Aziz eal. 2008) to extract the 16S rDNA, DNA gyrase subunit B (gyrB), and translation initiation factor IF-2 (infB) gene sequences that were deposited in GenBank under accession numbers PP329908.1 for 16S rDNA, PP496481 for infB, and PP328920.1 for gyrB. Homology analysis using CLC Genomics Workbench 22.0.2 (QIAGEN) and BLASTn against the GenBank nucleotide database resulted in a 99.74% match (1543/ 1547 bp) of the 16S sequence, 99.59% match (2674/ 2685 bp) of the infB sequence, and 99.42% match (2396/ 2410 bp) of the gyrB sequence with Pantoea ananatis strain AJ13355 (AP012032). To test pathogenicity, seeds of spring wheat breeding line SD4892 were planted in 30 cm × 30 cm pots in a greenhouse under a 16 h light photoperiod. The inoculum was prepared from 48-h-old NA plates of SD101 rinsed with 1X Phosphate Buffer Saline (PBS buffer), adjusted to an OD600 = 1.0, and amended with two drops of Tween 20 (polyoxyethylene sorbitol ester, Millipore Sigma). PBS with Tween 20 was used as a negative control. The inoculum was sprayed on 15 replicates of 15-day-old seedlings, kept at 95% relative humidity for 48 h, then moved to the greenhouse at 23 to 25°C. The symptoms appeared as water soaking that later turned to necrotic streaks with surrounding chlorosis on all 15 inoculated plants while control plants remained healthy. The pathogen was re-isolated from the leaves as described above. The 16S rDNA, infB, and gyrB sequences amplified and sequenced were identical to the gene sequences from the whole genome sequencing. The experiment was repeated with the same results, completing Koch's postulates. Although P. ananatis is pathogenic on corn, rice, and other plant species in the United States (Coutinho et al. 2009), and was reported pathogenic on wheat in Poland (Krawczyk et al. 2020), this is the first report of its pathogenicity on wheat in the United States. The prevalence, and incidence of BLS disease caused by P. ananatis in wheat is needed to estimate its threat to wheat production and to develop management strategies.

Dispersal patterns and potential distribution prediction of three rice planthopper species in China based on the ensemble model

Dispersal patterns and potential distribution prediction of three rice planthopper species in China based on the ensemble model

Estimation of Photosynthetic Induction Is Significantly Affected by Light Environments of Local Leaves and Whole Plants in Oryza Genus.

Photosynthetic induction and stomatal kinetics are acknowledged as pivotal factors in regulating both plant growth and water use efficiency under fluctuating light conditions. However, the considerable variability in methodologies and light regimes used to assess the dynamics of photosynthesis (A) and stomatal conductance (gs) during light induction across studies poses challenges for comparison across species. Moreover, the influence of stomatal morphology on both steady-state and non-steady-state gs remains poorly understood. In this study, we show the strong impact of IRGA Chamber Illumination and Whole Plant Illumination on the photosynthetic induction of two rice species. Our findings reveal that these illuminations significantly enhance photosynthetic induction by modulating both stomatal and biochemical processes. Moreover, we observed that a higher density of smaller stomata plays a critical role in enhancing the stomatal opening and photosynthetic induction to fluctuating light conditions, although it exerts minimal influence on steady-state gs and A under constant light conditions. Therefore, future studies aiming to estimate photosynthetic induction and stomatal kinetics should consider the light environments at both the leaf and whole plant levels.

Genome-wide characterization and functional analysis of heat shock transcription factors in wild and cultivated rice (Oryza sativa L.)

Due to domestication, the genetic diversity in cultivated rice is lower than that of wild rice species. Recent progress in sequencing the genomes of wild and cultivated rice genus is an important step in identifying their genetic differences associated with abiotic and biotic stresses-resistant ability. Thus, in this study, heat shock transcription factor (Hsf) genes in 6 wild rice accessions, including Oryza barthii, Oryza glumaepatula, Oryza meridionalis, Oryza nivara, Oryza punctate and Oryza rufipogon, and 1 cultivated rice variety Nipponbare were firstly identified, and the evolution of rice Hsf genes were analyzed. Totally, 22, 23, 24, 24, 25, 25 and 25 Hsf genes were identified in the 7 tested rice genomes, Oryza barthii, Oryza glumaepatula, Oryza meridionalis, Oryza nivara, Oryza punctate, Oryza rufipogon and Oryza sativa, respectively. The evolutionary analysis of Hsf genes revealed that Oryza rufipogon was the immediate ancestral progenitor of Oryza sativa. The variation in the number of Hsf genes between wild and cultivated rice genotypes was mainly due to segmental duplication and whole genome duplication (WGD) events, which might contribute to the different stress-tolerant ability between the wild and cultivated rice varieties. Secondly, the function of the Hsf genes in wild and cultivated rice in response to salinity stress was compared. Under salt stress, four Hsf genes, HsfA2b, HsfB4b, HsfB4c and HsfB4d, were exclusively down-regulated in Oryza rufipogon shoots. Whilst, another four Hsf genes, HsfA7a, HsfB2c, HsfC1b and HsfC2b, were up-regulated in the shoots of both the cultivated rice and its ancestral progenitor Oryza rufipogon. Meanwhile, genomic comparison results showed that 1, 1, 5 and 5 nsSNPs were detected in these 4 Hsf genes respectively, which might alter the functions of these genes. RT-qPCR results further confirmed the expression profile of one of these 4 Hsf genes, HsfB2c. The expression pattern of this gene in the cultivated rice variety in response to salt stress was similar with the previously known salt stress-tolerant gene, WRKY28. This indicated that these 4 Hsf genes might be among the conserved genes related to salt stress tolerance in the wild and cultivated rice. In summary, these results provide novel clues to the further functional studies of Hsf genes in rice for breeding programs.

Isolation of endophytic fungi from wild rice species for disease management and growth promotion in cultivated rice (Oryza sativa L.)

ABSTRACT The focus of plant health management is shifting from synthetic chemicals to bio-agents, and endophytes are beneficial for this purpose. In the present study, we isolated eleven endophytic fungi from seven wild rice species. Independent treatment of endophytic fungi in rice showed significant improvements in plant growth, higher tillering and percent fertility, panicle number/hill and filled grain number in endophyte-inoculated plants compared to control plants. Growth promotion activities of two endophytes Curvularia lunata (NRRI EF-11) and Hypocreals sp. (NRRI EF-8) were recorded with increased rice yield. These isolates also exhibited higher plant growth promoting chemicals namely, Indole acetic acid (IAA) and Inorganic phosphate (IP) which was realised into better growth promotion in rice. The biocontrol efficacy of endophytic fungi was highest in NRRI EF-11among all isolates as indicated by inhibition of radial growth of pathogens by 76.98–77.06% and in NRRI EF-8 by 74.81–76.61%, which is due to higher production of prussic acid. Defense induction was confirmed by analyzing the expression of catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) defense enzymes, where expression of CAT, POD and SOD increased by 19.44–25.86, 2.70–3.16, 11.14–12.95 Units g−1 in treated NRRI EF-11 plants and 18.39–25.84, 2.16–2.94, 10.96–12.62 Units g−1 in treated NRRI EF-8 plants, respectively. These two endophytes have the potentiality to manage crop health in a sustainable way.

OlCHR, encoding a chromatin remodeling factor, is a killer causing hybrid sterility between rice species Oryza sativa and O. longistaminata

OlCHR, encoding a chromatin remodeling factor, is a killer causing hybrid sterility between rice species Oryza sativa and O. longistaminata

Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen.

Oryza alta Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource. A new wild rice line, Huaye 5, was developed from Oryza alta Swallen in our lab. Whole genome re-sequencing and pan-genomic analysis were employed to analyze its genomic variations and novel genes. More than ten million genomic variations were detected when compared with Asian cultivar. Among the variational genes, 724, 197 and 710 genes coded protein kinase, synthetase and transcription factor, respectively. A total of 353, 131 and 135 variational genes were associated with morphological trait, physiological trait, resistance or tolerance, respectively. A total of 62 were NBS-LRR genes were detected, in which 11 NBS-LRR genes expressed in sheath and mature stem, and 26 expressed in young and mature roots expressed. The pan-genome sequences of wild rice species with CCDD genome were constructed by integrating 8 Oryza alta (OA), 2 Oryza grandiglumis (OG) and 18 Oryza latifolia (OL) accessions. A total of 28 non-reference NBS-LRR genes were revealed, and 7 of which were mainly expressed in mature roots. This research demonstrated rich DNA variation in the Oryza alta Swallen that may provide a new germplasm for rice resistance breeding.

Integrated environmental and genomic analysis reveals the drivers of fine‐scale divergence and local adaptation in northern populations of two wild rice species in China

Societal Impact StatementCrop wild relatives represent precious genetic resources for crop improvement. Investigating their local adaptation to marginal environments is important for the utilization of wild genetic resources. Oryza officinalis and Oryza granulata are wild relatives of cultivated rice and possess genes that convey resistance to insects, disease, and tolerance to shade and drought. The northern edge for the distribution of these two lies in China where populations are facing habitat destruction. This study found that the northern marginal populations of both species have adapted to local conditions, with specific implications for the conservation and utilization of wild rice.Summary O. officinalis and O. granulata, wild relatives of cultivated rice, represent important gene reservoirs with the potential to improve rice with respect to insect resistance and stress tolerance. However, the northern marginal populations of these two species in China are facing habitat destruction. Here, we investigated the genetic diversity and divergence of northern marginal populations of O. officinalis and O. granulata. The genomic variation of two species was examined by whole‐genome sequencing on 357 individuals. Generalized dissimilarity modeling was applied to investigate the effects of geographic and environmental isolation on population differentiation. Genetic‐environment association analysis and genome‐wide FST outlier scans were used to identify environmentally driven signals of selection. The marginal populations of both species exhibited low genetic diversity and obvious genetic differentiation stemmed from the joint effects of isolation by geographic distance and the environment. Both genomes exhibited specific signals of adaptation to cold environments in the north. Investigation of the divergence and adaptation of marginal populations of O. officinalis and O. granulata will help us to determine how wild rice can adapt to local environments, thus allowing for the development of scientific conservation policies and the identification of new genetic resources for rice with improved resistance.

Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminata.

Rhizomes are modified stems that grow underground and produce new individuals genetically identical to the mother plant. Recently, a breakthrough has been made in efforts to convert annual grains into perennial ones by utilizing wild rhizomatous species as donors, yet the developmental biology of this organ is rarely studied. Oryza longistaminata, a wild rice species featuring strong rhizomes, provides a valuable model for exploration of rhizome development. Here, we first assembled a double-haplotype genome of O. longistaminata, which displays a 48-fold improvement in contiguity compared to the previously published assembly. Furthermore, spatiotemporal transcriptomics was performed to obtain the expression profiles of different tissues in O. longistaminata rhizomes and tillers. Two spatially reciprocal cell clusters, the vascular bundle 2 cluster and the parenchyma 2 cluster, were determined to be the primary distinctions between the rhizomes and tillers. We also captured meristem initiation cells in the sunken area of parenchyma located at the base of internodes, which is the starting point for rhizome initiation. Trajectory analysis further indicated that the rhizome is regenerated through de novo generation. Collectively, these analyses revealed a spatiotemporal transcriptional transition underlying the rhizome initiation, providing a valuable resource for future perennial crop breeding.