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BACKGROUND: Water resource development projects, such as dams and irrigation schemes, have a positive impact on food security and poverty reduction. However, such projects could increase prevalence of vector borne disease, such as malaria. This study investigate the impact of different agroecosystems and prevalence of malaria infection in Southwest Ethiopia. METHODS: Two cross-sectional surveys were conducted in the dry and wet seasons in irrigated and non-irrigated clusters of Arjo sugarcane and Gambella rice development areas of Ethiopia in 2019. A total of 4464 and 2176 study participants from 1449 households in Arjo and 546 households in Gambella enrolled in the study and blood samples were collected, respectively. All blood samples were microscopically examined and a subset of microscopy negative blood samples (n = 2244) were analysed by qPCR. Mixed effect logistic regression and generalized estimating equation were used to determine microscopic and submicroscopic malaria infection and the associated risk factors, respectively. RESULTS: Prevalence by microscopy was 2.0% (88/4464) in Arjo and 6.1% (133/2176) in Gambella. In Gambella, prevalence was significantly higher in irrigated clusters (10.4% vs 3.6%) than in non-irrigated clusters (p < 0.001), but no difference was found in Arjo (2.0% vs 2.0%; p = 0.993). On the other hand, of the 1713 and 531 samples analysed by qPCR from Arjo and Gambella the presence of submicroscopic infection was 1.2% and 12.8%, respectively. Plasmodium falciparum, Plasmodium vivax, and Plasmodium ovale were identified by qPCR in both sites. Irrigation was a risk factor for submicroscopic infection in both Arjo and Gambella. Irrigation, being a migrant worker, outdoor job, < 6 months length of stay in the area were risk factors for microscopic infection in Gambella. Moreover, school-age children and length of stay in the area for 1-3 years were significant predictors for submicroscopic malaria in Gambella. However, no

Accurately detecting nitrogen (N) deficiency and determining the need for additional N fertilizer is a key challenge to achieving precise N management in many crops, including rice (Oryza sativa L.). Many remotely sensed vegetation indices (VIs) have shown promise in this regard; however, it is not well-known if VIs measured from different sensors can be used interchangeably. The objective of this study was to quantitatively test and compare the ability of VIs measured from an aerial and proximal sensor to predict the crop yield response to top-dress N fertilizer in rice. Nitrogen fertilizer response trials were established across two years (six site-years) throughout the Sacramento Valley rice-growing region of California. At panicle initiation (PI), unmanned aircraft system (UAS) Normalized Difference Red-Edge Index (NDREUAS) and GreenSeeker (GS) Normalized Difference Vegetation Index (NDVIGS) were measured and expressed as a sufficiency index (SI) (VI of N treatment divided by VI of adjacent N-enriched area). Following reflectance measurements, each plot was split into subplots with and without top-dress N fertilizer. All metrics evaluated in this study indicated that both NDREUAS and NDVIGS performed similarly with respect to predicting the rice yield response to top-dress N at PI. Utilizing SI measurements prior to top-dress N fertilizer application resulted in a 113% and 69% increase (for NDREUAS and NDVIGS, respectively) in the precision of the rice yield response differentiation compared to the effect of applying top-dress N without SI information considered. When the SI measured via NDREUAS and NDVIGS at PI was ≤0.97 and 0.96, top-dress N applications resulted in a significant (p < 0.05) increase in crop yield of 0.19 and 0.21 Mg ha-1, respectively. These results indicate that both aerial NDREUAS and proximal NDVIGS have the potential to accurately predict the rice yield response to PI top-dress N fertilizer in this system and could serve as the basis fo

Rorqual foraging behavior varies with species, prey type and foraging conditions, and can be a determining factor for their fitness. Little is known about the foraging ecology of Rice's whales (Balaenoptera ricei), an endangered species with a population of fewer than 100 individuals. Suction cup tags were attached to two Rice's whales to collect information on their diving kinematics and foraging behavior. The tagged whales primarily exhibited lunge-feeding near the sea bottom and to a lesser extent in the water-column and at the sea surface. During 6-10 min foraging dives, the whales typically circled their prey before executing one or two feeding lunges. Longer duration dives and dives with more feeding-lunges were followed by an increase in their breathing rate. The median lunge rate of one lunge per dive of both animals was much lower than expected based on comparative research on other lunge-feeding baleen whales, and may be associated with foraging on fish instead of krill or may be an indication of different foraging conditions. Both animals spent extended periods of the night near the sea surface, increasing the risk for ship strike. Furthermore, their circling before lunging may increase the risk for entanglement in bottom-longline fishing gear. Overall, these data show that Rice's whale foraging behavior differs from other lunge feeding rorqual species and may be a significant factor in shaping our understanding of their foraging ecology. Efforts to mitigate threats to Rice's whales will benefit from improved understanding of patterns in their habitat use and fine-scale ecology.

Rice straw cellulose nanofibrils from the optimal 2,2,6,6-tetramethylpiperidine-1-oxyl oxidation/blending process carrying 1.17 mmol/g surface carboxyls were protonated to varying charged (COO-Na+) and uncharged (COOH) surfaces. Reducing the electrostatic repulsion of surface charges by protonation with hydrochloric acid from 11 to 45 and 100% surface carboxylic acid most prominently reduced the aerogel densities from 8.0 to 6.6 and 5.2 mg/cm3 while increasing the mostly open cell pore volumes from 125 to 152 and 196 mL/g. Irrespective of charge levels, all aerogels were amphiphilic, super-absorptive, stable at pH 2 for up to 30 days, and resilient for up to 10 repetitive squeezing-absorption cycles. While these aerogels exhibited density-dependent dry [11.3 to 1.5 kPa/(mg/cm3)] and reduced wet [3.3 to 1.4 kPa/(mg/cm3)] moduli, the absorption of organic liquids stiffened the saturated aerogels. These data support protonation as a critical yet simple approach toward precise control of aerogels' dry and wet properties.

The soil microbiome is a driver of nitrous oxide (N2O) emissions in terrestrial ecosystems. Identifying the core microbiome of N2O emissions and its temperature sensitivity from trillions of soil microorganisms is a great challenge and is essential to improving the predictability of soil-climate feedback related to increasing temperature. Here, the integrated soil microbiome covering archaeal, bacterial, fungal, algal, and microfaunal communities was studied to disengage the potential linkage with its N2O emissions and its temperature sensitivity in paddy fields by hunting for core species pairs. The results showed that between-group interactions of core bacterial and archaeal members and the within-group interactions of core bacterial members jointly contributed to the N2O emissions and its temperature sensitivity. The contribution of between-group interactions (32 to 33%) was greater than that of within groups (10 to 18%). These results suggested that N2O emissions and their fluctuations related to climate warming are affected by the within- and between-group interactions of the soil microbiome. Our results help advance the knowledge on the importance of microbial keystone species and network associations in controlling N2O production and their responses to increasing temperature. IMPORTANCE Soil microorganisms drive emissions of nitrous oxide from soils; this is a powerful greenhouse gas and the dominant ozone-depleting agent. N2O emissions can be partly predicted from soil properties and specific microbial groups, whereas a possible role of below-ground microbial interactions has largely been overlooked. Here, the integrated soil microbiome covering archaeal, bacterial, fungal, algal, and microfaunal communities was studied to disengage the potential linkage with the N2O emissions and temperature sensitivity of the microbiome in paddy fields by hunting for core species pairs. The results showed that between-group interactions of core bacterial and archaeal membe

A major threat to rice production is the disease epidemics caused by insect-borne viruses that emerge and re-emerge with undefined origins. It is well known that some human viruses have zoonotic origins from wild animals. However, it remains unknown whether native plants host uncharacterized endemic viruses with spillover potential to rice (Oryza sativa) as emerging pathogens. Here, we discovered rice tiller inhibition virus (RTIV), a novel RNA virus species, from colonies of Asian wild rice (O. rufipogon) in a genetic reserve by metagenomic sequencing. We identified the specific aphid vector that is able to transmit RTIV and found that RTIV would cause low-tillering disease in rice cultivar after transmission. We further demonstrated that an infectious molecular clone of RTIV initiated systemic infection and causes low-tillering disease in an elite rice variety after Agrobacterium-mediated inoculation or stable plant transformation, and RTIV can also be transmitted from transgenic rice plant through its aphid vector to cause disease. Finally, global transcriptome analysis indicated that RTIV may disturb defense and tillering pathway to cause low tillering disease in rice cultivar. Thus, our results show that new rice viral pathogens can emerge from native habitats, and RTIV, a rare aphid-transmitted rice viral pathogen from native wild rice, can threaten the production of rice cultivar after spillover.

Switchgrass (Panicum virgatum) is a bioenergy model crop valued for its energy efficiency and drought tolerance. The related monocot species rice (Oryza sativa) and maize (Zea mays) deploy species-specific, specialized metabolites as core stress defenses. By contrast, specialized chemical defenses in switchgrass are largely unknown. To investigate specialized metabolic drought responses in switchgrass, we integrated tissue-specific transcriptome and metabolite analyses of the genotypes Alamo and Cave-in-Rock that feature different drought tolerance. The more drought-susceptible Cave-in-Rock featured an earlier onset of transcriptomic changes and significantly more differentially expressed genes in response to drought compared to Alamo. Specialized pathways showed moderate differential expression compared to pronounced transcriptomic alterations in carbohydrate and amino acid metabolism. However, diterpenoid-biosynthetic genes showed drought-inducible expression in Alamo roots, contrasting largely unaltered triterpenoid and phenylpropanoid pathways. Metabolomic analyses identified common and genotype-specific flavonoids and terpenoids. Consistent with transcriptomic alterations, several root diterpenoids showed significant drought-induced accumulation, whereas triterpenoid abundance remained predominantly unchanged. Structural analysis verified select drought-responsive diterpenoids as oxygenated furanoditerpenoids. Drought-dependent transcriptome and metabolite profiles provide the foundation to understand the molecular mechanisms underlying switchgrass drought responses. Accumulation of specialized root diterpenoids and corresponding pathway transcripts supports a role in drought stress tolerance.

Introducing asexual reproduction through seeds - apomixis - into crop species could revolutionize agriculture by allowing F1 hybrids with enhanced yield and stability to be clonally propagated. Engineering synthetic apomixis has proven feasible in inbred rice through the inactivation of three genes (MiMe), which results in the conversion of meiosis into mitosis in a line ectopically expressing the BABYBOOM1 (BBM1) parthenogenetic trigger in egg cells. However, only 10-30% of the seeds are clonal. Here, we show that synthetic apomixis can be achieved in an F1 hybrid of rice by inducing MiMe mutations and egg cell expression of BBM1 in a single step. We generate hybrid plants that produce more than 95% of clonal seeds across multiple generations. Clonal apomictic plants maintain the phenotype of the F1 hybrid along successive generations. Our results demonstrate that there is no barrier to almost fully penetrant synthetic apomixis in an important crop species, rendering it compatible with use in agriculture.

Improving biological nitrogen fixation (BNF) in cereal crops is a long-sought objective; however, no successful modification of cereal crops showing increased BNF has been reported. Here, we described a novel approach in which rice plants were modified to increase the production of compounds that stimulated biofilm formation in soil diazotrophic bacteria, promoted bacterial colonization of plant tissues and improved BNF with increased grain yield at limiting soil nitrogen contents. We first used a chemical screening to identify plant-produced compounds that induced biofilm formation in nitrogen-fixing bacteria and demonstrated that apigenin and other flavones induced BNF. We then used CRISPR-based gene editing targeting apigenin breakdown in rice, increasing plant apigenin contents and apigenin root exudation. When grown at limiting soil nitrogen conditions, modified rice plants displayed increased grain yield. Biofilm production also modified the root microbiome structure, favouring the enrichment of diazotrophic bacteria recruitment. Our results support the manipulation of the flavone biosynthetic pathway as a feasible strategy for the induction of biological nitrogen fixation in cereals and a reduction in the use of inorganic nitrogen fertilizers.

Cellulose and lignin are the two main components of secondary plant cell walls with substantial impact on stalk in the field and on straw during industrial processing. The amount of fermentable sugar that can be accessed is another important parameter affecting various industrial applications. In the present study, genetic variability of rice (Oryza sativa L.) genotypes for cellulose, lignin, and fermentable sugars contents was analyzed in rice straw. A genome-wide association study of 33,484 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) >0.05 was performed. The genome-wide association study identified seven, three, and three genomic regions to be significantly associated with cellulose, lignin, and fermentable sugar contents, respectively. Candidate genes in the associated genomic regions were enzymes mainly involved in cell wall metabolism. Novel SNP markers associated with cellulose were tagged to GH16, peroxidase, GT6, GT8, and CSLD2. For lignin content, Villin protein, OsWAK1/50/52/53, and GH16 were identified. For fermentable sugar content, UTP-glucose-1-phosphate uridylyltransferase, BRASSINOSTEROID INSENSITIVE 1, and receptor-like protein kinase 5 were found. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in biosynthesis, turnover, and modification of major cell wall components and saccharides in rice straw., QC 20220615

Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

Plant TRANS-ACTING SIRNA3 (TAS3)-derived short interfering RNAs (siRNAs) include tasiR-AUXIN RESPONSE FACTORs (ARFs), which are functionally conserved in targeting ARF genes, and a set of non-tasiR-ARF siRNAs, which have rarely been studied. In this study, TAS3 siRNAs were systematically characterized in rice (Oryza sativa). Small RNA sequencing results showed that an overwhelming majority of TAS3 siRNAs belong to the non-tasiR-ARF group, while tasiR-ARFs occupy a diminutive fraction. Phylogenetic analysis of TAS3 genes across dicot and monocot plants revealed that the siRNA-generating regions were highly conserved in grass species, especially in the Oryzoideae. Target genes were identified for not only tasiR-ARFs but also non-tasiR-ARF siRNAs by analyzing rice Parallel Analysis of RNA Ends datasets, and some of these siRNA-target interactions were experimentally confirmed using tas3 mutants generated by genome editing. Consistent with the de-repression of target genes, phenotypic alterations were observed for mutants in three TAS3 loci in comparison to wild-type rice. The regulatory role of ribosomes in the TAS3 siRNA-target interactions was further revealed by the fact that TAS3 siRNA-mediated target cleavage, in particular tasiR-ARFs targeting ARF2/3/14/15, occurred extensively in rice polysome samples. Altogether, our study sheds light into TAS3 genes in plants and expands our knowledge about rice TAS3 siRNA-target interactions.

The zygote, a totipotent stem cell, is crucial to the life cycle of sexually reproducing organisms. It is produced by the fusion of two differentiated cells-the egg and sperm, which in plants have radically different siRNA transcriptomes from each other and from multicellular embryos. Owing to technical challenges, the epigenetic changes that accompany the transition from differentiated gametes to totipotent zygote are poorly understood. Because siRNAs serve as both regulators and outputs of the epigenome, we characterized small RNA transcriptomes of zygotes from rice. Zygote small RNAs exhibit extensive maternal carryover and an apparent lack of paternal contribution, indicated by absence of sperm signature siRNAs. Zygote formation is accompanied by widespread redistribution of 24-nt siRNAs relative to gametes, such that ∼70% of the zygote siRNA loci do not overlap any egg cell siRNA loci. Newly detected siRNA loci in zygote are gene-proximal and not associated with centromeric heterochromatin, similar to canonical siRNAs, in sharp contrast to gametic siRNA loci that are gene-distal and heterochromatic. In addition, zygote but not egg siRNA loci are associated with high DNA methylation in the mature embryo. Thus, the zygote begins transitioning before the first embryonic division to an siRNA profile that is associated with future RdDM in embryogenesis. These findings indicate that, in addition to changes in gene expression, the transition to totipotency in the plant zygote is accompanied by resetting of the epigenetic reprogramming that occurred during gamete formation.

Plant transcription factors (TFs), such as basic helix-loop-helix (bHLH) and AT-rich zinc-binding proteins (PLATZ), play critical roles in regulating the expression of developmental genes in cereals. We identified the bHLH protein TaPGS1 (T. aestivum Positive Regulator of Grain Size 1) specifically expressed in the seeds at 5-20 days post-anthesis in wheat. TaPGS1 was ectopically overexpressed (OE) in wheat and rice, leading to increased grain weight (up to 13.81% in wheat and 18.55% in rice lines) and grain size. Carbohydrate and total protein levels also increased. Scanning electron microscopy results indicated that the starch granules in the endosperm of TaPGS1 OE wheat and rice lines were smaller and tightly embedded in a proteinaceous matrix. Furthermore, TaPGS1 was bound directly to the E-box motif at the promoter of the PLATZ TF genes TaFl3 and OsFl3 and positively regulated their expression in wheat and rice. In rice, the OsFl3 CRISPR/Cas9 knockout lines showed reduced average thousand-grain weight, grain width, and grain length in rice. Our results reveal that TaPGS1 functions as a valuable trait-associated gene for improving cereal grain yield.

BackgroundOne of the ways genomes respond to stress is by producing extrachromosomal circular DNAs (eccDNAs). EccDNAs can contain genes and dramatically increase their copy number. They can also reinsert into the genome, generating structural variation. They have been shown to provide a source of phenotypic and genotypic plasticity in several species. However, whole circularome studies have so far been limited to a few model organisms. Fungal plant pathogens are a serious threat to global food security in part because of their rapid adaptation to disease prevention strategies. Understanding the mechanisms fungal pathogens use to escape disease control is paramount to curbing their threat.ResultsWe present a whole circularome sequencing study of the rice blast pathogen, Magnaporthe oryzae. We find that M. oryzae has a highly diverse circularome that contains many genes and shows evidence of large LTR retrotransposon activity. We find that genes enriched on eccDNAs in M. oryzae occur in genomic regions prone to presence-absence variation and that disease-associated genes are frequently on eccDNAs. Finally, we find that a subset of genes is never present on eccDNAs in our data, which indicates that the presence of these genes on eccDNAs is selected against.ConclusionsOur study paves the way to understanding how eccDNAs contribute to adaptation in M. oryzae. Our analysis also reveals how M. oryzae eccDNAs differ from those of other species and highlights the need for further comparative characterization of eccDNAs across species to gain a better understanding of these molecules.

In this article, we describe the development of the plant immunity field, starting with efforts to understand the genetic basis for disease resistance, which ∼30 y ago led to the discovery of diverse classes of immune receptors that recognize and respond to infectious microbes. We focus on knowledge gained from studies of the rice XA21 immune receptor that recognizes RaxX (required for activation of XA21 mediated immunity X), a sulfated microbial peptide secreted by the gram-negative bacterium Xanthomonas oryzae pv. oryzae. XA21 is representative of a large class of plant and animal immune receptors that recognize and respond to conserved microbial molecules. We highlight the complexity of this large class of receptors in plants, discuss a possible role for RaxX in Xanthomonas biology, and draw attention to the important role of sulfotyrosine in mediating receptor-ligand interactions.

The recently named Rice's whale in the Gulf of Mexico is one of the most endangered whales in the world, and improved knowledge of spatiotemporal occurrence patterns is needed to support their recovery and conservation. Passive acoustic monitoring methods for determining spatiotemporal occurrence patterns require identifying the species' call repertoire. Rice's whale call repertoire remains unvalidated though several potential call types have been identified. This study uses sonobuoys and passive acoustic tagging to validate the source of potential call types and to characterize Rice's whale calls. During concurrent visual and acoustic surveys, acoustic-directed approaches were conducted to obtain visual verifications of sources of localized sounds. Of 28 acoustic-directed approaches, 79% led to sightings of balaenopterid whales, of which 10 could be positively identified to species as Rice's whales. Long-moan calls, downsweep sequences, and tonal-sequences are attributed to Rice's whales based on these matches, while anthropogenic sources are ruled out. A potential new call type, the low-frequency downsweep sequence, is characterized from tagged Rice's whale recordings. The validation and characterization of the Rice's whale call repertoire provides foundational information needed to use passive acoustic monitoring for better understanding and conservation of these critically endangered whales.

Rice blast, caused by Pyricularia oryzae, is one of the most destructive diseases in agriculture leading to severe impacts on rice crop harvests worldwide. In a previous study, we showed that rice genes OsDjA2 and OsERF104, encoding a chaperone protein and an APETELA2/ethylene-responsive factor, respectively, were strongly induced in a compatible interaction with blast fungus, and also had their function in plant susceptibility validated through gene silencing. Here, we report the CRISPR/Cas9 knockout of OsDjA2 and OsERF104 genes resulting in considerable improvement of blast resistance. A total of 15 OsDjA2 (62.50%) and 17 OsERF104 (70.83%) T0 transformed lines were identified from 24 regenerated plants for each target and used in downstream experiments. Phenotyping of homozygous T1 mutant lines revealed not only a significant decrease in the number of blast lesions but also a reduction in the percentage of diseased leaf area, compared with the wild-type infected control plants. Our results supported CRISPR/Cas9-mediated target mutation in rice susceptibility genes as a potential and alternative breeding strategy for building resistance to blast disease.

The zygote, a totipotent stem cell, is crucial to the life cycle of sexually reproducing organisms. It is produced by the fusion of two differentiated cells-the egg and sperm, which in plants have radically different siRNA transcriptomes from each other and from multicellular embryos. Owing to technical challenges, the epigenetic changes that accompany the transition from differentiated gametes to totipotent zygote are poorly understood. Because siRNAs serve as both regulators and outputs of the epigenome, we characterized small RNA transcriptomes of zygotes from rice. Zygote small RNAs exhibit extensive maternal carryover and an apparent lack of paternal contribution, indicated by absence of sperm signature siRNAs. Zygote formation is accompanied by widespread redistribution of 24-nt siRNAs relative to gametes, such that ∼70% of the zygote siRNA loci do not overlap any egg cell siRNA loci. Newly detected siRNA loci in zygote are gene-proximal and not associated with centromeric heterochromatin, similar to canonical siRNAs, in sharp contrast to gametic siRNA loci that are gene-distal and heterochromatic. In addition, zygote but not egg siRNA loci are associated with high DNA methylation in the mature embryo. Thus, the zygote begins transitioning before the first embryonic division to an siRNA profile that is associated with future RdDM in embryogenesis. These findings indicate that, in addition to changes in gene expression, the transition to totipotency in the plant zygote is accompanied by resetting of the epigenetic reprogramming that occurred during gamete formation.

Plant transcription factors (TFs), such as basic helix-loop-helix (bHLH) and AT-rich zinc-binding proteins (PLATZ), play critical roles in regulating the expression of developmental genes in cereals. We identified the bHLH protein TaPGS1 (T. aestivum Positive Regulator of Grain Size 1) specifically expressed in the seeds at 5-20 days post-anthesis in wheat. TaPGS1 was ectopically overexpressed (OE) in wheat and rice, leading to increased grain weight (up to 13.81% in wheat and 18.55% in rice lines) and grain size. Carbohydrate and total protein levels also increased. Scanning electron microscopy results indicated that the starch granules in the endosperm of TaPGS1 OE wheat and rice lines were smaller and tightly embedded in a proteinaceous matrix. Furthermore, TaPGS1 was bound directly to the E-box motif at the promoter of the PLATZ TF genes TaFl3 and OsFl3 and positively regulated their expression in wheat and rice. In rice, the OsFl3 CRISPR/Cas9 knockout lines showed reduced average thousand-grain weight, grain width, and grain length in rice. Our results reveal that TaPGS1 functions as a valuable trait-associated gene for improving cereal grain yield.

In this article, we describe the development of the plant immunity field, starting with efforts to understand the genetic basis for disease resistance, which ∼30 y ago led to the discovery of diverse classes of immune receptors that recognize and respond to infectious microbes. We focus on knowledge gained from studies of the rice XA21 immune receptor that recognizes RaxX (required for activation of XA21 mediated immunity X), a sulfated microbial peptide secreted by the gram-negative bacterium Xanthomonas oryzae pv. oryzae. XA21 is representative of a large class of plant and animal immune receptors that recognize and respond to conserved microbial molecules. We highlight the complexity of this large class of receptors in plants, discuss a possible role for RaxX in Xanthomonas biology, and draw attention to the important role of sulfotyrosine in mediating receptor-ligand interactions.

Rice blast, caused by Pyricularia oryzae, is one of the most destructive diseases in agriculture leading to severe impacts on rice crop harvests worldwide. In a previous study, we showed that rice genes OsDjA2 and OsERF104, encoding a chaperone protein and an APETELA2/ethylene-responsive factor, respectively, were strongly induced in a compatible interaction with blast fungus, and also had their function in plant susceptibility validated through gene silencing. Here, we report the CRISPR/Cas9 knockout of OsDjA2 and OsERF104 genes resulting in considerable improvement of blast resistance. A total of 15 OsDjA2 (62.50%) and 17 OsERF104 (70.83%) T0 transformed lines were identified from 24 regenerated plants for each target and used in downstream experiments. Phenotyping of homozygous T1 mutant lines revealed not only a significant decrease in the number of blast lesions but also a reduction in the percentage of diseased leaf area, compared with the wild-type infected control plants. Our results supported CRISPR/Cas9-mediated target mutation in rice susceptibility genes as a potential and alternative breeding strategy for building resistance to blast disease.

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in California's Central Valley have emerged as ecologically functioning floodplain rearing habitat for juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods to enhance habitat benefits for fall-run Chinook Salmon reared on winter-flooded rice fields in the Yolo Bypass, a modified floodplain managed for flood control, agriculture, and wildlife habitat in the Sacramento River Valley of California. Investigations included studying the effect of 1) post-harvest field substrate; 2) depth refugia; 3) duration of field drainage; and 4) duration of rearing occupancy on in-situ diet, growth and survival of juvenile salmon. Post-harvest substrate treatment had only a small effect on the lower trophic food web and an insignificant effect on growth rates or survival of rearing hatchery-origin, fall-run Chinook Salmon. Similarly, depth refugia, created by trenches dug to various depths, also had an insignificant effect on survival. Rapid field drainage yielded significantly higher survival compared to drainage methods drawn out over longer periods. A mortality of approximately one third was observed in the first week after fish were released in the floodplain. This initial mortality event was followed by high, stable survival rates for the remainder of the 6-week duration of floodplain rearing study. Across years, in-field survival ranged 7.4-61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in California's recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incr

XA21 encodes a rice immune receptor that confers robust resistance to most strains of the Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo). XA21-mediated immunity is triggered by recognition of a small protein called RaxX-sY (required for activation of XA21-mediated immunity X, tyrosine-sulfated) secreted by Xoo. To identify components regulating XA21-mediated immunity, we generated and screened a mutant population of fast-neutron-mutagenized rice expressing Ubi:Myc-XA21 for those susceptible to Xoo. Here, we report the characterization of one of these rice mutants, named sxi2 (suppressor of XA21-mediated immunity-2). Whole-genome sequencing revealed that sxi2 carries a deletion of the PALADIN (PALD) gene encoding a protein with three putative protein tyrosine phosphatase-like domains (PTP-A, -B, and -C). Expression of PALD in the sxi2 genetic background was sufficient to complement the susceptible phenotype, which requires the catalytic cysteine of the PTP-A active site to restore resistance. PALD co-immunoprecipitated with the full-length XA21 protein, whose levels are positively regulated by the presence of the PALD transgene. Furthermore, we foundd that sxi2 retains many hallmarks of XA21-mediated immunity, similar to the wild type. These results reveal that PALD, a previously uncharacterized class of phosphatase, functions in rice innate immunity, and suggest that the conserved cysteine in the PTP-A domain of PALD is required for its immune function.

Plants encounter various microbes in nature and must respond appropriately to symbiotic or pathogenic ones. In rice, the receptor-like kinase OsCERK1 is involved in recognizing both symbiotic and immune signals. However, how these opposing signals are discerned via OsCERK1 remains unknown. Here, we found that receptor competition enables the discrimination of symbiosis and immunity signals in rice. On the one hand, the symbiotic receptor OsMYR1 and its short-length chitooligosaccharide ligand inhibit complex formation between OsCERK1 and OsCEBiP and suppress OsCERK1 phosphorylating the downstream substrate OsGEF1, which reduces the sensitivity of rice to microbe-associated molecular patterns. Indeed, OsMYR1 overexpression lines are more susceptible to the fungal pathogen Magnaporthe oryzae, whereas Osmyr1 mutants show higher resistance. On the other hand, OsCEBiP can bind OsCERK1 and thus block OsMYR1-OsCERK1 heteromer formation. Consistently, the Oscebip mutant displayed a higher rate of mycorrhizal colonization at early stages of infection. Our results indicate that OsMYR1 and OsCEBiP receptors compete for OsCERK1 to determine the outcome of symbiosis and immunity signals.

Intensive systems with two or three rice (Oryza sativa L.) crops per year account for about 50% of the harvested area for irrigated rice in Asia. Any reduction in productivity or sustainability of these systems has serious implications for global food security. Rice yield trends in the world's longest-running long-term continuous cropping experiment (LTCCE) were evaluated to investigate consequences of intensive cropping and to draw lessons for sustaining production in Asia. Annual production was sustained at a steady level over the 50-y period in the LTCCE through continuous adjustment of management practices and regular cultivar replacement. Within each of the three annual cropping seasons (dry, early wet, and late wet), yield decline was observed during the first phase, from 1968 to 1990. Agronomic improvements in 1991 to 1995 helped to reverse this yield decline, but yield increases did not continue thereafter from 1996 to 2017. Regular genetic and agronomic improvements were sufficient to maintain yields at steady levels in dry and early wet seasons despite a reduction in the yield potential due to changing climate. Yield declines resumed in the late wet season. Slower growth in genetic gain after the first 20 y was associated with slower breeding cycle advancement as indicated by pedigree depth. Our findings demonstrate that through adjustment of management practices and regular cultivar replacement, it is possible to sustain a high level of annual production in irrigated systems under a changing climate. However, the system was unable to achieve further increases in yield required to keep pace with the growing global rice demand.

The purpose of the current study was to assess the effects of substituting corn with ground brown rice on growth performance, immune status, and gut microbiota in weanling pigs. Seventy-two weanling pigs (28 d old with 6.78 ± 0.94 kg body weight [BW]) were randomly allotted to two dietary treatments with six pens and six pigs (three barrows and gilts) per pen within a randomized complete block design. The control pigs were fed a typical diet for weanling pigs based on corn and soybean meal diet (control diet: CON), and the other pigs were fed a formulated diet with 100% replacement of corn with ground brown rice for 35d (treatment diet: GBR). Growth performance, immune status, and gut microbiota of weanling pigs were measured. The substitution of corn with GBR did not affect growth performance or diarrhea frequency. Additionally, there were no differences in white blood cell number, hematocrit, cortisol, C-reactive protein, and serum tumor necrosis factor-alpha levels between pigs fed CON or GBR for the first 2 wk after weaning. However, weanling pigs fed GBR had lower (P < 0.05) serum transforming growth factor-beta 1 level than those fed CON. Furthermore, weanling pigs fed GBR had increased (P < 0.05) relative abundance of phylum Firmicutes and genus Lactobacillus and Streptococcus and decreased (P < 0.05) relative abundance of phylum Bacteroidetes and genus Clostridium and Prevotella in the gut microbiota compared with those fed CON. In conclusion, there was no significant difference in growth performance when corn was replaced with ground brown rice in diets for weanling pigs. Furthermore, the substitution of corn with ground brown rice in weaning diet modulated immune status and gut microbiota of pigs by increasing beneficial microbial communities and reducing harmful microbial communities. Overall, ground brown rice-based diet is a potential alternative to corn-based diet without negative effects on growth performance, immune status, and gut microbiot

The microbial compositions, quality characteristics, and structural changes in fresh brown rice noodles (FBRN) during storage were investigated. Total plate count and mold and yeast counts increased while the pH decreased during storage. Metagenomic sequencing revealed that the microbial composition of FBRN changed throughout storage. A comprehensive investigation of the variation in lipid content demonstrated that hydrolytic rancidity was responsible for lipid deterioration. LF-NMR showed an increase in the proportion of bound water and a decrease in the proportion of free water in FBRN. Moreover, significant changes in edible qualities were observed. The cooking loss increased three-fold and noodles hardness reduced by approximately 23%. Further, the high initial aldehyde content of FBRN diminished almost completely, while that of alcohols and esters increased, leading to significant flavor deterioration. The correlation and factor analysis suggested that the TPC and MY counts could be used as key indicators of FBRN deterioration.

Structural biology has the potential to illuminate the evolution of pathogen effectors and their commonalities that cannot be readily detected at the primary sequence level. Recent breakthroughs in protein structure modeling have demonstrated the feasibility to predict the protein folds without depending on homologous templates. These advances enabled a genome-wide computational structural biology approach to help understand proteins based on their predicted folds. In this study, we employed structure prediction methods on the secretome of the destructive fungal pathogen Magnaporthe oryzae. Out of 1,854 secreted proteins, we predicted the folds of 1,295 proteins (70%). We showed that template-free modeling by TrRosetta captured 514 folds missed by homology modeling, including many known effectors and virulence factors, and that TrRosetta generally produced higher quality models for secreted proteins. Along with sensitive homology search, we employed structure-based clustering, defining not only homologous groups with divergent members but also sequence-unrelated structurally analogous groups. We demonstrate that this approach can reveal new putative members of structurally similar MAX effectors and novel analogous effector families present in M. oryzae and possibly in other phytopathogens. We also investigated the evolution of expanded putative ADP-ribose transferases with predicted structures. We suggest that the loss of catalytic activities of the enzymes might have led them to new evolutionary trajectories to be specialized as protein binders. Collectively, we propose that computational structural genomics approaches can be an integral part of studying effector biology and provide valuable resources that were inaccessible before the advent of machine learning-based structure prediction.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

BackgroundIrrigation schemes may result in subsequent changes in malaria disease dynamics. Understanding the mechanisms and effects of irrigation on malaria vector bionomics and transmission intensity is essential to develop new or alternative surveillance and control strategies to reduce or control malaria risk. This study was designed to assess the effect of rice irrigation on malaria vector bionomics and transmission intensity in the Gambella Region, Ethiopia.MethodsComparative cross-sectional study was conducted in Abobo District of the Gambella Region, Ethiopia. Accordingly, clusters (kebeles) were classified into nearby and faraway clusters depending on their proximity to the irrigation scheme. Adult mosquito survey was conducted in February, August and November 2018 from three nearby and three faraway clusters using Centers for Disease Control and Prevention (CDC) light traps (LTs). During the November survey, human landing catch (HLC) and pyrethrum spray catch (PSC) were also conducted. The collected mosquitoes were morphologically identified to species and tested for Plasmodium infection using circumsporozoite protein enzyme-linked immunosorbent assay (CSP-ELISA). Furthermore, species-specific polymerase chain reaction (PCR) was performed to identify member species of the Anopheles gambiae complex. Chi-square and t-tests were used to analyze the data using the SPSS version 20 software package.ResultsA total of 4319 female anopheline mosquitoes comprising An. gambiae sensu lato, An. funestus group, An. pharoensis, An. coustani complex and An. squamosus were collected. Overall, 84.5% and 15.5% of the anopheline mosquitoes were collected from the nearby and faraway clusters, respectively. Anopheles gambiae s.l. was the predominant (56.2%) anopheline species in the area followed by An. pharoensis (15.7%). The density of anopheline mosquitoes was significantly higher in the nearby clusters in both HLCs [t(3) = 5.14, P = 0.0143] and CDC LT catches [t(271.97)

This study examined the role of intermittent illumination/dark conditions coupled with MnO2-ammendments to regulate the mobility of As and Fe in flooded arsenic-enriched soils. Addition of MnO2 particles with intermittent illumination led to a pronounced increase in the reductive-dissolution of Fe(III) and As(V) from flooded soils compared to a corresponding dark treatments. A higher MnO2 dosage (0.10 vs 0.02 g) demonstrated a greater effect. Over a 49-day incubation, maximum Fe concentrations mobilized from the flooded soils amended with 0.10 and 0.02 g MnO2 particles were 2.39 and 1.85-fold higher than for non-amended soils under dark conditions. The corresponding maximum amounts of mobilized As were at least 92 % and 65 % higher than for non-amended soils under dark conditions, respectively. Scavenging of excited holes by soil humic/fulvic compounds increased mineral photoelectron production and boosted Fe(III)/As(V) reduction in MnO2-amended, illuminated soils. Additionally, MnO2 amendments shifted soil microbial community structure by enriching metal-reducing bacteria (e.g., Anaeromyxobacter, Bacillus and Geobacter) and increasing c-type cytochrome production. This microbial diversity response to MnO2 amendment facilitated direct contact extracellular electron transfer processes, which further enhanced Fe/As reduction. Subsequently, the mobility of released Fe(II) and As(III) was partially attenuated by adsorption, oxidation, complexation and/or coprecipitation on active sites generated on MnO2 surfaces during MnO2 dissolution. These results illustrated the impact of a semiconducting MnO2 mineral in regulating the biogeochemical cycles of As/Fe in soil and demonstrated the potential for MnO2-based bioremediation strategies for arsenic-polluted soils.

BackgroundSmall RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) serve as core players in gene silencing at transcriptional and post-transcriptional levels in plants, but their subcellular localization has not yet been well studied, thus limiting our mechanistic understanding of sRNA action.ResultsWe investigate the cytoplasmic partitioning of sRNAs and their targets globally in maize (Zea mays, inbred line "B73") and rice (Oryza sativa, cv. "Nipponbare") by high-throughput sequencing of polysome-associated sRNAs and 3' cleavage fragments, and find that both miRNAs and a subset of 21-nucleotide (nt)/22-nt siRNAs are enriched on membrane-bound polysomes (MBPs) relative to total polysomes (TPs) across different tissues. Most of the siRNAs are generated from transposable elements (TEs), and retrotransposons positively contributed to MBP overaccumulation of 22-nt TE-derived siRNAs (TE-siRNAs) as opposed to DNA transposons. Widespread occurrence of miRNA-mediated target cleavage is observed on MBPs, and a large proportion of these cleavage events are MBP-unique. Reproductive 21PHAS (21-nt phasiRNA-generating) and 24PHAS (24-nt phasiRNA-generating) precursors, which were commonly considered as noncoding RNAs, are bound by polysomes, and high-frequency cleavage of 21PHAS precursors by miR2118 and 24PHAS precursors by miR2275 is further detected on MBPs. Reproductive 21-nt phasiRNAs are enriched on MBPs as opposed to TPs, whereas 24-nt phasiRNAs are nearly completely devoid of polysome occupancy.ConclusionsMBP overaccumulation is a conserved pattern for cytoplasmic partitioning of sRNAs, and endoplasmic reticulum (ER)-bound ribosomes function as an independent regulatory layer for miRNA-induced gene silencing and reproductive phasiRNA biosynthesis in maize and rice.

Early root growth is critical for plant establishment and survival. We have identified a molecular pathway required for helical root tip movement known as circumnutation. Here, we report a multiscale investigation of the regulation and function of this phenomenon. We identify key cell signaling events comprising interaction of the ethylene, cytokinin, and auxin hormone signaling pathways. We identify the gene Oryza sativa histidine kinase-1 (HK1) as well as the auxin influx carrier gene OsAUX1 as essential regulators of this process in rice. Robophysical modeling and growth challenge experiments indicate circumnutation is critical for seedling establishment in rocky soil, consistent with the long-standing hypothesis that root circumnutation facilitates growth past obstacles. Thus, the integration of robotics, physics, and biology has elucidated the functional importance of root circumnutation and uncovered the molecular mechanisms underlying its regulation.

There is growing global interest in the bioremediation of cadmium (Cd) using combinations of biochar and microorganisms. However, the interactions among biochar, introduced and indigenous microorganisms remain unclear. Accordingly, a 90 day microcosm experiment was conducted to investigate this by adding Bacillus sp. K1 strain inoculated rice straw biochar (SBB) and magnetic straw biochar (MBB) into a Cd contaminated paddy soil from Hunan, China. All treatments were incubated aerobically (60% water holding capacity) or anaerobically for 90 d. During both soil incubations, Bacillus sp. K1 successfully colonized in soil with composites applications. Soil pH was significantly increased from acid to neutral, and available Cd decreased with the addition of both composites. The better remediation efficiency of MBB than SBB under anerobic conditions was attributed to the transformation of acetic acid-extractable Cd into the residual fraction, caused by Cd2+ bonding with crystal Fe3O4. The application of the two kinds of composites caused similar changes to both microbial communities. There was a slight decrease in indigenous microbial alpha diversity with the MBB aerobic application, while the total population number of bacteria was increased by 700%. Both the redundancy analysis and Mantel analyses indicated that pH and microbial biomass C contributed to the colonization of Bacillus sp. K1 with SBB under aerobic conditions, and with MBB under anerobic conditions, respectively. The research provides a new insight into interactive effects and investigates immobilization mechanisms involved of bacterial/biochar composites in anaerobic and aerobic soils.

In angiosperms, endosperm development comprises a series of developmental transitions controlled by genetic and epigenetic mechanisms that are initiated after double fertilization. Polycomb repressive complex 2 (PRC2) is a key component of these mechanisms that mediate histone H3 lysine 27 trimethylation (H3K27me3); the action of PRC2 is well described in Arabidopsis thaliana but remains uncertain in cereals. In this study, we demonstrate that mutation of the rice (Oryza sativa) gene EMBRYONIC FLOWER2a (OsEMF2a), encoding a zinc-finger containing component of PRC2, causes an autonomous endosperm phenotype involving proliferation of the central cell nuclei with separate cytoplasmic domains, even in the absence of fertilization. Detailed cytological and transcriptomic analyses revealed that the autonomous endosperm can produce storage compounds, starch granules, and protein bodies specific to the endosperm. These events have not been reported in Arabidopsis. After fertilization, we observed an abnormally delayed developmental transition in the endosperm. Transcriptome and H3K27me3 ChIP-seq analyses using endosperm from the emf2a mutant identified downstream targets of PRC2. These included >100 transcription factor genes such as type-I MADS-box genes, which are likely required for endosperm development. Our results demonstrate that OsEMF2a-containing PRC2 controls endosperm developmental programs before and after fertilization.

Parent-of-origin-dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin-specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA-producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions-the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.

Large changes have taken place in smallholder farming systems in South Asia's coastal areas in recent decades, particularly related to cropping intensity, input availability, climate risks, and off-farm activities. However, few studies have investigated the extent to which these changes have impacted farm-level crop productivity, which is a key driver of food security and poverty in rainfed, low-input, rice-based systems. The objective of this study was to conduct an integrated assessment of variables related to socioeconomic status, farm characteristics, and crop management practices to understand the major factors influencing crop productivity and identify promising leverage points for sustainable development in coastal Bangladesh. Using a panel survey dataset of 32 variables from 502 farm households located within polder (coastal embankment) and outside polder systems during 2005-2015, we employed statistical factor analysis to characterize five independent latent factors named here as Farming Challenges, Economic Status, Crop Management Practices, Asset Endowment, and Farm Characteristics. The factor Farming Challenges explained the most variation among households (31%), with decreases observed over time, specifically households located outside polders. Individual variables contributing to this factor included perceived cyclone severity, household distance to main roads and input-output markets, cropping intensity, and access to extension services. The most important factors for increasing crop productivity on a household and per unit area basis were Asset Endowment and Crop Management Practices, respectively. The former highlights the need for increasing gross cropped area, which can be achieved through greater cropping intensity, while the latter was associated with increased fertilizer, labor, and pesticide input use. Despite the importance of these factors, household poverty trajectory maps showed that changes in off-farm income had played the strongest role

The microbial compositions, quality characteristics, and structural changes in fresh brown rice noodles (FBRN) during storage were investigated. Total plate count and mold and yeast counts increased while the pH decreased during storage. Metagenomic sequencing revealed that the microbial composition of FBRN changed throughout storage. A comprehensive investigation of the variation in lipid content demonstrated that hydrolytic rancidity was responsible for lipid deterioration. LF-NMR showed an increase in the proportion of bound water and a decrease in the proportion of free water in FBRN. Moreover, significant changes in edible qualities were observed. The cooking loss increased three-fold and noodles hardness reduced by approximately 23%. Further, the high initial aldehyde content of FBRN diminished almost completely, while that of alcohols and esters increased, leading to significant flavor deterioration. The correlation and factor analysis suggested that the TPC and MY counts could be used as key indicators of FBRN deterioration.

Production landscapes depend on, but also affect, ecosystem services. In the Rejoso watershed (East Java, Indonesia), uncontrolled groundwater use for paddies reduces flow of lowland pressure-driven artesian springs that supply drinking water to urban stakeholders. Analysis of the water balance suggested that the decline by about 30% in spring discharge in the past decades is attributed for 47 and 53%, respectively, to upland degradation and lowland groundwater abstraction. Consequently, current spring restoration efforts support upland agroforestry development while aiming to reduce lowland groundwater wasting. To clarify spatial and social targeting of lowland interventions five clusters (replicable patterns) of lowland paddy farming were distinguished from spatial data on, among other factors, reliance on river versus artesian wells delivering groundwater, use of crop rotation, rice yield, fertiliser rates and intensity of rodent control. A survey of farming households (461 respondents), complemented and verified through in-depth interviews and group discussions, identified opportunities for interventions and associated risks. Changes in artesian well design, allowing outflow control, can support water-saving, sustainable paddy cultivation methods. With rodents as a major yield-reducing factor, solutions likely depend on more synchronized planting calendars and thus on collective action for effectiveness at scale. Interventions based on this design are currently tested.

There is growing global interest in the bioremediation of cadmium (Cd) using combinations of biochar and microorganisms. However, the interactions among biochar, introduced and indigenous microorganisms remain unclear. Accordingly, a 90 day microcosm experiment was conducted to investigate this by adding Bacillus sp. K1 strain inoculated rice straw biochar (SBB) and magnetic straw biochar (MBB) into a Cd contaminated paddy soil from Hunan, China. All treatments were incubated aerobically (60% water holding capacity) or anaerobically for 90 d. During both soil incubations, Bacillus sp. K1 successfully colonized in soil with composites applications. Soil pH was significantly increased from acid to neutral, and available Cd decreased with the addition of both composites. The better remediation efficiency of MBB than SBB under anerobic conditions was attributed to the transformation of acetic acid-extractable Cd into the residual fraction, caused by Cd2+ bonding with crystal Fe3O4. The application of the two kinds of composites caused similar changes to both microbial communities. There was a slight decrease in indigenous microbial alpha diversity with the MBB aerobic application, while the total population number of bacteria was increased by 700%. Both the redundancy analysis and Mantel analyses indicated that pH and microbial biomass C contributed to the colonization of Bacillus sp. K1 with SBB under aerobic conditions, and with MBB under anerobic conditions, respectively. The research provides a new insight into interactive effects and investigates immobilization mechanisms involved of bacterial/biochar composites in anaerobic and aerobic soils.

The purpose of the current study was to assess the effects of substituting corn with ground brown rice on growth performance, immune status, and gut microbiota in weanling pigs. Seventy-two weanling pigs (28 d old with 6.78 ± 0.94 kg body weight [BW]) were randomly allotted to two dietary treatments with six pens and six pigs (three barrows and gilts) per pen within a randomized complete block design. The control pigs were fed a typical diet for weanling pigs based on corn and soybean meal diet (control diet: CON), and the other pigs were fed a formulated diet with 100% replacement of corn with ground brown rice for 35d (treatment diet: GBR). Growth performance, immune status, and gut microbiota of weanling pigs were measured. The substitution of corn with GBR did not affect growth performance or diarrhea frequency. Additionally, there were no differences in white blood cell number, hematocrit, cortisol, C-reactive protein, and serum tumor necrosis factor-alpha levels between pigs fed CON or GBR for the first 2 wk after weaning. However, weanling pigs fed GBR had lower (P < 0.05) serum transforming growth factor-beta 1 level than those fed CON. Furthermore, weanling pigs fed GBR had increased (P < 0.05) relative abundance of phylum Firmicutes and genus Lactobacillus and Streptococcus and decreased (P < 0.05) relative abundance of phylum Bacteroidetes and genus Clostridium and Prevotella in the gut microbiota compared with those fed CON. In conclusion, there was no significant difference in growth performance when corn was replaced with ground brown rice in diets for weanling pigs. Furthermore, the substitution of corn with ground brown rice in weaning diet modulated immune status and gut microbiota of pigs by increasing beneficial microbial communities and reducing harmful microbial communities. Overall, ground brown rice-based diet is a potential alternative to corn-based diet without negative effects on growth performance, immune status, and gut microbiot

In angiosperms, endosperm development comprises a series of developmental transitions controlled by genetic and epigenetic mechanisms that are initiated after double fertilization. Polycomb repressive complex 2 (PRC2) is a key component of these mechanisms that mediate histone H3 lysine 27 trimethylation (H3K27me3); the action of PRC2 is well described in Arabidopsis thaliana but remains uncertain in cereals. In this study, we demonstrate that mutation of the rice (Oryza sativa) gene EMBRYONIC FLOWER2a (OsEMF2a), encoding a zinc-finger containing component of PRC2, causes an autonomous endosperm phenotype involving proliferation of the central cell nuclei with separate cytoplasmic domains, even in the absence of fertilization. Detailed cytological and transcriptomic analyses revealed that the autonomous endosperm can produce storage compounds, starch granules, and protein bodies specific to the endosperm. These events have not been reported in Arabidopsis. After fertilization, we observed an abnormally delayed developmental transition in the endosperm. Transcriptome and H3K27me3 ChIP-seq analyses using endosperm from the emf2a mutant identified downstream targets of PRC2. These included >100 transcription factor genes such as type-I MADS-box genes, which are likely required for endosperm development. Our results demonstrate that OsEMF2a-containing PRC2 controls endosperm developmental programs before and after fertilization.

Revealing belowground-aboveground relationships (BAR) is essential to drive ecological processes to address agriculture dysfunctions, especially in the management of aboveground plant diseases. Earthworms are one of the most important soil organisms involved in BAR, and silicon (Si) has been identified as a crucial element regulating aboveground plant health. How earthworm-Si interactions induce BAR in poor- and rich-nutrient soil contexts is still poorly understood, despite a growing interest in agricultural sustainability. We investigated the potential of BAR induced by the earthworm-silicon interaction to control the severity of rice blast disease in a Ferralsol in Madagascar, with or without NPK fertilization. We conducted a greenhouse microcosm experiment in which we manipulated the presence of the endogeic earthworm Pontoscolex corethrurus and the fungus Pyricularia oryzae in a Ferralsol supplied or not with Si and fertilized with macronutrients (nitrogen, phosphorus and potassium, i.e., NPK). After eight weeks of growth, plant biomass, nutrition and disease severity were measured. Our results validated the hypothesis that a dual treatment of earthworm inoculation and Si fertilization in a nutrient-poor tropical soil confers a higher tolerance of rainfed rice to P. oryzae, in comparison with treatments with only earthworms or Si, providing the optimal agronomic balance between a gain in biomass (and nutrition) and a reduction in disease severity. The supply of macronutrients altered this positive BAR by favouring the phenomenon of N-induced susceptibility. The aboveground plant C:N ratio of 15 is a threshold below which any increase in N per C unit likely enhances blast disease. The role of belowground interactions to counteract agricultural dysfunctions is supported by our study. To accomplish ecological intensification and provision of ecosystem services such as disease regulation, our findings recommend replacing excessive use of macronutrient fertilizer wi

For many smallholder farmers in East and Southeast Asia, farming represents a decreasing share of their income-generating activities, leading to increasing limits to investing family labour in farming. This process has been particularly marked in regions where farmers face limited access to land, water and markets. This study asks whether irrigated farms in central Thailand are on a similar pathway. It analyses how these farms have evolved to face existing constraints and their future prospects. The farms have adapted to constraints including lack of fresh water in the dry season, floods, and sometimes insufficient labour. In almost all farming families, farming is still the main income-generating activity for at least one household member. Most of the farmers involved in fish and shrimp farming had already identified a successor in their family or considered it was possible. This was also the case of rice farmers who had made quite high investments in their farms, most of whom cultivated relatively large areas. However, another group of rice farmers had become trapped in a vicious circle of low farm profitability, the increasing age of the farmers and the fact their farms held little attraction for younger generations. Thai agricultural policies did not provide sufficient means to break this cycle. The future of these vulnerable rice farms thus appears to be uncertain. Breaking this cycle may require a comprehensive approach that explicitly addresses the issue of farm structure.

Knowledge of the genetic architecture of importantly agronomical traits can speed up genetic improvement in cultivated rice (Oryza sativa L.). Many recent investigations have leveraged genome-wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs), associated with agronomic traits in various rice populations. The reported trait-relevant SNPs appear to be arbitrarily distributed along the genome, including genic and nongenic regions. Whether the SNPs in different genomic regions play different roles in trait heritability and which region is more responsible for phenotypic variation remains opaque. We analyzed a natural rice population of 524 accessions with 3,616,597 SNPs to compare the genetic contributions of functionally distinct genomic regions for five agronomic traits, i.e., yield, heading date, plant height, grain length, and grain width. An analysis of heritability in the functionally partitioned rice genome showed that regulatory or intergenic regions account for the most trait heritability. A close look at the trait-associated SNPs (TASs) indicated that the majority of the TASs are located in nongenic regions, and the genetic effects of the TASs in nongenic regions are generally greater than those in genic regions. We further compared the predictabilities using the genetic variants from genic regions with those using nongenic regions. The results revealed that nongenic regions play a more important role than genic regions in trait heritability in rice, which is consistent with findings in humans and maize. This conclusion not only offers clues for basic research to disclose genetics behind these agronomic traits, but also provides a new perspective to facilitate genomic selection in rice.

Gametes constitute a critical stage of the plant life cycle during which the genome undergoes reprogramming in preparation for embryogenesis. Here, we examined genome-wide distributions of small RNAs in the sperm and egg cells of rice. We found that 24-nt siRNAs, which are a hallmark of RNA-directed DNA methylation (RdDM) in plants, were depleted from heterochromatin boundaries in both gametes relative to vegetative tissues, reminiscent of siRNA patterns in DDM1-type nucleosome remodeler mutants. In sperm cells, 24-nt siRNAs were spread across heterochromatic regions, while in egg cells, 24-nt siRNAs were concentrated at a smaller number of heterochromatic loci throughout the genome, especially at loci which also produced siRNAs in other tissues. In both gametes, patterns of CHH methylation, typically a strong indicator of RdDM, were similar to vegetative tissues, although lower in magnitude. These findings indicate that the small RNA transcriptome undergoes large-scale redistribution in both male and female gametes, which is not correlated with recruitment of DNA methyltransferases in gametes and suggestive of unexplored regulatory activities of gamete small RNAs.

Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.

Biopharmaceutical protein production using transgenic plant cell bioreactor processes offers advantages over microbial and mammalian cell culture platforms in its ability to produce complex biologics with simple chemically defined media and reduced biosafety concerns. A disadvantage of plant cells from a traditional batch bioprocessing perspective is their slow growth rate which has motivated us to develop semicontinuous and/or perfusion processes. Although the economic benefits of plant cell culture bioprocesses are often mentioned in the literature, to our knowledge no rigorous technoeconomic models or analyses have been published. Here we present technoeconomic models in SuperPro Designer® for the large-scale production of recombinant butyrylcholinesterase (BChE), a prophylactic/therapeutic bioscavenger against organophosphate nerve agent poisoning, in inducible transgenic rice cell suspension cultures. The base facility designed to produce 25 kg BChE per year utilizing two-stage semicontinuous bioreactor operation manufactures a single 400 mg dose of BChE for $263. Semicontinuous operation scenarios result in 4-11% reduction over traditional two-stage batch operation scenarios. In addition to providing a simulation tool that will be useful to the plant-made pharmaceutical community, the model also provides a computational framework that can be used for other semicontinuous or batch bioreactor-based processes.