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In the present study, 15 accessions of wild rice species belonging to genome groups different from that of Oryza sativa were tested for their adaptive response to flooding at the seedling and mature stages. Under complete submergence at the seedling stage, reduced underwater shoot elongation and high survival rate after the recovery period were observed in the accessions of O. minuta as well as tetraploid O. punctata, O. eichingeri, O. officinalis, O. alta, O. grandiglumis, O. latifolia, and O. australiensis. This suggests that these species exhibit submergence tolerance at the seedling stage. During gradual submergence at mature stage, promoted internodal elongation was observed in the accessions of diploid and tetraploid O. punctata, O. alta, O. grandiglumis, O. latifolia, and O. brachyantha. This suggests that these species possess floating ability. Remarkably, two CCDD genome species, namely O. grandiglumis and O. latifolia, strongly displayed both submergence tolerance at the seedling stage and floating ability at mature stage, suggesting that these species are valuable genetic resources for improving rice adaptability to flooding. SUB1A and SNORKEL genes are known to confer submergence tolerance and floating ability to O. sativa, respectively. However, SUB1A, SNORKEL1, and SNORKEL2 genes were not detected in any of the wild rice accessions investigated in the present study. Our results suggest that adaptive responses to flooding in the investigated wild rice species can be achieved independently of the presence or absence of SUB1A and SNORKEL genes.

Abstract Background Events of gene fusion have been reported in several organisms. However, the general role of gene fusion as part of new gene origination remains unknown. Results We conduct genome-wide interrogations of four Oryza genomes by designing and implementing novel pipelines to detect fusion genes. Based on the phylogeny of ten plant species, we detect 310 fusion genes across four Oryza species. The estimated rate of origination of fusion genes in the Oryza genus is as high as 63 fusion genes per species per million years, which is fixed at 16 fusion genes per species per million years and much higher than that in flies. By RNA sequencing analysis, we find more than 44% of the fusion genes are expressed and 90% of gene pairs show strong signals of purifying selection. Further analysis of CRISPR/Cas9 knockout lines indicates that newly formed fusion genes regulate phenotype traits including seed germination, shoot length and root length, suggesting the functional significance of these genes. Conclusions We detect new fusion genes that may drive phenotype evolution in Oryza. This study provides novel insights into the genome evolution of Oryza.

Rice nucleolin (OsNUC1), consisting of two isoforms, OsNUC1-L and OsNUC1-S, is a multifunctional protein involved in salt-stress tolerance. Here, OsNUC1-S's function was investigated using transgenic rice lines overexpressing OsNUC1-S. Under non-stress conditions, the transgenic lines showed a lower yield, but higher net photosynthesis rates, stomatal conductance, and transpiration rates than wild type only in the second leaves, while in the flag leaves, these parameters were similar among the lines. However, under salt-stress conditions at the booting stage, the higher yields in transgenic lines were detected. Moreover, the gas exchange parameters of the transgenic lines were higher in both flag and second leaves, suggesting a role for OsNUC1-S overexpression in photosynthesis adaptation under salt-stress conditions. Moreover, the overexpression lines could maintain light-saturation points under salt-stress conditions, while a decrease in the light-saturation point owing to salt stress was found in wild type. Based on a transcriptome comparison between wild type and a transgenic line, after 3 and 9 days of salt stress, the significantly differentially expressed genes were enriched in the metabolic process of nucleic acid and macromolecule, photosynthesis, water transport, and cellular homeostasis processes, leading to the better performance of photosynthetic processes under salt-stress conditions at the booting stage.

BackgroundCalmodulin (CaM) is an important calcium sensor protein that transduces Ca2+ signals in plant stress signaling pathways. A previous study has revealed that transgenic rice over-expressing the calmodulin gene OsCam1-1 (LOC_Os03g20370) is more tolerant to salt stress than wild type. To elucidate the role of OsCam1-1 in the salt stress response mechanism, downstream components of the OsCam1-1-mediated response were identified and investigated by transcriptome profiling and target identification.ResultsTranscriptome profiling of transgenic 'Khao Dawk Mali 105' rice over-expressing OsCam1-1 and wild type rice showed that overexpression of OsCam1-1 widely affected the expression of genes involved in several cellular processes under salt stress, including signaling, hormone-mediated regulation, transcription, lipid metabolism, carbohydrate metabolism, secondary metabolism, photosynthesis, glycolysis, tricarboxylic acid (TCA) cycle and glyoxylate cycle. Under salt stress, the photosynthesis rate in the transgenic rice was slightly lower than in wild type, while sucrose and starch contents were higher, suggesting that energy and carbon metabolism were affected by OsCam1-1 overexpression. Additionally, four known and six novel CaM-interacting proteins were identified by cDNA expression library screening with the recombinant OsCaM1. GO terms enriched in their associated proteins that matched those of the differentially expressed genes affected by OsCam1-1 overexpression revealed various downstream cellular processes that could potentially be regulated by OsCaM1 through their actions.ConclusionsThe diverse cellular processes affected by OsCam1-1 overexpression and possessed by the identified CaM1-interacting proteins corroborate the notion that CaM signal transduction pathways compose a complex network of downstream components involved in several cellular processes. These findings suggest that under salt stress, CaM activity elevates metabolic enzymes involved in central energy pathways, which promote or at least maintain the production of energy under the limitation of photosynthesis.

BackgroundPaddy soil dissolved organic matter (DOM) represents a major hotspot for soil biogeochemistry, yet we know little about its chemodiversity let alone the microbial community that shapes it. Here, we leveraged ultrahigh-resolution mass spectrometry, amplicon, and metagenomic sequencing to characterize the molecular distribution of DOM and the taxonomic and functional microbial diversity in paddy soils across China. We hypothesized that variances in microbial community significantly associate with changes in soil DOM molecular composition.ResultsWe report that both microbial and DOM profiles revealed geographic patterns that were associated with variation in mean monthly precipitation, mean annual temperature, and pH. DOM molecular diversity was significantly correlated with microbial taxonomic diversity. An increase in DOM molecules categorized as peptides, carbohydrates, and unsaturated aliphatics, and a decrease in those belonging to polyphenolics and polycyclic aromatics, significantly correlated with proportional changes in some of the microbial taxa, such as Syntrophobacterales, Thermoleophilia, Geobacter, Spirochaeta, Gaiella, and Defluviicoccus. DOM composition was also associated with the relative abundances of the microbial metabolic pathways, such as anaerobic carbon fixation, glycolysis, lignolysis, fermentation, and methanogenesis.ConclusionsOur study demonstrates the continental-scale distribution of DOM is significantly correlated with the taxonomic profile and metabolic potential of the rice paddy microbiome. Abiotic factors that have a distinct effect on community structure can also influence the chemodiversity of DOM and vice versa. Deciphering these associations and the underlying mechanisms can precipitate understanding of the complex ecology of paddy soils, as well as help assess the effects of human activities on biogeochemistry and greenhouse gas emissions in paddy soils.

BackgroundSwitchgrass (Panicum virgatum L.) is a promising bioenergy feedstock because it can be grown on marginal land and produces abundant biomass. Recalcitrance of the lignocellulosic components of the switchgrass cell wall to enzymatic degradation into simple sugars impedes efficient biofuel production. We previously demonstrated that overexpression of OsAT10, a BAHD acyltransferase gene, enhances saccharification efficiency in rice.ResultsHere we show that overexpression of the rice OsAT10 gene in switchgrass decreased the levels of cell wall-bound ferulic acid (FA) in green leaf tissues and to a lesser extent in senesced tissues, and significantly increased levels of cell wall-bound p-coumaric acid (p-CA) in green leaves but decreased its level in senesced tissues of the T0 plants under greenhouse conditions. The engineered switchgrass lines exhibit an approximate 40% increase in saccharification efficiency in green tissues and a 30% increase in senesced tissues.ConclusionOur study demonstrates that overexpression of OsAT10, a rice BAHD acyltransferase gene, enhances saccharification of lignocellulosic biomass in switchgrass.

Aproveitando-se a ocorrência de um evento espontâneo de baixas temperaturas (

The flavin monooxygenase (FMO) enzyme was discovered in mammalian liver cells that convert a carcinogenic compound, N-N′-dimethylaniline, into a non-carcinogenic compound, N-oxide. Since then, many FMOs have been reported in animal systems for their primary role in the detoxification of xenobiotic compounds. In plants, this family has diverged to perform varied functions like pathogen defense, auxin biosynthesis, and S-oxygenation of compounds. Only a few members of this family, primarily those involved in auxin biosynthesis, have been functionally characterized in plant species. Thus, the present study aims to identify all the members of the FMO family in 10 different wild and cultivated Oryza species. Genome-wide analysis of the FMO family in different Oryza species reveals that each species has multiple FMO members in its genome and that this family is conserved throughout evolution. Taking clues from its role in pathogen defense and its possible function in ROS scavenging, we have also assessed the involvement of this family in abiotic stresses. A detailed in silico expression analysis of the FMO family in Oryza sativa subsp. japonica revealed that only a subset of genes responds to different abiotic stresses. This is supported by the experimental validation of a few selected genes using qRT-PCR in stress-sensitive Oryza sativa subsp. indica and stress-sensitive wild rice Oryza nivara. The identification and comprehensive in silico analysis of FMO genes from different Oryza species carried out in this study will serve as the foundation for further structural and functional studies of FMO genes in rice as well as other crop types. [ABSTRACT FROM AUTHOR]

Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group. The miRNA-miRNA* duplex region is completely conserved across eleven Oryza species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the 'A10234287911' allele may promote better processing vis-à-vis the structure conferred by 'G10234287911' allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression. [ABSTRACT FROM AUTHOR]

Background: The cytoplasmic male sterility (CMS) of rice is caused by chimeric mitochondrial DNA (mtDNA) that is maternally inherited in the majority of multicellular organisms. Wild rice (Oryza rufipogon Griff.) has been regarded as the ancestral progenitor of Asian cultivated rice (Oryza sativa L.). To investigate the distribution of original CMS source, and explore the origin of gametophytic CMS gene, a total of 427 individuals with seventeen representative populations of O. rufipogon were collected in from Dongxiang of Jiangxi Province to Sanya of Hainan Province, China, for the PCR amplification of atp6, orfH79 and B-atp6-orfH79, respectively. Results: The B-atp6-orfH79 and its variants (B-atp6-GSV) were detected in five among seventeen populations (i.e. HK, GZ, PS, TL and YJ) through PCR amplification, which could be divided into three haplotypes, i.e., BH1, BH2, and BH3. The BH2 haplotype was identical to B-atp6-orfH79, while the BH1 and BH3 were the novel haplotypes of B-atp6-GSV. Combined with the high-homology sequences in GenBank, a total of eighteen haplotypes have been revealed, only with ten haplotypes in orfH79 and its variants (GSV) that belong to three species (i.e. O. rufipogon, Oryza nivara and Oryza sativa). Enough haplotypes clearly demonstrated the uniform structural characteristics of the B-atp6-orfH79 as follows: except for the conserved sequence (671 bp) composed of B-atp6 (619 bp) and the downstream followed the B-atp6 (52 bp, DS), and GSV sequence, a rich variable sequence (VS, 176 bp) lies between the DS and GSV with five insertion or deletion and more than 30 single nucleotide polymorphism. Maximum likelihood analysis showed that eighteen haplotypes formed three clades with high support rate. The hierarchical analysis of molecular variance (AMOVA) indicated the occurrence of variation among all populations (FST = 1; P < 0.001), which implied that the chimeric structure occurred independently. Three haplotypes (i.e., H1, H2 and H3) were detected by the primer of orfH79, which were identical to the GVS in B-atp6-GVS structure, respectively. All seventeen haplotypes of the orfH79, belonged to six species based on our results and the existing references. Seven existed single nucleotide polymorphism in GSV section can be translated into eleven various amino acid sequences. Conclusions: Generally, this study, indicating that orfH79 was always accompanied by the B-atp6, not only provide two original CMS sources for rice breeding, but also confirm the uniform structure of B-atp-orfH79, which contribute to revealing the origin of rice gametophytic CMS genes, and the reason about frequent recombination of mitochondrial DNA. [ABSTRACT FROM AUTHOR]

Weedy rice (Oryza spp.) is a notorious weed in direct‐seeding paddy fields. Because it has anatomical and physiological traits similar to those of cultivated rice, no selective herbicide is effective in controlling weedy rice growing among conventional rice cultivars. Imidazolinone (IMI)‐resistant rice lines JD372 and JJ818 have been planted with imazamox to control weedy rice in Jiangsu and Shanghai, China. Whole‐plant dose–response analysis showed that imazamox exhibited high efficacy against three populations of weedy rice. The ED90 of weedy rice populations FN‐5, GY‐8, and HY‐3 were 46.87, 61.43, and 52.17 g a.i. ha−1, respectively, close to the recommended field dose (50 g a.i. ha−1) of imazamox. Conversely, the ED10 values of JD372 and JJ818 were slightly lower than 50 g a.i. ha−1. These findings indicate that imazamox can control weedy rice production in JD372 and JJ818 fields. The acetolactate synthase (ALS) sensitivity of JD372 in vitro was 1714.89‐fold lower to imazamox than was that of FN‐5. ALS gene sequencing revealed a Ser653Asn point mutation—a common mutation that confers resistance to IMI herbicides in JD372. In addition, higher ALS expression levels in JD372 were found at 24 and 72 h after imazamox treatment. ALS overexpression might partially compensate for the ALS activity of JD372 that was suppressed by imazamox. [ABSTRACT FROM AUTHOR]

The domestication syndrome is defined as a collection of domestication-related traits that have undergone permanent genetic changes during the domestication of cereals. Australian wild rice populations have not been exposed to gene flow from domesticated rice populations. A high level of natural variation of the sequences at domestication loci (e.g., seed shattering, awn development, and grain size) was found in Australian AA genome wild rice from the primary gene pool of rice. This natural variation is much higher than that found in Asian cultivated rice and wild Asian rice populations. The Australian Oryza meridionalis populations exhibit a high level of homozygous polymorphisms relative to domesticated rice, inferring the fixation of distinct wild and domesticated alleles. Alleles of the seed shattering genes (SH4/SHA1 and OsSh1/SH1) present in the shattering-prone O. meridionalis populations are likely to be functional, while the dysfunctional alleles of these seed shattering genes are found in domesticated rice. This confirms that unlike Asian wild rice populations, Australian wild rice populations have remained genetically isolated from domesticated rice, retaining pre-domestication alleles in their wild populations that uniquely allow the impact of domestication on the rice genome to be characterized. This study also provides key information about the domestication loci in Australian wild rice populations that will be valuable in the utilization of these genetic resources in crop improvement and de novo domestication. [ABSTRACT FROM AUTHOR]

Partial submergence of Oryza sativa deepwater rice elicits enhancement of internodal elongation, referred to as deepwater response, conferred by three types of genes, SNORKEL1/2 (SK1/2), SEMIDWARF1 (SD1), and ACCELERATOR OF INTERNODE ELONGATION 1 (ACE1). We investigated the presence and expression of these genes in the African cultivated rice Oryza glaberrima and the relationship between these genes and the deepwater response of O. glaberrima. In 49 of the 50 accessions tested, one or two SK genes were identified, which could be divided into three types of SK1 and four types of SK2. The accessions with the SK2 type whose expression was induced by submergence demonstrated rapid internodal elongation under submergence. In most of these accessions, submergence also increased the expression of SD1 and ACE1 genes. However, the accessions did not possess the haplotype of SD1 that is associated with high deepwater response in O. sativa. In contrast, they possessed the type of ACE1 gene similar to that in O. sativa deepwater rice. These results indicate that the molecular mechanisms underlying induction of deepwater response in O. glaberrima are similar to that found in deepwater rice of O. sativa and suggest that most O. glaberrima cultivars, including upland cultivars, can exhibit rapid internodal elongation under submergence. [ABSTRACT FROM AUTHOR]

Water-limiting conditions can severely affect rice yield. Therefore, increasing plant tolerance to water stress is a priority for many rice breeding programs. However, improving rice tolerance to this abiotic stress comes with several complications related to the seeding practices, the adopted water management system and the growth stage where water stress occurs. For this reason, it is challenging to outline single ideotypes showing traits suitable for overcoming drought at different times during the life cycle of rice in diverse cropping ecosystems. The current knowledge of genomics and biochemicals can contribute to drawing rice ideotypes flexible towards diverse water availability conditions. Traits identified in accessions of the wild ancestor of cultivated rice, as well as other wild rice species, in Oryza glaberrima and weedy rice were demonstrated to confer enhanced tolerance to water stress, while screenings of cultivated rice germplasms identified several genes/loci improving water stress resistance. New frontiers are represented by the dissection of the epigenetic control of stress tolerance and the implementation of the contribution of favorable microbiota. Innovative breeding technologies, whose feasibility is related to advancements in genomic analyses, are contributing to enhancing the knowledge-based development of water stress-tolerant rice varieties. [ABSTRACT FROM AUTHOR]

Plant breeding efforts to boost rice productivity have focused on developing a haploid development pipeline. CENH3 gene has emerged as a leading player that can be manipulated to engineer haploid induction system. Currently, allele mining for the OsCENH3 gene was done by PCR-based resequencing of 33 wild species accessions of genus Oryza and in silico mining of alleles from pre-existing data. We have identified and characterized CENH3 variants in genus Oryza. Our results indicated that the majority CENH3 alleles present in the Oryza gene pool carry synonymous substitutions. A few non-synonymous substitutions occur in the N-terminal Tail domain (NTT). SNP A/G at position 69 was found in accessions of AA genome and non-AA genome species. Phylogenetic analysis revealed that non-synonymous substitutions carrying alleles follow pre-determined evolutionary patterns. O. longistaminata accessions carry SNPs in four codons along with indels in introns 3 and 6. Fifteen haplotypes were mined from our panel; representative mutant alleles exhibited structural variations upon modeling. Structural analysis indicated that more than one structural variant may be exhibited by different accessions of single species (Oryza barthii). NTT allelic mutants, though not directly implicated in HI, may show variable interactions. HI and interactive behavior could be ascertained in future investigations. [ABSTRACT FROM AUTHOR]

Cultivated rice is a staple food for more than half of the world's population, providing approximately 20% of the world's food energy needs. A broad spectrum of pathogenic microorganisms causes rice diseases leading to huge yield losses worldwide. Wild and cultivated rice species are known to possess a wide variety of antimicrobial secondary metabolites, known as phytoalexins, which are part of their active defense mechanisms. These compounds are biosynthesized transiently by rice in response to pathogens and certain abiotic stresses. Rice phytoalexins have been intensively studied for over half a century, both for their biological role and their potential application in agronomic and pharmaceutical fields. In recent decades, the growing interest of the research community, combined with advances in chemical, biological, and biomolecular investigation methods, has led to a notable acceleration in the growth of knowledge on rice phytoalexins. This review provides an overview of the knowledge gained in recent decades on the diversity, distribution, biosynthesis, chemical synthesis, and bioactivity of rice phytoalexins, with particular attention to the most recent advances in this research field. [ABSTRACT FROM AUTHOR]

The world's population may reach 10 billion by 2050, but 10% still suffer from food shortages. At the same time, global warming threatens food security by decreasing crop yields, so it is necessary to develop crops with enhanced resistance to high temperatures in order to secure the food supply. In this review, the role of Rubisco activase as an important factor in plant heat tolerance is summarized, based on the conclusions of recent findings. Rubisco activase is a molecular chaperone determining the activation of Rubisco, whose heat sensitivity causes reductions of photosynthesis at high temperatures. Thus, the thermostability of Rubisco activase is considered to be critical for improving plant heat tolerance. It has been shown that the introduction of thermostable Rubisco activase through gene editing into Arabidopsis thaliana and from heat-adapted wild Oryza species or C4 Zea mays into Oryza sativa improves Rubisco activation, photosynthesis, and plant growth at high temperatures. We propose that developing a universal thermostable Rubisco activase could be a promising direction for further studies. [ABSTRACT FROM AUTHOR]

Crop breeding programs can improve traits associated with desirable phenotypic characteristics to different local environmental conditions. In rice, such improvements were achieved depending on genetic diversity among local populations. Here, we examined whether differences in traits of elite varieties are due to genetic differences and from what the genetic differences are derived. Previously, we identified one quantitative trait locus (QTLs) associated with heading date, i.e., the quantitative trait locus for days to heading on chromosome 3 (qDTH3). Using 592 plants of the F2 generation, fine mapping narrowed the qDTH3 locus down to a 158-kb region of the corresponding rice reference genome. Based on the genome sequences of a 656-kb region including the qDTH3 locus among four Oryza species collections, we propose the historic evolutionary process of cultivated rice, considering nucleotide polymorphisms and intrapopulation recombination. Phenotypic differences in qDTH3 in elite varieties may be derived from a different lineage split from the ancestor. [ABSTRACT FROM AUTHOR]

SOil-surface Roots (SORs) are roots that elongate over or near the soil surface. They allow plants to escape waterlogging-caused hypoxia and high salinity that are often present in deeper soil. Quantitative evaluation is essential for understanding SOR function and identifying the genes and quantitative trait loci (QTLs) that control it. However, existing methods to evaluate SOR formation are laborious/slow or semiquantitative. Here, we describe a high-throughput quantitative SOR evaluation system that uses an overhead scanner. We evaluated SORs in 56 wild rice (Oryza glumaepatula) introgression lines (ILs) with the genetic background of O. sativa. The method can quantify the SOR area of a plant in less than 90 sec. During the image analysis process, multithreshold segmentation on the scanned images reduced the reflection noise of the digital image and improved the accuracy of the estimation of SORs formation. The root surface areas of SORs of the O. glumaepatula ILs varied widely, which should make them well-suited for identifying SOR-related QTLs. The overhead scanner method has the potential to quantitatively and rapidly evaluate SORs developed on the soil surface. [ABSTRACT FROM AUTHOR]

Wild rice (Oryza barthii) is increasingly used in Sudan as a food crop. Wild rice is a whole grain, rich in minerals, vitamins, protein, starch, dietary fiber and various phytochemicals; and yet low in fat, with a beneficial fatty acids profile. The objective of this study was to evaluate the socioeconomic significance of wild rice as a famine food crop in Darfur state of Sudan. A study was conducted in five districts (Tullus, Gadad, Demso, Katila, and Umshtoor) in South Darfur in Sudan. Primary data were obtained through a face-to-face semi-questionnaire interview on 146 households; supplemented with interviews of key informants and group discussions. All respondents (100%) not only attested to knowing wild rice and its growth habits, but also consumption (93.8%) of the crop. Wild rice reportedly grows naturally and widely in valleys, although it was dismally exploited by the local population. It is harvested manually and traditionally; and sold mostly in the local markets, without post-harvest value additions. The crop is consumed in various meals, but mainly in the form of porridge. Some respondents (13%) used the crop in times of famine. Wild rice is stored in traditional containers (95.9%) for periods ranging from 8 to 12 years without visible storage problems. [ABSTRACT FROM AUTHOR]

Bcl-2-associated anthogenes (BAGs), chaperone regulators are known to regulate programmed cell death in plants. In the present study, we have identified eight BAG genes in the rice (Oryza sativa) genome. Subsequently, to understand the evolution, 78 BAG homologs were identified in other nine Oryza species. In addition to the signature ubiquitin-like domain, an additional conserved sequence of 12 amino acids was found in all the class I BAG genes except few exceptions in wild species. A significantly variable number of BAG genes was identified in different Oryza species indicates the expansion of BAG genes due to segmental duplication. Based on whole genome resequencing information available for 4726 rice genotypes, haplotype diversity and the functional effect of variations in BAG genes were predicted. Transcriptomic analyses further suggested the multifunctional roles of BAG genes during both developmental and defense response in Oryza species. Differential expression of BAG genes particularly BAG3 and BAG5 was observed under heavy metal stress. Similarly, higher expression of OsBAG1 and OsBAG2 were found in resistant rice cultivar in response to Magnaporthe oryzae infection and OsBAG2 showed upregulation in response to Xanthomonas oryzae infection as well. A similar expression of BAG genes was observed in the qRT-PCR analysis. Furthermore, heterologous transient expression of OInBAG6 protein tagged with yellow fluorescent protein in tobacco leaves showed the subcellular localization in both nucleus and plasma membrane. This study will help to understand the evolution of BAG genes and their role in cell death under stress conditions in rice. [ABSTRACT FROM AUTHOR]

Stomata control carbon and water exchange between the leaves and the ambient. However, the plasticity responses of stomatal traits to growth conditions are still unclear, especially for monocot leaves. The current study investigated the leaf anatomical traits, stomatal morphological traits on both adaxial and abaxial leaf surfaces, and photosynthetic traits of Oryza leaves developed in two different growth conditions. Substantial variation exists across the Oryza species in leaf anatomy, stomatal traits, photosynthetic rate, and stomatal conductance. The abaxial stomatal density was higher than the adaxial stomatal density in all the species, and the stomatal ratios ranged from 0.35 to 0.46 across species in two growth environments. However, no difference in the stomatal ratio was observed between plants in the growth chamber and outdoors for a given species. Photosynthetic capacity, stomatal conductance, leaf width, major vein thickness, minor vein thickness, inter-vein distance, and stomatal pore width values for leaves grown outdoors were higher than those for plants grown in the growth chamber. Our results indicate that a broad set of leaf anatomical, stomatal, and photosynthetic traits of Oryza tend to shift together during plasticity to diverse growing conditions, but the previously projected sensitive trait, stomatal ratio, does not shape growth conditions. [ABSTRACT FROM AUTHOR]

Summary: Salinity is one of the major environmental stresses limiting growth and yield of rice. The objective of the present study was to analyze the impact of NaCl on yield-related parameters of Oryza glaberrima. Two contrasted cultivars of Oryza glaberrima previously tested for salt resistance at the vegetative stage [salt-resistant (TOG5307) and salt-sensitive (TOG5949)] were irrigated with a saline solution containing 30 mM NaCl (EC: 3 dS.m−1 NaCl). After 6 months of treatments, mineral nutrient and yield-related parameters were assessed. Proline was quantified in the panicle leaf at the start of the grain filling stage. NaCl treatment affected most yield-related parameters: panicle length, panicle leaf dry weight, number of branches per panicle, panicle leaf length, days to 50% heading, straw fresh weight per plant, grain yield per plant, number of spikelets per panicle, and number of filled grains per panicle. The weight of 1,000 grains decreased in the salt-sensitive cultivar only, suggesting that grain filling processes were compromised. The salt-resistant cultivar TOG5307 was less affected than the salt-sensitive TOG5949 and accumulated lower amounts of Na+ in the grains. For both cultivars, hulls contained higher concentration of Na+ and K+ than grains. TOG5307 also contained more proline in the panicle leaf than TOG5949, suggesting that TOG5307 can cope with the osmotic component of salt stress. The cultivar exhibiting the highest salt resistance at the vegetative stage also exhibited the highest resistance at the reproductive one. [ABSTRACT FROM AUTHOR]

Seeds are continuously exposed to a wide variety of microorganisms in the soil. In addition, seeds contain large amounts of carbon and nitrogen sources that support initial growth after germination. Thus, seeds in the soil can easily promote microbial growth, and seeds are susceptible to decay. Therefore, seed defense against microorganisms is important for plant survival. Seed-microbe interactions are also important issues from the perspective of food production, in seed quality and shelf life. However, seed-microbe interactions remain largely unexplored. In this study, we established a simple and rapid assay system for the antibacterial activity of rice seed crude extracts by colorimetric quantification methods by the reduction of tetrazolium compound. Using this experimental system, the diversity of effects of rice seed extracts on microbial growth was analyzed using Escherichia coli as a bacterial model. We used collections of cultivated rice, comprising 50 accessions of Japanese landraces, 52 accessions of world rice core collections, and of 30 wild Oryza accessions. Furthermore, we attempted to find genetic factors responsible for the diversity by genome-wide association analysis. Our results demonstrate that this experimental system can easily analyze the effects of seed extracts on bacterial growth. It also suggests that there are various compounds in rice seeds that affect microbial growth. Overall, this experimental system can be used to clarify the chemical entities and genetic control of seed-microbe interactions and will open the door for understanding the diverse seed-microbe interactions through metabolites. [ABSTRACT FROM AUTHOR]

Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient's genetic background. CSSLs are an ideal genetic population for mapping quantitative traits loci (QTLs). In this study, 59 CSSLs from the common wild rice (Oryza rufipogon Griff.) accession DP15 under the indica rice cultivar (O. sativa L. ssp. indica) variety 93-11 background were constructed through multiple backcrosses and marker-assisted selection (MAS). Through high-throughput whole genome re-sequencing (WGRS) of parental lines, 12,565 mapped InDels were identified and designed for polymorphic molecular markers. The 59 CSSLs library covered 91.72% of the genome of common wild rice accession DP15. The DP15-CSSLs displayed variation in six economic traits including grain length (GL), grain width (GW), thousand-grain weight (TGW), grain length-width ratio (GLWR), plant height (PH), and leaf margin color (LMC), which were finally attributed to 22 QTLs. A homozygous CSSL line and a purple leave margin CSSL line were selected to construct two secondary genetic populations for the QTLs mapping. Thus, the PH-controlling QTL qPH1.1 was mapped to a region of 4.31-Mb on chromosome 1, and the LMC-controlling QTL qLMC6.1 was mapped to a region of 370-kb on chromosome 6. Taken together, these identified novel QTLs/genes from common wild rice can potentially promote theoretical knowledge and genetic applications to rice breeders worldwide. [ABSTRACT FROM AUTHOR]

Dongxiang wild rice (DXWR) is one of the most valuable germplasm resources of rice. It is important to conserve the genetic diversity and uncover the population differentiation of DXWR. In this study, we analyzed the genetic diversity and population differentiation of DXWR based on whole-genome resequencing of 220 DXWR lines collected from nine natural populations in an ex situ conservation nursery. Almost half of the SNPs and Indels detected in these DXWR lines were absent in cultivated rice or other common wild rice, indicating the potential and importance of DXWR in rice breeding. Based on Structure and PCA analysis, these DXWR lines could be divided into two subpopulations, in which subpopulation G1 had more specific SNPs and Indels and was genetically more genetically diverse than subpopulation G2. The average Fst of regions with low relative genetic diversity between G1 and G2 were significantly lower than whole-genomic Fst, indicating directional selection in these regions. Some functional genes and QTLs were found to locate in highly differentiated regions between G1 and G2. Moreover, the deep root ratios of G2 were significantly higher than G1. Our results would be helpful to the conservation and utilization of DXWR germplasm. [ABSTRACT FROM AUTHOR]

Wild species are known to be reservoir for agronomically important traits including disease resistance in crops. Bacterial blight (BB) is one of the major diseases of rice causing significant yield reduction, and host plant resistance plays a major role in the management of the disease. In this study, we employed backcross introgression lines (BILs) of 'Swarna' containing wild introgressions from two accessions of Oryza nivara IRGC81848 and IRGC81832 in order to map quantitative trait loci (QTLs) for BB resistance. A total of 22 and 43 QTLs for BB resistance were detected respectively on 12 chromosomes, which explained between 2.5% to 18.09% of the phenotypic variance in the two populations. Of the significant QTLs, qBB‐1‐1 (RM259‐RM9) and qBB‐10‐1 (RM474‐RM271) were detected across the two populations and the resistance contributing alleles were from donor wild accessions. Two major QTLs in 'Swarna'/O. nivara IRGC81848 (NPS lines) and seven QTLs in 'Swarna'/O. nivara IRGC81832 (NPK lines) were consistently detected across the years in the respective populations. Novel QTLs qBB‐10‐1 and qBB‐12‐1 are identified as candidate genomic regions for further fine mapping. These stable QTLs identified can be utilized for enhancing BB resistance in elite rice genotypes via marker‐assisted or genomic selection strategies. [ABSTRACT FROM AUTHOR]

The dehydration-responsive element-binding (DREB) genes are types of plant-specific transcription factors that bind to DRE/CRT elements in response to abiotic stresses. It belongs to the AP2 superfamily and contains highly conserved APETELA2 (AP2) domain. In this study, comparative analysis of DREB2A gene from diploid Oryza species was performed using BLASTN approach. The OglDREB2A sequence (KU159742.1) was used as query against 11 diploid Oryza species in the Gramene database for identification of DREB2A orthologs. Molecular characterization, subcellular localization, conserved motifs and promoter analysis were also performed using bioinformatics tools. Molecular characterization of DREB2A protein in the diploid Oryza showed an AP2 conserved domain and nuclear localized protein which is similar to putative transcription factor involved in stress responses. Motif analysis using MEME suites identified 7 significant motifs across all the diploid Oryza species with motif 2, 3, 4 and 5 as the common motifs with ~50 amino acids length. Analysis of 1kb upstream of TSS of DREB2A of the 11 diploid Oryza species revealed many CAREs associated with stress (DRE, LTRE, ERE, G-box, TCC-motif and Sp1) and hormonal regulations (ABREs, MeJA, GARE, and GC-motif) with ABRE as the common element in all the diploid species. Additionally, wild species has more number of cis elements than the cultivated species suggesting a possible role in genome evolution. Overall, the 11 DREB2A orthologs are conserved in terms of sequence homology and protein structure but cultivated species has less number of transcripts than their progenitors suggesting gene retrogression in cultivated Oryza species. [ABSTRACT FROM AUTHOR]

This study identified the genetic diversity of amylase-producing lactic acid bacteria from brown rice (Oryza nivara) Wakawondu cultivar based on the 16S rRNA gene. The ten lactic acid bacteria strains were isolated from the fermented Wakawondu rice washing water; two isolates, SBM3D and SBM4A, displayed strong amylase activity. The two isolates had the same characteristics according to both morphological and biochemical examination. The effect of fermentation time on SBM3D bacterial isolates revealed that bacterial growth at 12 h with OD values and enzyme activity, respectively, of 0.856 and 175 mU/mL, was nearly identical to the growth at 27 h with OD values of 0.886 and 176 mU/mL consecutively. Meanwhile, the bacterial isolate of SBM4A showed a significant increase in growth at 15 h with an OD value of 0.552 and enzyme activity of 99 U/mL. The maximum growth was seen at 18 h with an OD value of 0.657 and enzyme activity of 126 mU/mL. Cladogram of an SBM3D isolate with Pediococcus pentosaceus strains SL001 CP039378.1 and SRCM102740 CP028269.1 forming a sister group clad. Pediococcus pentosaceus strains SRCM102739 CP028266.1 and SRCM102738 CP028264.1 form a sister group in the cladogram of the SBM4A isolate. SBM3D and SBM4A, which are amylase-producing Pediococcus pentosaceus, can be used in food, chemical, health, and other industries. [ABSTRACT FROM AUTHOR]

While crop models are increasingly applied to large-scale areas, inadequate observation data make it difficult to calibrate the model's phenological parameters at the regional scale. The present study proposed a simple mathematical method for estimating rice phenological parameters across spatial scales for the ORYZA model. The method establishes the cumulative function of the phenological parameters (CFPP). By fitting the CFPP with the so-called growth curve, the 4 phenological parameters of the ORYZA model were transformed into 3 fitted parameters in the equation of CFPP. Functions between the fitted parameters and several meteorological and field management factors were established. These established functions were substituted back into CFPP to construct a modified CFPP. Due to the inter-translational relationship between CFPP and the original phenological parameters, the values of phenological parameters could be estimated by the modified CFPP based on meteorological and field management factors. The newly proposed mathematical method was applied in the Yangtze River Basin (YRB), China. The results indicated that the multi-station average of the absolute value of relative errors for the rice panicle initiation, flowering, and maturity dates within the YRB were 12.3 %, 10.5 %, and 8.7 %, respectively, which were at most 4.8 % larger than that simulated using parameters calibrated using each station's phenological data. The phenological parameters estimated by the novel mathematical method had close performance to those calibrated directly based on observed data at most stations in terms of rice phenology simulation. The present study provided a new solution for phenological parameter calibration for crop models when applied in a large-scale area. [Display omitted] • Cumulative function of phenological parameters (CFPP) for the ORYZA model was constructed. • The phenological parameters and CFPP can be transformed into each other. • The spatial variation of parameters in CFPP were investigated. • A modified CFPP for estimating the phenological parameters across regional scales was constructed. [ABSTRACT FROM AUTHOR]

The escalating salinity levels in cultivable soil pose a significant threat to agricultural productivity and, consequently, human sustenance. This problem is being exacerbated by natural processes and human activities, coinciding with a period of rapid population growth. Developing halophytic crops is needed to ensure food security is not impaired and land resources can be used sustainably. Evolution has created many close halophyte relatives of our major glycophytic crops, such as Puccinellia tenuiflora (relative of barley and wheat), Oryza coarctata (relative of rice) and Glycine soja (relative of soybean). There are also some halophytes have been subjected to semi-domestication and are considered as minor crops, such as Chenopodium quinoa. In this paper, we examine the prevailing comprehension of robust salinity resilience in halophytes. We summarize the existing strategies and technologies that equip researchers with the means to enhance the salt tolerance capabilities of primary crops and investigate the genetic makeup of halophytes. • Developing halophytic crops is needed to ensure food security is not impaired and land resources can be used sustainably. • The study of these halophytes will help us improve the salt tolerance of our existing crops and diversify the human diets. • We conclude the available strategies and technologies that enable the researchers to improve the salt tolerance performance of the major crops and the genetics of halophytes. [ABSTRACT FROM AUTHOR]

The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in land plants. However, current knowledge about the evolution of the PPR gene family remains largely limited. In this study, we performed a comparative genomic analysis of the PPR gene family in O. sativa and its wild progenitor, O. rufipogon, and outlined a comprehensive landscape of gene duplications. Our findings suggest that the majority of PPR genes originated from dispersed duplications. Although segmental duplications have only expanded approximately 11.30% and 13.57% of the PPR gene families in the O. sativa and O. rufipogon genomes, we interestingly obtained evidence that segmental duplication promotes the structural diversity of PPR genes through incomplete gene duplications. In the O. sativa and O. rufipogon genomes, 10 (~33.33%) and 22 pairs of gene duplications (~45.83%) had non-PPR paralogous genes through incomplete gene duplication. Segmental duplications leading to incomplete gene duplications might result in the acquisition of domains, thus promoting functional innovation and structural diversification of PPR genes. This study offers a unique perspective on the evolution of PPR gene structures and underscores the potential role of segmental duplications in PPR gene structural diversity.

The strigolactones, a class of plant hormones, regulate many aspects of plant physiology. In the inhibition of shoot branching, the α/β hydrolase D14-which metabolizes strigolactone-interacts with the F-box protein D3 to ubiquitinate and degrade the transcription repressor D53. Despite the fact that multiple modes of interaction between D14 and strigolactone have recently been determined, how the hydrolase functions with D3 to mediate hormone-dependent D53 ubiquitination remains unknown. Here we show that D3 has a C-terminal α-helix that can switch between two conformational states. The engaged form of this α-helix facilitates the binding of D3 and D14 with a hydrolysed strigolactone intermediate, whereas the dislodged form can recognize unmodified D14 in an open conformation and inhibits its enzymatic activity. The D3 C-terminal α-helix enables D14 to recruit D53 in a strigolactone-dependent manner, which in turn activates the hydrolase. By revealing the structural plasticity of the SCFD3-D14 ubiquitin ligase, our results suggest a mechanism by which the E3 coordinates strigolactone signalling and metabolism.

Inorganic arsenic (iAs) is carcinogenic and highly concentrated in rice. Dietary exposure to iAs is concerning among adolescents due to their developmental stage and iAs's long-latency effects. This paper aimed to assess iAs exposure from rice and related lifetime cancer risks (LCR) among adolescents in Kunming, China. A comprehensive literature review of iAs levels in rice and LCR in humans was also conducted. Average daily consumption of rice (ADC) was estimated from 267 adolescents (15⁻18 years). Rice samples obtained from 6 markets were analyzed for iAs concentration (AC). Estimated daily intake (EDI) of iAs was calculated using ADC, AC, and average body weight (BW). Lifetime Cancer Risk (LCR) was calculated using EDI and U.S. EPA derived iAs oral slope factor. The AC was 0.058 mg/kg and the average BW and ADC were 67.5 kg and 410 g/day for males and 55.5 kg and 337 g/day for females. The EDI and LCR were 3.52 × 10-4 mg/kg-BW/day and 5.28 × 10-4 for both males and females, with LCR 5 times above the U.S. LCR upper limit of 1.0 × 10-4. While the AC was below the Chinese maximum contaminant level of 0.2 mg/kg, study results indicated that Kunming adolescents may be at increased risk for iAs-related cancers.

The recently developed CRISPR (clustered regularly interspaced short palindromic repeats)/Cpf1 system expands the range of genome editing and is emerging as an alternative powerful tool for both plant functional genomics and crop improvement. Cpf1-CRISPR RNA (crRNA) produces double strand DNA breaks (DSBs) with long 5'-protruding ends, which may facilitate the pairing and insertion of repair templates through homology-directed repair (HDR) for targeted gene replacement and introduction of the desired DNA elements at specific gene loci for crop improvement. However, the potential mechanism underlying HDR of DSBs generated by Cpf1-crRNA remains to be investigated, and the inherent low efficiency of HDR and poor availability of exogenous donor DNA as repair templates strongly impede the use of HDR for precise genome editing in crop plants. Here, we provide evidence of synthesis-dependent repair of Cpf1-induced DSBs, which enables us precisely to replace the wild-type ALS gene with the intended mutant version that carries two discrete point mutations conferring herbicide resistance to rice plants. Our observation that the donor repair template (DRT) with only the left homologous arm is sufficient for precise targeted allele replacement offers a better understanding of the mechanism underlying HDR in plants, and greatly simplifies the design of DRTs for precision genome editing in crop improvement.

Anthropogenic land use change, including agriculture, can alter mosquito larval habitat quality, increase mosquito abundance, and increase incidence of vector-borne disease. Rice is a staple food crop for more than half of the world's population, with ∼1% of global production occurring within the United States (US). Flooded rice fields provide enormous areas of larval habitat for mosquito species and may be hotspots for mosquito-borne pathogens, including West Nile virus (WNV). West Nile virus was introduced into the Americas in 1999 and causes yearly epidemics in the US with an average of approximately 1,400 neuroinvasive cases and 130 deaths per year. We examined correlations between rice cultivation and WNV disease incidence in rice-growing regions within the US. Incidence of WNV disease increased with the fraction of each county under rice cultivation in California but not in the southern US. We show that this is likely due to regional variation in the mosquitoes transmitting WNV. Culex tarsalis was an important vector of WNV in California, and its abundance increased with rice cultivation, whereas in rice-growing areas of the southern US, the dominant WNV vector was Culex quinquefasciatus, which rarely breeds in rice fields. These results illustrate how cultivation of particular crops can increase disease risk and how spatial variation in vector ecology can alter the relationship between land cover and disease.

Many statistical methods are available for genomic selection (GS) through which genetic values of quantitative traits are predicted for plants and animals using whole-genome SNP data. A large number of predictors with much fewer subjects become a major computational challenge in GS. Principal components regression (PCR) and its derivative, i.e., partial least squares regression (PLSR), provide a solution through dimensionality reduction. In this study, we show that PCR can perform better than PLSR in cross validation. PCR often requires extracting more components to achieve the maximum predictive ability than PLSR and thus may be associated with a higher computational cost. However, application of the HAT method (a strategy of describing the relationship between the fitted and observed response variables with a hat matrix) to PCR circumvents conventional cross validation in testing predictive ability, resulting in substantially improved computational efficiency over PLSR where cross validation is mandatory. Advantages of PCR over PLSR are illustrated with a simulated trait of a hypothetical population and four agronomical traits of a rice population. The benefit of using PCR in genomic selection is further demonstrated in an effort to predict 1000 metabolomic traits and 24,973 transcriptomic traits in the same rice population.

Glycosylinositol phosphorylceramides (GIPCs), which have a ceramide core linked to a glycan headgroup of varying structures, are the major sphingolipids in the plant plasma membrane. Recently, we identified the major biosynthetic genes for GIPC glycosylation in Arabidopsis (Arabidopsis thaliana) and demonstrated that the glycan headgroup is essential for plant viability. However, the function of GIPCs and the significance of their structural variation are poorly understood. Here, we characterized the Arabidopsis glycosyltransferase GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) and showed that it is responsible for the glycosylation of a subgroup of GIPCs found in seeds and pollen that contain GlcNAc and GlcN [collectively GlcN(Ac)]. In Arabidopsis gint1 plants, loss of the GlcN(Ac) GIPCs did not affect vegetative growth, although seed germination was less sensitive to abiotic stress than in wild-type plants. However, in rice, where GlcN(Ac) containing GIPCs are the major GIPC subgroup in vegetative tissue, loss of GINT1 was seedling lethal. Furthermore, we could produce, de novo, "rice-like" GlcN(Ac) GIPCs in Arabidopsis leaves, which allowed us to test the function of different sugars in the GIPC headgroup. This study describes a monocot GIPC biosynthetic enzyme and shows that its Arabidopsis homolog has the same biochemical function. We also identify a possible role for GIPCs in maintaining cell-cell adhesion.

Weed evolution from crops involves changes in key traits, but it is unclear how genetic and phenotypic variation contribute to weed diversification and productivity. Weedy rice is a conspecific weed of rice (Oryza sativa) worldwide. We used principal component analysis and hierarchical clustering to understand how morphologically and evolutionarily distinct US weedy rice populations persist in rice fields in different locations under contrasting management regimes. Further, we used a representative subset of 15 sequence-tagged site fragments of expressed genes from global Oryza to assess genome-wide sequence variation among populations.Crop hull color and crop-overlapping maturity dates plus awns, seed (panicle) shattering (> 50%), pigmented pericarp and stature variation (30.2% of total phenotypic variance) characterize genetically less diverse California weedy rice. By contrast, wild-like hull color, seed shattering (> 50%) and stature differences (55.8% of total phenotypic variance) typify genetically diverse weedy rice ecotypes in Arkansas.Recent de-domestication of weedy species - such as in California weedy rice - can involve trait combinations indistinguishable from the crop. This underscores the need for strict seed certification with genetic monitoring and proactive field inspection to prevent proliferation of weedy plant types. In established populations, tillage practice may affect weed diversity and persistence over time. © 2017 Society of Chemical Industry.

Recombinant butyrylcholinesterase produced in a metabolically regulated transgenic rice cell culture (rrBChE) was purified to produce a highly pure (95%), active form of enzyme. The developed downstream process uses common manufacturing friendly operations including tangential flow filtration, anion-exchange chromatography, and affinity chromatography to obtain a process recovery of 42% active rrBChE. The purified rrBChE was then characterized to confirm its comparability to the native human form of the molecule (hBChE). The recombinant and native enzyme demonstrated comparable enzymatic behavior and had an identical amino acid sequence. However, rrBChE differs in that it contains plant-type complex N-glycans, including an α-1,3 linked core fucose, and a β-1,2 xylose, and lacking a terminal sialic acid. Despite this difference, rrBChE is demonstrated to be an effective stoichiometric bioscavenger for five different organophosphorous nerve agents in vitro. Together, the efficient downstream processing scheme and functionality of rrBChE confirm its promise as a cost-effective alternative to hBChE for prophylactic and therapeutic use.

Paddy soils from mercury (Hg)-contaminated rice fields in Guizhou, China were studied with respect to total mercury (THg) and methylmercury (MeHg) concentrations as well as Bacterial and Archaeal community composition. Total Hg (0.25-990 μg g-1) and MeHg (1.3-30.5 ng g-1) varied between samples. Pyrosequencing (454 FLX) of the hypervariable v1-v3 regions of the 16S rRNA genes showed that Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Euryarchaeota, and Crenarchaeota were dominant in all samples. The Bacterial α-diversity was higher in samples with relatively Low THg and MeHg and decreased with increasing THg and MeHg concentrations. In contrast, Archaeal α-diversity increased with increasing of MeHg concentrations but did not correlate with changes in THg concentrations. Overall, the methylation gene hgcAB copy number increased with both increasing THg and MeHg concentrations. The microbial communities at High THg and High MeHg appear to be adapted by species that are both Hg resistant and carry hgcAB genes for MeHg production. The relatively high abundance of both sulfate-reducing δ-Proteobacteria and methanogenic Archaea, as well as their positive correlations with increasing THg and MeHg concentrations, suggests that these microorganisms are the primary Hg-methylators in the rice paddy soils in Guizhou, China.

BACKGROUND:Pathogen perception by plants is mediated by plasma membrane-localized immune receptors that have varied extracellular domains. Lectin receptor kinases (LecRKs) are among these receptors and are subdivided into 3 classes, C-type LecRKs (C-LecRKs), L-type LecRKs (L-LecRKs) and G-type LecRKs (G-LecRKs). While C-LecRKs are represented by one or two members in all plant species investigated and have unknown functions, L-LecRKs have been characterized in a few plant species and have been shown to play roles in plant defense against pathogens. Whereas Arabidopsis G-LecRKs have been characterized, this family of LecRKs has not been studied in tomato. RESULTS:This investigation updates the current characterization of Arabidopsis G-LecRKs and characterizes the tomato G-LecRKs, using LecRKs from the monocot rice and the basal eudicot columbine to establish a basis for comparisons between the two core eudicots. Additionally, revisiting parameters established for Arabidopsis nomenclature for LecRKs is suggested for both Arabidopsis and tomato. Moreover, using phylogenetic analysis, we show the relationship among and between members of G-LecRKs from all three eudicot plant species. Furthermore, investigating presence of motifs in G-LecRKs we identified conserved motifs among members of G-LecRKs in tomato and Arabidopsis, with five present in at least 30 of the 38 Arabidopsis members and in at least 45 of the 73 tomato members. CONCLUSIONS:This work characterized tomato G-LecRKs and added members to the currently characterized Arabidopsis G-LecRKs. Additionally, protein sequence analysis showed an expansion of this family in tomato as compared to Arabidopsis, and the existence of conserved common motifs in the two plant species as well as conserved species-specific motifs.

Identification of trait-associated metabolites will advance the knowledge and understanding of the biosynthetic and catabolic pathways that are relevant to the complex traits of interest. In the past, the association between metabolites (treated as quantitative traits) and genetic variants (e.g., SNPs) has been extensively studied using metabolomic quantitative trait locus (mQTL) mapping. Nevertheless, the research on the association between metabolites with agronomic traits has been inadequate. In practice, the regular approaches for QTL mapping analysis may be adopted for metabolites-phenotypes association analysis due to the similarity in data structure of these two types of researches. In the study, we compared four regular QTL mapping approaches, i.e., simple linear regression (LR), linear mixed model (LMM), Bayesian analysis with spike-slab priors (Bayes B) and least absolute shrinkage and selection operator (LASSO), by testing their performances on the analysis of metabolome-phenotype associations. Simulation studies showed that LASSO had the higher power and lower false positive rate than the other three methods. We investigated the associations of 839 metobolites with five agronomic traits in a collection of 533 rice varieties. The results implied that a total of 25 metabolites were significantly associated with five agronomic traits. Literature search and bioinformatics analysis indicated that the identified 25 metabolites are significantly involved in some growth and development processes potentially related to agronomic traits. We also explored the predictability of agronomic traits based on the 839 metabolites through cross-validation, which showed that metabolomic prediction was efficient and its application in plant breeding has been justified.

Crops carrying broad-spectrum resistance loci provide an effective strategy for controlling infectious disease because these loci typically confer resistance to diverse races of a pathogen or even multiple species of pathogens. Despite their importance, only a few crop broad-spectrum resistance loci have been reported. Here, we report the identification and characterization of the rice bsr-k1 (broad-spectrum resistance Kitaake-1) mutant, which confers broad-spectrum resistance against Magnaporthe oryzae and Xanthomonas oryzae pv oryzae with no major penalty on key agronomic traits. Map-based cloning reveals that Bsr-k1 encodes a tetratricopeptide repeats (TPRs)-containing protein, which binds to mRNAs of multiple OsPAL (OsPAL1-7) genes and promotes their turnover. Loss of function of the Bsr-k1 gene leads to accumulation of OsPAL1-7 mRNAs in the bsr-k1 mutant. Furthermore, overexpression of OsPAL1 in wild-type rice TP309 confers resistance to M. oryzae, supporting the role of OsPAL1 Our discovery of the bsr-k1 allele constitutes a significant conceptual advancement and provides a valuable tool for breeding broad-spectrum resistant rice.

Bacterial communities associated with roots impact the health and nutrition of the host plant. The dynamics of these microbial assemblies over the plant life cycle are, however, not well understood. Here, we use dense temporal sampling of 1,510 samples from root spatial compartments to characterize the bacterial and archaeal components of the root-associated microbiota of field grown rice (Oryza sativa) over the course of 3 consecutive growing seasons, as well as 2 sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth and then stabilized compositionally for the remainder of the life cycle. Bacterial and archaeal taxa conserved between field sites were defined as predictive features of rice plant age by modeling using a random forest approach. The age-prediction models revealed that drought-stressed plants have developmentally immature microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle.

Abiotic stress-induced senescence in crops is a process particularly affecting the photosynthetic apparatus, decreasing photosynthetic activity and inducing chloroplast degradation. A pathway for stress-induced chloroplast degradation that involves the CHLOROPLAST VESICULATION (CV) gene was characterized in rice (Oryza sativa) plants. OsCV expression was up-regulated with the age of the plants and when plants were exposed to water-deficit conditions. The down-regulation of OsCV expression contributed to the maintenance of the chloroplast integrity under stress. OsCV-silenced plants displayed enhanced source fitness (i.e. carbon and nitrogen assimilation) and photorespiration, leading to water-deficit stress tolerance. Co-immunoprecipitation, intracellular co-localization, and bimolecular fluorescence demonstrated the in vivo interaction between OsCV and chloroplastic glutamine synthetase (OsGS2), affecting source-sink relationships of the plants under stress. Our results would indicate that the OsCV-mediated chloroplast degradation pathway is involved in the regulation of nitrogen assimilation during stress-induced plant senescence.

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.

Rice blast, caused by the ascomycete Magnaporthe oryzae, is one of the most destructive rice diseases worldwide. Even though the disease has been present in California since 1996, there is no data for the pathogen population biology in the state. Using amplified fragment length polymorphisms and mating-type markers, the M. oryzae population diversity was investigated using isolates collected when the disease was first established in California and isolates collected a decade later. While in the 1990 samples, a single multilocus genotype (MLG) was identified (MLG1), over a decade later, we found 14 additional MLGs in the 2000 isolates. Some of these MLGs were found to infect the only rice blast-resistant cultivar (M-208) available for commercial production in California. The same samples also had a significant decrease of MLG1. MLG1 was found infecting the resistant rice cultivar M-208 on one occasion whereas MLG7 was the most common genotype infecting the M-208. MLG7 was identified in the 2000 samples, and it was not present in the M. oryzae population a decade earlier. Our results demonstrate a significant increase in genotypic diversity over time with no evidence of sexual reproduction and suggest a recent introduction of new virulent race(s) of the pathogen. In addition, our data could provide information regarding the durability of the Pi-z resistance gene of the M-208. This information will be critical to plant breeders in developing strategies for deployment of other rice blast resistance genes/cultivars in the future.

A field experiment was conducted to determine the persistence of metamifop in transplanted rice crop for two seasons. Metamifop 10% EC was applied at two doses: 100 g a.i. ha-1 and 200 g a.i. ha-1 at 2-3 leaf stage of Echinochloa crusgalli. The residues of metamifop along with its major metabolite, N-(2-fluorophenyl)-2-hydroxy-N-methylpropionamide (HFMPA), were estimated in rice plant, field water and soil using Liquid Chromatography Mass Spectrometry. Limit of detection and limit of quantification of the method for both the compounds were set at 0.003 μg g-1 and 0.010 μg g-1 respectively. Metamifop showed less persistence in field water and rice plant as compared to soil samples. Presence of HFMPA was recorded in rice plant and soil. Both the compounds were found below level of quantification in harvest samples of straw, grains, husk and soil. A safe waiting period of 52 d was suggested for harvesting of rice when metamifop was applied at 100 g a.i. ha-1 (recommended dose).

The NHX-type cation/H+ transporters in plants have been shown to mediate Na+ (K+ )/H+ exchange for salinity tolerance and K+ homoeostasis. In this study, we identified and characterized two NHX homologues, HtNHX1 and HtNHX2 from an infertile and salinity tolerant species Helianthus tuberosus (cv. Nanyu No. 1). HtNHX1 and HtNHX2 share identical 5'- and 3'-UTR and coding regions, except for a 342-bp segment encoding 114 amino acids (L272 to Q385 ) which is absent in HtNHX2. Both hydroponics and soil culture experiments showed that the expression of HtNHX1 or HtNHX2 improved the rice tolerance to salinity. Expression of HtNHX2, but not HtNHX1, increased rice grain yield, harvest index, total nutrient uptake under K+ -limited salt-stress or general nutrient deficiency conditions. The results provide a novel insight into NHX function in plant mineral nutrition.