This service exclusively searches for literature that cites resources. Please be aware that the total number of searchable documents is limited to those containing RRIDs and does not include all open-access literature.
Polyploidization is a prominent process in plant evolution, whereas the mechanism and tempo-spatial process remained poorly understood. Oryza officinalis complex, a polyploid complex in the genus Oryza, could exemplify the issues not only for it covering a variety of ploidy levels, but also for the pantropical geographic pattern of its polyploids in Asia, Africa, Australia and Americas, in which a pivotal genome, the C-genome, witnessed all the polyploidization process.
Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice ( Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a single copy of the thb gene exist in Oryza sativa var. indica and O. sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit a very high affinity for O 2, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O 2. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O 2-transport, O 2-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice nshb and thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice nshbs and thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the cis-elements and trans-acting factors that regulate the expression of rice hb genes, and the partial understanding of the evolution of rice Hbs.
The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb de novo assembled genome sequence of Oryza brachyantha. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha. We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza.
Development and testing of reliable tools for simulating rice production in salt-affected areas are presented in this paper. New functions were implemented in existing crop models ORYZA v3 and the cropping systems modelling framework APSIM. Field experiments covering two years, two different sites, and three varieties were used to validate both improved models. We used the salt balance module in the systems model APSIM to simulate the observed daily soil salinity with acceptable accuracy (RMSEn <35%), whereas ORYZA v3 used measured soil salinity at a given interval of days as a model input. Both models presented similarly good accuracy in simulating aboveground biomass, leaf area index, and grain yield for IR64 over a gradient of salinity conditions. The model index of agreement ranged from 0.86 to 0.99. Variability of yield under stressed and non-stressed conditions was simulated with a RMSE, of 191 kg ha-1 and 222 kg ha-1 , respectively, for ORYZA v3 and APSIM-Oryza, corresponding to an RMSEn of 14.8% and 17.3%. These values are within the bounds of experimental error, therefore indicating acceptable model performance. The model test simulating genotypic variability of rice crop responses resulted in similar levels of acceptable model performance with RMSEn ranging from 11.3 to 39.9% for observed total above ground biomass for IR64 and panicle biomass for IR29, respectively. With the improved models, more reliable tools are now available for use in risk assessment and evaluation of suitable management options for rice production in salt-affected areas. The approach presented may also be applied in improving other non-rice crop models to integrate a response to soil salinity - particularly in process-based models which capture stage-related stress tolerance variability and resource use efficiency.
Oryza glumaepatula originates from South America continent and contains many valuable traits, such as tolerance to abiotic stress, high yield and good cooking qualities. However, hybrid sterility severely hindered the utilization of favorable genes of O. glumaepatula by interspecific hybridization. In order to further understand the nature of hybrid sterility between O. sativa and O. glumaepatula, a near isogenic line (NIL) was developed using a japonica variety Dianjingyou 1 as the recurrent parent and an accession of O. glumaepatula as the donor parent. A novel gene S56(t) for pollen sterility was mapped into the region between RM20797 and RM1093 on the short arm of chromosome 7, the physical distance between the two markers was about 469 kb. The genetic behavior of S56(t) followed one-locus allelic interaction model, the male gametes carrying the alleles of O. sativa in the heterozygotes were aborted completely. These results would help us clone S56(t) gene and understand the role of S56(t) in interspecific sterility.
Oryza officinalis is an accessible alien donor for genetic improvement of rice. Comparison across a representative panel of Oryza species showed that the wild O. officinalis and cultivated O. sativa ssp. japonica have similar cold tolerance potentials. The possibility that either distinct or similar genetic mechanisms are involved in the low temperature responses of each species was addressed by comparing their transcriptional networks. General similarities were supported by shared transcriptomic signatures indicative of equivalent metabolic, hormonal, and defense status. However, O. officinalis has maintained an elaborate cold-responsive brassinosteroid-regulated BES1-network that appeared to have been fragmented in O. sativa. BES1-network is potentially important for integrating growth-related responses with physiological adjustments and defenses through the protection of photosynthetic machinery and maintenance of stomatal aperture, oxidative defenses, and osmotic adjustment. Equivalent physiological processes are functional in O. sativa but their genetic mechanisms are under the direct control of ABA-dependent, DREB-dependent and/or oxidative-mediated networks uncoupled to BES1. While O. officinalis and O. sativa represent long periods of speciation and domestication, their comparable cold tolerance potentials involve equivalent physiological processes but distinct genetic networks. BES1-network represents a novel attribute of O. officinalis with potential applications in diversifying or complementing other mechanisms in the cultivated germplasm.
Wild relatives genetically close to cultivars are precious genetic resources for plant breeding. Oryza rufipogon, O. barthii, O. glumaepatula, O. meridionalis and O. longistaminata are such wild species, and are also categorized as AA genome species based on their structural similarities. Chromosome segment substitution lines (CSSLs) are a powerful resource in breeding and genetics, and numerous rice CSSLs have been produced. This study aimed to develop DNA markers for evaluation of CSSLs directly by PCR and subsequent gel electrophoresis. We confirmed that up to 155 of 188 markers developed for detection of japonica-indica INDELs could also detect INDELs between rice cultivars and wild AA-species accessions. Percentages of applicable markers were higher in O. rufipogon accessions (61.7 to 85.6%), and lower in accessions of other four AA species (39.8 to 51.4%). These markers were distributed throughout the rice chromosomes, and will be useful for genotyping of CSSLs and other genetic resources derived from crosses between rice cultivars and closely related wild species.
Oryza coarctata plant, collected from Sundarban delta of West Bengal, India, has been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time the draft genome with the coverage of 85.71 % and deposited the raw data in NCBI SRA, with BioProject ID PRJNA396417.
The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content. We validated our assembly by a comparative linkage analysis and by examining well-characterized gene families. This genome assembly will be a useful resource to exploit beneficial alleles found in O. longistaminata. Our results also show that it is possible to generate a high-quality, functionally complete rice genome assembly from moderate SMRT read coverage by exploiting synteny in a closely related Oryza species.
Long terminal repeat (LTR) retrotransposons constitute a major fraction of the genomes of higher plants. For example, retrotransposons comprise more than 50% of the maize genome and more than 90% of the wheat genome. LTR retrotransposons are believed to have contributed significantly to the evolution of genome structure and function. The genome sequencing of selected experimental and agriculturally important species is providing an unprecedented opportunity to view the patterns of variation existing among the entire complement of retrotransposons in complete genomes.
Seeds are the most important plant storage organ and play a central role in the life cycle of plants. Since little is known about the protein composition of rice (Oryza sativa) seeds, in this work we used proteomic methods to obtain a reference map of rice seed proteins and identify important molecules. Overall, 480 reproducible protein spots were detected by two-dimensional electrophoresis on pH 4-7 gels and 302 proteins were identified by MALDI-TOF MS and database searches. Together, these proteins represented 252 gene products and were classified into 12 functional categories, most of which were involved in metabolic pathways. Database searches combined with hydropathy plots and gene ontology analysis showed that most rice seed proteins were hydrophilic and were related to binding, catalytic, cellular or metabolic processes. These results expand our knowledge of the rice proteome and improve our understanding of the cellular biology of rice seeds.
Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were identified in O. sativa ssp. japonica, O. sativa ssp. indica, Oryza rufipogon, Oryza nivara, Oryza punctata, and Oryza glumaepatula, respectively. Gene duplication events, structural features, conserved motifs, a phylogenetic analysis, chromosome locations, and Ka/Ks ratios of this important family were found to be strictly conservative across these six Oryza species/subspecies, suggesting that the expansion of the GH3 gene family in Oryza species might be attributed to duplication events, and this expansion could occur in the common ancestor of Oryza species, even in common ancestor of rice tribe (Oryzeae) (23.07~31.01 Mya). The RNA-seq results of different tissues displayed that OsGH3 genes had significantly different expression profiles. Remarkably, the qRT-PCR result after NaCl treatment indicated that the majority of OsGH3 genes play important roles in salinity stress, especially OsGH3-2 and OsGH3-8. This study provides important insights into the evolution of the GH3 gene family in Oryza species and will assist with further investigation of OsGH3 genes' functions under salinity stress.
Cultivated rice (Oryza sativa L.) is frequently exposed to multiple stresses, including Schizotetranychus oryzae mite infestation. Rice domestication has narrowed the genetic diversity of the species, leading to a wide susceptibility. This work aimed to analyze the response of two African rice species (Oryza barthii and Oryza glaberrima), weedy rice (O. sativa f. spontanea), and O. sativa cv. Nipponbare to S. oryzae infestation. Surprisingly, leaf damage, histochemistry, and chlorophyll concentration/fluorescence indicated that the African species present a higher level of leaf damage, increased accumulation of H2O2, and lower photosynthetic capacity when compared to O. sativa plants under infested conditions. Infestation decreased tiller number, except in Nipponbare, and caused the death of O. barthii and O. glaberrima plants during the reproductive stage. While infestation did not affect the weight of 1,000 grains in both O. sativa, the number of panicles per plant was affected only in O. sativa f. spontanea, and the percentage of full seeds per panicle and seed length were increased only in Nipponbare. Using proteomic analysis, we identified 195 differentially abundant proteins when comparing susceptible (O. barthii) and tolerant (Nipponbare) plants under control and infested conditions. O. barthii presents a less abundant antioxidant arsenal and is unable to modulate proteins involved in general metabolism and energy production under infested condition. Nipponbare presents high abundance of detoxification-related proteins, general metabolic processes, and energy production, suggesting that the primary metabolism is maintained more active compared to O. barthii under infested condition. Also, under infested conditions, Nipponbare presents higher levels of proline and a greater abundance of defense-related proteins, such as osmotin, ricin B-like lectin, and protease inhibitors (PIs). These differentially abundant proteins can be used as biotechnological tools in breeding programs aiming at increased tolerance to mite infestation.
A long awn is one of the distinct morphological features of wild rice species. This organ is thought to aid in seed dispersal and prevent predation by animals. Most cultivated varieties of Oryza sativa and Oryza glaberrima, however, have lost the ability to form long awns. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Here, we evaluated three sets of chromosome segment substitution lines (CSSLs) in a common O. sativa genetic background (cv. Koshihikari) that harbor genomic fragments from Oryza nivara, Oryza rufipogon, and Oryza glaberrima donors. Phenotypic analyses of these libraries revealed the existence of three genes, Regulator of Awn Elongation 1 (RAE1), RAE2, and RAE3, involved in the loss of long awns in cultivated rice. Donor segments at two of these genes, RAE1 and RAE2, induced long awn formation in the CSSLs whereas an O. sativa segment at RAE3 induced long awn formation in O. glaberrima. These results suggest that the two cultivated rice species, O. sativa and O. glaberrima, have taken independent paths to become awnless.
The introduction of closely related species genomic fragments is an effective way to enrich genetic diversity and creates new germplasms in crops. Here, we studied the genetic diversity of an introgression line (IL) population composed of 106 ILs derived from an interspecific tetra cross between O. glaberrima and O. sativa (RAM3/Jin23B//Jin23B///YuetaiB). The proportion of O. glaberrima genome (PGG) in the ILs ranged from 0.3% to 36.7%, with an average value of 12.32% which is close to the theoretically expected proportion. A total of 250 polymorphic alleles were amplified by 21 AFLP primer combinations with an average of 12 alleles per primer. Population structure analysis revealed that the IL population can be divided into four genetically distinct subpopulations. Both principal component analysis and neighbor-joining tree analysis showed that ILs with a higher PGG displayed greater genetic diversity. Canonical discriminant analysis identified six phenotypic traits (plant height, yield per plant, filled grain percentage, panicle length, panicle number and days to flowering) as the main discriminatory traits among the ILs and between the subpopulations and showed significant phenotypic distances between subpopulations. The effects of PGG on phenotypic traits in the ILs were estimated using a linear admixed model, which showed a significant positive effect on grain yield per plant (0.286±0.117), plant height (0.418 ± 0.132), panicle length (0.663 ± 0.107), and spikelet number per panicle (0.339 ± 0.128), and a significant negative effect on filled grain percentage (-0.267 ± 0.123) and days to flowering (-0.324 ± 0.075). We found that an intermediate range (10% - 20%) of PGG was more effective for producing ILs with favorable integrated agronomic traits. Our results confirm that construction of IL population carrying O. glaberrima genomic fragments could be an effective approach to increase the genetic diversity of O. sativa genome and an appropriate level of PGG could facilitate pyramiding more favorable genes for developing more adaptive and productive rice.
Grain size and weight are important target traits determining grain yield and quality in rice. Wild rice species possess substantial elite genes that can be served as an important resource for genetic improvement of rice. In this study, we identify and validate a novel QTL on chromosome 7 affecting the grain size and weight using introgression lines from cross of Oryza sativa and Oryza minuta.
The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.
A number of genes that contribute to the domestication traits of cultivated rice have been identified. These include Sh4, Rc, PROG1 and LABA1, which are associated with non-shattering rachis, white pericarp, erect growth and barbless awns, respectively. The mutations giving rise to the "domestication alleles" of these genes are either invariable in cultivated rice, or have variability that is strictly associated with the phenotypic trait. This observation forms the basis to those current rice domestication models that envisage a single origin for the domesticated phenotype. Such models assume that the domestication alleles are absent or rare in wild rice, emerged under cultivation and spread across all rice groups by introgressive hybridization. We examined whole-genome sequencing datasets for wild and cultivated rice to test the former two assumptions. We found that the rc and laba1 alleles occur in wild rice with broad geographical distribution, and reach frequencies as high as 13 and 15%, respectively. These results are in agreement with previous observations of the prog1 and sh4 domestication alleles in wild populations. We also show that the diversity of the genomic regions surrounding the rc, laba1, prog1 and sh4 alleles in wild accessions is greater than that in cultivated rice, suggesting that these alleles emerged prior to domestication. Our findings indicate that the possibility that independent rice groups obtained identical domestication alleles directly from the wild population needs to be considered.
Chimeric retroposition is a process by which RNA is reverse transcribed and the resulting cDNA is integrated into the genome along with flanking sequences. This process plays essential roles and drives genome evolution. Although the origination rates of chimeric retrogenes are high in plant genomes, the evolutionary patterns of the retrogenes and their parental genes are relatively uncharacterised in the rice genome. In this study, we evaluated the substitution ratio of 24 retrogenes and their parental genes to clarify their evolutionary patterns. The results indicated that seven gene pairs were under positive selection. Additionally, soon after new chimeric retrogenes were formed, they rapidly evolved. However, an unexpected pattern was also revealed. Specifically, after an undefined period following the formation of new chimeric retrogenes, the parental genes, rather than the new chimeric retrogenes, rapidly evolved under positive selection. We also observed that one retro chimeric gene (RCG3) was highly expressed in infected calli, whereas its parental gene was not. Finally, a comparison of our Ka/Ks analysis with that of other species indicated that the proportion of genes under positive selection is greater for chimeric retrogenes than for non-chimeric retrogenes in the rice genome.
Welcome to the FDI Lab - SciCrunch.org Resources search. From here you can search through a compilation of resources used by FDI Lab - SciCrunch.org and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that FDI Lab - SciCrunch.org has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on FDI Lab - SciCrunch.org then you can log in from here to get additional features in FDI Lab - SciCrunch.org such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into FDI Lab - SciCrunch.org you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter your papers by.
From here we'll present any options for the literature, such as exporting your current results.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Year:
Count: