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To integrate the genomic information of the rice pan-genome, we performed comparative analyses and established a user-friendly Rice Gene Index (RGI,https://riceome.hzau.edu.cn) platform with 16 platinum standard reference genomes and supplementary transcriptome data. To logically organize and scientifically the index of 744,233 genes among rice accessions, we detected 112,658 Ortholog Gene Indices, and provide ‘GeneCard’ pages to query genomic, transcriptomic, and homology information for each gene. The RGI allows users to search for relationships and comprehensive information of genes in keyword-based, sequence-based, and relationship-based ways. Furthermore, users can visualize these relationships at local and global scales corresponding to ‘Microcollinearity’ and ‘Macrocollinearity’ modules.

Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Utilizing 16 high-quality genomes that represent the subpopulation structure of Asian rice (O. sativa), plus the genomes of two close relatives (O. rufipogon and O. punctata), we built a pan-genome inversion index of 1,054 non-redundant inversions that span an average of ∼ 14% of the O. sativa cv. Nipponbare reference genome sequence. Using this index we estimated an inversion rate of 1,100 inversions per million years in Asian rice, which is 37 to 73 times higher than previously estimated for plants. Detailed analyses of these inversions showed evidence of their effects on gene regulation, recombination rate, linkage disequilibrium and agronomic trait performance. Our study uncovers the prevalence and scale of large inversions (≥ 100 kb) across the pan-genome of Asian rice, and hints at their largely unexplored role in functional biology and crop performance.

Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation. ispartof: NATURE PLANTS vol:8 issue:5 pages:491-+ ispartof: location:England status: published

Seeds of 15 diverse rice accessions, representing aus, indica, temperate japonica and tropical japonica subpopulations, were produced under temperate climate conditions in Korea and used for vitamin E analysis and seed storage experiments at 45°C and 10.9% seed moisture content. High γ-tocotrienol was significantly positively correlated with seed longevity. In addition, a high β-tocopherol proportion relative to δ-tocopherol was significantly negatively correlated with seed longevity. Using high-density single-nucleotide polymorphism marker data, DNA haplotype analysis showed clear allelic variations in the region of two S-adenosylmethionine synthetase genes: LOC_Os04g42095 and LOC_Os11g15410, which regulate the conversion of δ-tocopherol into β-tocopherol. Four indica accessions with rare and subpopulation-specific alleles showed a 2.3-fold lower β-/δ-tocopherol ratio compared with accessions from other subpopulations.

The aus rice variety group originated in stress-prone regions and is a promising source for the development of new stress-tolerant rice cultivars. In this study, an aus panel (~220 genotypes) was evaluated in field trials under well-watered and drought conditions and in the greenhouse (basket, herbicide and lysimeter studies) to investigate relationships between grain yield and root architecture, and to identify component root traits behind the composite trait of deep root growth. In the field trials, high and stable grain yield was positively related to high and stable deep root growth (r = 0.16), which may indicate response to within-season soil moisture fluctuations (i.e., plasticity). When dissecting component traits related to deep root growth (including angle, elongation and branching), the number of nodal roots classified as 'large-diameter' was positively related to deep root growth (r = 0.24), and showed the highest number of colocated genome-wide association study (GWAS) peaks with grain yield under drought. The role of large-diameter nodal roots in deep root growth may be related to their branching potential. Two candidate loci that colocated for yield and root traits were identified that showed distinct haplotype distributions between contrasting yield/stability groups and could be good candidates to contribute to rice improvement.

Seed longevity is a key trait to secure seed viability and vigor of farmer’s seed lots under the increased temperatures and humidity associated with climate change. While previous studies have found quantitative trait loci (QTL) for improved longevity in temperate japonica rice varieties, there are no available QTL identified that can potentially enhance seed longevity in tropical japonica rice, which are grown in ASEAN countries and highly vulnerable to the impact of climate change. Here, we present QTL and candidate genes identified in an F3 bi-parental QTL mapping population developed from a tropical japonica × indica cross, using 1 k single nucleotide polymorphism (SNP) markers. To accelerate seed ageing through a seed storage experiment, seed moisture content (MC) was elevated by equilibrating seeds at 60 % relative humidity (RH) and 20 °C, after which seeds were stored at 10.9 % seed MC and 45 °C for 56 days. Within a QTL identified on chromosome 2 (2.9 Mb size), there were 45 annotated genes potentially relevant to seed longevity mechanisms such as oxidative stress reduction and repair of damaged DNA. Within the QTL, the preponderance of genes expressed largely in reproductive tissues, seeds or embryo make this a dependable QTL. Based on coexpression and network analysis, we highlight eight genes as potentially important candidate genes, consistent with previous studies suggesting their role in seed germination and longevity.

Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual SV calls that grouped into 1.5 million allelic variants. We found enrichment of long SVs in promoters and an excess of shorter variants in 5′ UTRs. Across the rice genomes, we identified regions of high SV frequency enriched in stress response genes. We demonstrated how SVs may help in finding causative variants in genome-wide association analysis. These new insights into rice genome biology are valuable for understanding the effects SVs have on gene function, with the prospect of identifying novel agronomically important alleles that can be utilized to improve cultivated rice.

In-depth studies on the genetic diversity of crops indicate that domestication is likely a drawn-out process that differs from the traditional representation of a simple rapid bottleneck. Asian cultivated rice provides a clear picture of multiple foundations of crop diversity. Among them, Japonica rice is likely the group derived from the first human manipulations of this species. We make use of the 3,000 Rice Genomes (3K RG) data set, first described in 2018, to explore the genetic diversity of traditional Japonica rice. After delineating introgressions from the Indica and cAus cultivar groups, we mask these traces to analyse Japonica diversity in more depth. We find differentiation between the established “temperate”, “subtropical” and “tropical” subgroups, and identify stream-like traces of highly divergent sources from broad geographic ranges and subgroups. We characterize five such streams, most visible respectively in: 1) Indonesia, 2) continental Southeast Asia, 3) China, 4) uplands of Japan, and 5) Bhutan. These streams likely consist of ancient alien introgressions propagated through geneflow to different degrees. They currently appear as long genome segments conserved among specific germplasm groups, as well as shorter segments more broadly distributed across diverse germplasm along what could be adaptive corridors. They are all represented in the Japonica component of cBasmati varieties, thought to have emerged over two millennia ago. We thus provide strong evidence that Japonica, the group posited as being the most direct product of a simple domestication process in China, is an aggregate derived from multiple waves of admixture and represents a composite gene pool with ancient Asia-wide population dynamics.

As the human population grows from 7.8 billion to 10 billion over the next 30 years, breeders must do everything possible to create crops that are highly productive and nutritious, while simultaneously having less of an environmental footprint. Rice will play a critical role in meeting this demand and thus, knowledge of the full repertoire of genetic diversity that exists in germplasm banks across the globe is required. To meet this demand, we describe the generation, validation and preliminary analyses of transposable element and long-range structural variation content of 12 near-gap-free reference genome sequences (RefSeqs) from representatives of 12 of 15 subpopulations of cultivated Asian rice. When combined with 4 existing RefSeqs, that represent the 3 remaining rice subpopulations and the largest admixed population, this collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to map resequencing data to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice., Measurement(s)genome • DNA • sequence_assembly • sequence feature annotation • physical mapTechnology Type(s)DNA sequencing • PacBio Sequel System • sequence assembly process • transposable elements annotation • Optical Mapping Illumina sequencingFactor Type(s)Oryza sativa cv. varietySample Characteristic - OrganismOryza sativa Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11950596

As the human population grows from 7.8 billion to 10 billion over the next 30 years, breeders must do everything possible to create crops that are highly productive and nutritious, while simultaneously having less of an environmental footprint. Rice will play a critical role in meeting this demand and thus, knowledge of the full repertoire of genetic diversity that exists in germplasm banks across the globe is required. To meet this demand, we describe the generation, validation and preliminary analyses of transposable element and long-range structural variation content of 12 near-gap-free reference genome sequences (RefSeqs) from representatives of 12 of 15 subpopulations of cultivated rice. When combined with 4 existing RefSeqs, that represent the 3 remaining rice subpopulations and the largest admixed population, this collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a pan-genome template to map resequencing data to detect virtually all standing natural variation that exists in the pan-cultivated rice genome.

To secure the world’s food supply it is essential that we improve our knowledge of the genetic underpinnings of complex agronomic traits. In this paper, we report our findings from performing trait prediction and association mapping using marker stability in diverse rice landraces. We used the least absolute shrinkage and selection operator as our marker selection algorithm, and considered twelve real agronomic traits and a hundred simulated traits using a population with approximately a hundred thousand markers. For trait prediction, we considered several statistical/machine learning methods. We found that some of the methods considered performed best when preselected markers using marker stability were used. However, our results also show that one might need to make a trade-off between model size and performance for some learning methods. For association mapping, we compared marker stability to the genome-wide efficient mixed-model analysis (GEMMA), and for the simulated traits, we found that marker stability significantly outperforms GEMMA. For the real traits, marker stability successfully identifies multiple associated markers, which often entail those selected by GEMMA. Further analysis of the markers selected for the real traits using marker stability showed that they are located in known quantitative trait loci (QTL) using the QTL Annotation Rice Online database. Furthermore, co-functional network prediction of the selected markers using RiceNet v2 also showed association to known controlling genes. We argue that a wide adoption of the marker stability approach for the prediction of agronomic traits and association mapping could improve global rice breeding efforts.

Modern rice cultivars are adapted to a range of environmental conditions and human preferences. At the root of this diversity is a marked genetic structure, owing to multiple foundation events. Admixture and recurrent introgression from wild sources have played upon this base to produce the myriad adaptations existing today. Genome-wide studies bring support to this idea, but understanding the history and nature of particular genetic adaptations requires the identification of specific patterns of genetic exchange. In this study, we explore the patterns of haplotype similarity along the genomes of a subset of rice cultivars available in the 3,000 Rice Genomes data set. We begin by establishing a custom method of classification based on a combination of dimensionality reduction and kernel density estimation. Through simulations, the behavior of this classifier is studied under scenarios of varying genetic divergence, admixture, and alien introgression. Finally, the method is applied to local haplotypes along the genome of a Core set of Asian Landraces. Taking the Japonica, Indica, and cAus groups as references, we find evidence of reciprocal introgressions covering 2.6% of reference genomes on average. Structured signals of introgression among reference accessions are discussed. We extend the analysis to elucidate the genetic structure of the group circum-Basmati: we delimit regions of Japonica, cAus, and Indica origin, as well as regions outlier to these groups (13% on average). Finally, the approach used highlights regions of partial to complete loss of structure that can be attributed to selective pressures during domestication.

Tolerance of anaerobic germination (AG) is a key trait in the development of direct seeded rice. Through rapid and sustained coleoptile elongation, AG tolerance enables robust seedling establishment under flooded conditions. Previous attempts to fine map and characterize AG2 (qAG7.1), a major centromere-spanning AG tolerance QTL, derived from the indica variety Ma-Zhan Red, have failed. Here, a novel approach of “enriched haplotype” genome-wide association study based on the Ma-Zhan Red haplotype in the AG2 region was successfully used to narrow down AG2 from more than 7 Mb to less than 0.7 Mb. The AG2 peak region contained 27 genes, including the Rc gene, responsible for red pericarp development in pigmented rice. Through comparative variant and transcriptome analysis between AG tolerant donors and susceptible accessions several candidate genes potentially controlling AG2 were identified, among them several regulatory genes. Genome-wide comparative transcriptome analysis suggested differential regulation of sugar metabolism, particularly trehalose metabolism, as well as differential regulation of cell wall modification and chloroplast development to be implicated in AG tolerance mechanisms.

The 3000 Rice Genomes Project generated a large dataset of genomic variation to the world’s most important crop, Oryza sativa L. Using the Burrows-Wheeler Aligner (BWA) and the Genome Analysis Toolkit (GATK) variant calling on this dataset, we identified ∼40 M single-nucleotide polymorphisms (SNPs). Five reference genomes of rice representing the major variety groups were used: Nipponbare (temperate japonica ), IR 64 ( indica ), 93–11 ( indica ), DJ 123 ( aus ), and Kasalath ( aus ). The results are accessible through the Rice SNP-Seek Database ( http://snp-seek.irri.org ) and through web services of the application programming interface (API). We incorporated legacy phenotypic and passport data for the sequenced varieties originating from the International Rice Genebank Collection Information System (IRGCIS) and gene models from several rice annotation projects. The massive genotypic data in SNP-Seek are stored using hierarchical data format 5 (HDF5) files for quick retrieval. Germplasm, phenotypic, and genomic data are stored in a relational database management system (RDBMS) using the Chado schema, allowing the use of controlled vocabularies from biological ontologies as query constraints in SNP-Seek. In this paper, we discuss the datasets stored in SNP-Seek, architecture of the database and web application, interoperability methodologies in place, and discuss a few use cases demonstrating the utility of SNP-Seek for diversity analysis and molecular breeding.

The advent of next generation sequencing, and more recently third generation sequencing, has enabled researchers to begin interrogating the genomic information of thousands of accessions of conserved genetic resources as well as cultivated varieties. Here, we describe recent results from the 3,000 Rice Genomes Project (3K RGP) and summarize a few of the projects for other crop species. The 3K RGP has served as the catalyst to create a digital rice genebank with the intent to sequence many more of the conserved accessions held in the International Rice Genebank Collection in the coming years. We are progressing with generating high quality reference builds for the 15 subpopulations defined by the 3K RG analyses. These along with reference builds of the wild relatives will allow access to the unique genomic regions specific to particular cultivated types and wild relatives. We have also begun efforts to sequence a further 10,000 accessions of rice in collaboration with partners in China. Yet, in-depth sequence data and initial comparative bioinformatic analyses are not enough to promote efficient use. Hence, high throughput phenomic screening in multiple environments, development of novel genetic populations, computational genetics and modeling will be necessary to understand the link between genotype to phenotype and its environmental control. The combination of these approaches underpinned by computational analyses will allow identification of novel genes and alleles that can be deployed into elite varieties for sustainable crop improvement.

We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/), which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs × 3 K rice lines) and web interface for convenient querying. The database allows quick retrieving of SNP alleles for all varieties in a given genome region, finding different alleles from predefined varieties and querying basic passport and morphological phenotypic information about sequenced rice lines. SNPs can be visualized together with the gene structures in JBrowse genome browser. Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.

Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence–absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding., Analyses of genetic variation and population structure based on over 3,000 cultivated rice (Oryza sativa) genomes reveal subpopulations that correlate with geographic location and patterns of introgression consistent with multiple rice domestication events.

We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org.

We analyzed functionality and relative distribution of genetic variants across the complete Oryza sativa genome, using the 40 million single nucleotide polymorphisms (SNPs) dataset from the 3,000 Rice Genomes Project (http://snp-seek.irri.org), the largest and highest density SNP collection for any higher plant. We have shown that the DNA-binding transcription factors (TFs) are the most conserved group of genes, whereas kinases and membrane-localized transporters are the most variable ones. TFs may be conserved because they belong to some of the most connected regulatory hubs that modulate transcription of vast downstream gene networks, whereas signaling kinases and transporters need to adapt rapidly to changing environmental conditions. In general, the observed profound patterns of nucleotide variability reveal functionally important genomic regions. As expected, nucleotide diversity is much higher in intergenic regions than within gene bodies (regions spanning gene models), and protein-coding sequences are more conserved than untranslated gene regions. We have observed a sharp decline in nucleotide diversity that begins at about 250 nucleotides upstream of the transcription start and reaches minimal diversity exactly at the transcription start. We found the transcription termination sites to have remarkably symmetrical patterns of SNP density, implying presence of functional sites near transcription termination. Also, nucleotide diversity was significantly lower near 3′ UTRs, the area rich with regulatory regions.

The global temperatures are predicted to rise due to climate change. However, knowledge on the mechanisms underlying the effect of high temperature (HT) on plant pathogen interaction is limited. We investigated the effect of elevated temperature on host phenotypic, biochemical and gene expression patterns in the rice-Magnaporthe oryzae (Mo) pathosystem using two genetic backgrounds, Co39 (Oryzae sativa-indica) and LTH (O. sativa-japonica) with (CO and LT) and without (Co39 and LTH) R gene (Pi54). After exposure to 28°C and 35°C the two genetic backgrounds showed contrasting responses to Mo. At 28°C, CO, Co39 and LTH displayed a more severe disease phenotype than LT. Surprisingly, CO became resistant to Mo after exposure to 35°C. CO and LT were used for further analysis to determine the defence related biochemical and transcriptome changes associated with HT induced resistance. Pre-exposure to 35°C triggered intense callose deposits and cell wall fluorescence of the attacked epidermal cells, as well as, increased hydrogen peroxide (H2O2) and salicylic acid (SA) levels. Transcriptional changes due to combined stress (35°C+Mo) were largely overridden by pathogen infection in both backgrounds, suggesting that the plants tended to shift their response to the pathogen. However, significant differences in global gene expression patterns occurred between CO and LT in response to both single (35°C and Mo) and double stress (35°C+Mo). Collectively, our results suggest that rice lines carrying Pi54 respond to Mo by rapid induction of callose and H2O2, and that these resistance mechanisms are amplified at HT. The relative difference in disease severity between CO and LT at 28°C suggests that the genetic background of japonica rice facilitates the function of Pi54 more than the background of indica rice. The phenotypic plasticity and gene expression differences between CO and LT reveal the presence of intricate background specific molecular signatures that may potentially influence adaptation to plant stresses.

We propose a notion of algebra of twisted chiral differential operators over algebraic manifolds with vanishing 1st Pontrjagin class. We show that such algebras possess families of modules depending on infinitely many complex parameters, which we classify in terms of the corresponding algebra of twisted differential operators. If the underlying manifold is a flag manifold, our construction recovers modules over an affine Lie algebra parameterized by opers over the Langlands dual Lie algebra. The spaces of global sections of “smallest” such modules are irreducible \({{\hat{{\mathfrak{g}}}}}\) -modules, and all irreducible \({{\mathfrak{g}}}\) -integrable \({{\hat{{\mathfrak{g}}}}}\) -modules at the critical level arise in this way.

The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools that can infer multiple origins. Misclassification of such individuals can lead to incorrect and costly misinterpretations of genomic data, primarily in disease studies and drug trials. We present an advanced tool to infer ancestry that can identify the biogeographic origins of highly mixed individuals. reAdmix is an online tool available at http://chcb.saban-chla.usc.edu/reAdmix/., presented at ISMB 2014, VariSIG