EU-OSTID: a collection of transposon insertional mutants for functional genomics in rice

Plant Functional Genomics Based on High-Throughput CRISPR Library Knockout Screening: A Perspective

Plant biology studies in the post-genome era have been focused on annotating genome sequences' functions. The established plant mutant collections have greatly accelerated functional genomics research in the past few decades. However, most plant genome sequences' roles and the underlying regulatory networks remain substantially unknown. Clustered, regularly interspaced short palindromic repeat (CRISPR)-associated systems are robust, versatile tools for manipulating plant genomes with various targeted DNA perturbations, providing an excellent opportunity for high-throughput interrogation of DNA elements' roles. This study compares methods frequently used for plant functional genomics and then discusses different DNA multi-targeted strategies to overcome gene redundancy using the CRISPR-Cas9 system. Next, this work summarizes recent reports using CRISPR libraries for high-throughput gene knockout and function discoveries in plants. Finally, this work envisions the future perspective of optimizing and leveraging CRISPR library screening in plant genomes' other uncharacterized DNA sequences.

Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration

BACKGROUND

Plants have the remarkable ability to generate callus, a pluripotent cell mass that acquires competence for subsequent tissue regeneration. Global chromatin remodeling is required for this cell fate transition, but how the process is regulated is not fully understood. Chromatin-enriched noncoding RNAs (cheRNAs) are thought to play important roles in maintaining chromatin state. However, whether cheRNAs participate in somatic cell regeneration in plants has not yet been clarified.

RESULTS

To uncover the characteristics and functions of cheRNAs during somatic cell reprogramming in plants, we systematically investigate cheRNAs during callus induction, proliferation and regeneration in rice. We identify 2284 cheRNAs, most of which are novel long non-coding RNAs or small nucleolar RNAs. These cheRNAs, which are highly conserved across plant species, shuttle between chromatin and the nucleoplasm during somatic cell regeneration. They positively regulate the expression of neighboring genes via specific RNA motifs, which may interact with DNA motifs around cheRNA loci. Large-scale mutant analysis shows that cheRNAs are associated with plant size and seed morphology. Further detailed functional investigation of two che-lncRNAs demonstrates that their loss of function impairs cell dedifferentiation and plant regeneration, highlighting the functions of cheRNAs in regulating the expression of neighboring genes via specific motifs. These findings support cis- regulatory roles of cheRNAs in influencing a variety of rice traits.

CONCLUSIONS

cheRNAs are a distinct subclass of regulatory non-coding RNAs that are required for somatic cell regeneration and regulate rice traits. Targeting cheRNAs has great potential for crop trait improvement and breeding in future.

SET DOMAIN GROUP 721 protein functions in saline-alkaline stress tolerance in the model rice variety Kitaake

To isolate the genetic locus responsible for saline-alkaline stress tolerance, we developed a high-throughput activation tagging-based T-DNA insertion mutagenesis method using the model rice (Oryza sativa L.) variety Kitaake. One of the activation-tagged insertion lines, activation tagging 7 (AC7), showed increased tolerance to saline-alkaline stress. This phenotype resulted from the overexpression of a gene that encodes a SET DOMAIN GROUP 721 protein with H3K4 methyltransferase activity. Transgenic plants overexpressing OsSDG721 showed saline-alkaline stress-tolerant phenotypes, along with increased leaf angle, advanced heading and ripening dates. By contrast, ossdg721 loss-of-function mutants showed increased sensitivity to saline-alkaline stress characterized by decreased survival rates and reduction in plant height, grain size, grain weight and leaf angle. RNA sequencing (RNA-seq) analysis of wild-type Kitaake and ossdg721 mutants indicated that OsSDG721 positively regulates the expression level of HIGH-AFFINITY POTASSIUM (K⁺ ) TRANSPORTER1;5 (OsHKT1;5), which encodes a Na⁺ -selective transporter that maintains K⁺ /Na⁺ homeostasis under salt stress. Furthermore, we showed that OsSDG721 binds to and deposits the H3K4me3 mark in the promoter and coding region of OsHKT1;5, thereby upregulating OsHKT1;5 expression under saline-alkaline stress. Overall, by generating Kitaake activation-tagging pools, we established that the H3K4 methyltransferase OsSDG721 enhances saline-alkaline stress tolerance in rice.

Era-like GTP protein gene expression in rice

The mutations are genetic changes in the genome sequences and have a significant role in biotechnology, genetics, and molecular biology even to find out the genome sequences of a cell DNA along with the viral RNA sequencing. The mutations are the alterations in DNA that may be natural or spontaneous and induced due to biochemical reactions or radiations which damage cell DNA. There is another cause of mutations which is known as transposons or jumping genes which can change their position in the genome during meiosis or DNA replication. The transposable elements can induce by self in the genome due to cellular and molecular mechanisms including hypermutation which caused the localization of transposable elements to move within the genome. The use of induced mutations for studying the mutagenesis in crop plants is very common as well as a promising method for screening crop plants with new and enhanced traits for the improvement of yield and production. The utilization of insertional mutations through transposons or jumping genes usually generates stable mutant alleles which are mostly tagged for the presence or absence of jumping genes or transposable elements. The transposable elements may be used for the identification of mutated genes in crop plants and even for the stable insertion of transposable elements in mutated crop plants. The guanine nucleotide-binding (GTP) proteins have an important role in inducing tolerance in rice plants to combat abiotic stress conditions.

Collection, preservation and distribution of Oryza genetic resources by the National Bioresource Project RICE (NBRP-RICE)

Biological resources are the basic infrastructure of bioscience research. Rice (Oryza sativa L.) is a good experimental model for research in cereal crops and monocots and includes important genetic materials used in breeding. The availability of genetic materials, including mutants, is important for rice research. In addition, Oryza species are attractive to researchers for both finding useful genes for breeding and for understanding the mechanism of genome evolution that enables wild plants to adapt to their own habitats. NBRP-RICE contributes to rice research by promoting the usage of genetic materials, especially wild Oryza accessions and mutant lines. Our activity includes collection, preservation and distribution of those materials and the provision of basic information on them, such as morphological and physiological traits and genomic information. In this review paper, we introduce the activities of NBRP-RICE and our database, Oryzabase, which facilitates the access to NBRP-RICE resources and their genomic sequences as well as the current situation of wild Oryza genome sequencing efforts by NBRP-RICE and other institutes.

Mutagenesis in Rice: The Basis for Breeding a New Super Plant

The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.

Insertional Mutagenesis Approaches and Their Use in Rice for Functional Genomics

Insertional mutagenesis is an indispensable tool for engendering a mutant population using exogenous DNA as the mutagen. The advancement in the next-generation sequencing platform has allowed for faster screening and analysis of generated mutated populations. Rice is a major staple crop for more than half of the world's population; however, the functions of most of the genes in its genome are yet to be analyzed. Various mutant populations represent extremely valuable resources in order to achieve this goal. Here, we have reviewed different insertional mutagenesis approaches that have been used in rice, and have discussed their principles, strengths, and limitations. Comparisons between transfer DNA (T-DNA), transposons, and entrapment tagging approaches have highlighted their utilization in functional genomics studies in rice. We have also summarised different forward and reverse genetics approaches used for screening of insertional mutant populations. Furthermore, we have compiled information from several efforts made using insertional mutagenesis approaches in rice. The information presented here would serve as a database for rice insertional mutagenesis populations. We have also included various examples which illustrate how these populations have been useful for rice functional genomics studies. The information provided here will be very helpful for future functional genomics studies in rice aimed at its genetic improvement.

Cas9/sgRNA-based genome editing and other reverse genetic approaches for functional genomic studies in rice

One of the important and direct ways of investigating the function of a gene is to characterize the phenotypic consequences associated with loss or gain-of-function of the corresponding gene. These mutagenesis strategies have been successfully deployed in Arabidopsis, and subsequently extended to crop species including rice. Researchers have made vast advancements in the area of rice genomics and functional genomics, as it is a diploid plant with a relatively smaller genome size unlike other cereals. The advent of rice genome research and the annotation of high-quality genome sequencing along with the developments in databases and computer searches have enabled the functional characterization of unknown genes in rice. Further, with the improvements in the efficiency of regeneration and transformation protocols, it has now become feasible to produce sizable mutant populations in indica rice varieties also. In this review, various mutagenesis methods, the current status of the mutant resources, limitations and strengths of insertional mutagenesis approaches and also results obtained with suitable screens for stress tolerance in rice are discussed. In addition, targeted genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) or Cas9/single-guide RNA system and its potential applications in generating transgene-free rice plants through genome engineering as an efficient alternative to classical transgenic technology are also discussed.

Development of iFOX-hunting as a functional genomic tool and demonstration of its use to identify early senescence-related genes in the polyploid Brassica napus

Functional genomic studies of many polyploid crops, including rapeseed (Brassica napus), are constrained by limited tool sets. Here we report development of a gain-of-function platform, termed 'iFOX (inducible Full-length cDNA OvereXpressor gene)-Hunting', for inducible expression of B. napus seed cDNAs in Arabidopsis. A Gateway-compatible plant gene expression vector containing a methoxyfenozide-inducible constitutive promoter for transgene expression was developed. This vector was used for cloning of random cDNAs from developing B. napus seeds and subsequent Agrobacterium-mediated transformation of Arabidopsis. The inducible promoter of this vector enabled identification of genes upon induction that are otherwise lethal when constitutively overexpressed and to control developmental timing of transgene expression. Evaluation of a subset of the resulting ~6000 Arabidopsis transformants revealed a high percentage of lines with full-length B. napus transgene insertions. Upon induction, numerous iFOX lines with visible phenotypes were identified, including one that displayed early leaf senescence. Phenotypic analysis of this line (rsl-1327) after methoxyfenozide induction indicated high degree of leaf chlorosis. The integrated B. napuscDNA was identified as a homolog of an Arabidopsis acyl-CoA binding protein (ACBP) gene designated BnACBP1-like. The early senescence phenotype conferred by BnACBP1-like was confirmed by constitutive expression of this gene in Arabidopsis and B. napus. Use of the inducible promoter in the iFOX line coupled with RNA-Seq analyses allowed mechanistic clues and a working model for the phenotype associated with BnACBP1-like expression. Our results demonstrate the utility of iFOX-Hunting as a tool for gene discovery and functional characterization of Brassica napus genome.

Whole Genome Characterization of a Few EMS-Induced Mutants of Upland Rice Variety Nagina 22 Reveals a Staggeringly High Frequency of SNPs Which Show High Phenotypic Plasticity Towards the Wild-Type

The Indian initiative, in creating mutant resources for the functional genomics in rice, has been instrumental in the development of 87,000 ethylmethanesulfonate (EMS)-induced mutants, of which 7,000 are in advanced generations. The mutants have been created in the background of Nagina 22, a popular drought- and heat-tolerant upland cultivar. As it is a pregreen revolution cultivar, as many as 573 dwarf mutants identified from this resource could be useful as an alternate source of dwarfing. A total of 541 mutants, including the macromutants and the trait-specific ones, obtained after appropriate screening, are being maintained in the mutant garden. Here, we report on the detailed characterizations of the 541 mutants based on the distinctness, uniformity, and stability (DUS) descriptors at two different locations. About 90% of the mutants were found to be similar to the wild type (WT) with high similarity index (>0.6) at both the locations. All 541 mutants were characterized for chlorophyll and epicuticular wax contents, while a subset of 84 mutants were characterized for their ionomes, namely, phosphorous, silicon, and chloride contents. Genotyping of these mutants with 54 genomewide simple sequence repeat (SSR) markers revealed 93% of the mutants to be either completely identical to WT or nearly identical with just one polymorphic locus. Whole genome resequencing (WGS) of four mutants, which have minimal differences in the SSR fingerprint pattern and DUS characters from the WT, revealed a staggeringly high number of single nucleotide polymorphisms (SNPs) on an average (16,453 per mutant) in the genic sequences. Of these, nearly 50% of the SNPs led to non-synonymous codons, while 30% resulted in synonymous codons. The number of insertions and deletions (InDels) varied from 898 to 2,595, with more than 80% of them being 1-2 bp long. Such a high number of SNPs could pose a serious challenge in identifying gene(s) governing the mutant phenotype by next generation sequencing-based mapping approaches such as Mutmap. From the WGS data of the WT and the mutants, we developed a genic resource of the WT with a novel analysis pipeline. The entire information about this resource along with the panicle architecture of the 493 mutants is made available in a mutant database EMSgardeN22 (http://14.139.229.201/EMSgardeN22).

Gene Overexpression Resources in Cereals for Functional Genomics and Discovery of Useful Genes

Identification and elucidation of functions of plant genes is valuable for both basic and applied research. In addition to natural variation in model plants, numerous loss-of-function resources have been produced by mutagenesis with chemicals, irradiation, or insertions of transposable elements or T-DNA. However, we may be unable to observe loss-of-function phenotypes for genes with functionally redundant homologs and for those essential for growth and development. To offset such disadvantages, gain-of-function transgenic resources have been exploited. Activation-tagged lines have been generated using obligatory overexpression of endogenous genes by random insertion of an enhancer. Recent progress in DNA sequencing technology and bioinformatics has enabled the preparation of genomewide collections of full-length cDNAs (fl-cDNAs) in some model species. Using the fl-cDNA clones, a novel gain-of-function strategy, Fl-cDNA OvereXpressor gene (FOX)-hunting system, has been developed. A mutant phenotype in a FOX line can be directly attributed to the overexpressed fl-cDNA. Investigating a large population of FOX lines could reveal important genes conferring favorable phenotypes for crop breeding. Alternatively, a unique loss-of-function approach Chimeric REpressor gene Silencing Technology (CRES-T) has been developed. In CRES-T, overexpression of a chimeric repressor, composed of the coding sequence of a transcription factor (TF) and short peptide designated as the repression domain, could interfere with the action of endogenous TF in plants. Although plant TFs usually consist of gene families, CRES-T is effective, in principle, even for the TFs with functional redundancy. In this review, we focus on the current status of the gene-overexpression strategies and resources for identifying and elucidating novel functions of cereal genes. We discuss the potential of these research tools for identifying useful genes and phenotypes for application in crop breeding.

Transposon Ds-Mediated Insertional Mutagenesis in Rice (Oryza sativa)

Rice (Oryza sativa) is the most important consumed staple food for a large and diverse population worldwide. Since databases of genomic sequences became available, functional genomics and genetic manipulations have been widely practiced in rice research communities. Insertional mutants are the most common genetic materials utilized to analyze gene function. To mutagenize rice genomes, we exploited the transpositional activity of an Activator/Dissociation (Ac/Ds) system in rice. To mobilize Ds in rice genomes, a maize Ac cDNA was expressed under the CaMV35S promoter, and a gene trap Ds was utilized to detect expression of host genes via the reporter gene GUS. Conventional transposon-mediated gene-tagging systems rely on genetic crossing and selection markers. Furthermore, the activities of transposases have to be monitored. By taking advantage of the fact that Ds becomes highly active during tissue culture, a plant regeneration system employing tissue culture was employed to generate a large Ds transposant population in rice. This system overcomes the requirement for markers and the monitoring of Ac activity. In the regenerated populations, more than 70% of the plant lines contained independent Ds insertions and 12% expressed GUS at seedling stages. This protocol describes the method for producing a Ds-mediated insertional population via tissue culture regeneration systems. © 2016 by John Wiley & Sons, Inc.

The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals

Plants are constantly exposed to a variety of biotic and abiotic stresses that reduce their fitness and performance. At the molecular level, the perception of extracellular stimuli and the subsequent activation of defense responses require a complex interplay of signaling cascades, in which protein phosphorylation plays a central role. Several studies have shown that some members of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family are involved in stress and developmental pathways. We report here a systematic analysis of the role of the members of this gene family by mutant phenotyping in the monocotyledon model plant rice, Oryza sativa. We have then targeted 176 of the ∼320 LRR-RLK genes (55.7%) and genotyped 288 mutant lines. Position of the insertion was confirmed in 128 lines corresponding to 100 LRR-RLK genes (31.6% of the entire family). All mutant lines harboring homozygous insertions have been screened for phenotypes under normal conditions and under various abiotic stresses. Mutant plants have been observed at several stages of growth, from seedlings in Petri dishes to flowering and grain filling under greenhouse conditions. Our results show that 37 of the LRR-RLK rice genes are potential targets for improvement especially in the generation of abiotic stress tolerant cereals.

High-throughput generation of an activation-tagged mutant library for functional genomic analyses in tobacco

Tobacco (Nicotiana tabacum L.) is an ideal model system for molecular biological and genetic studies. In this study, activation tagging was used to generate approximately 100,000 transgenic tobacco plants. Southern blot analysis indicated that there were 1.6 T-DNA inserts per line on average in our transformed population. The phenotypes observed include abnormalities in leaf and flower morphology, plant height, flowering time, branching, and fertility. Among 6,000 plants in the T0 generation, 57 displayed obvious phenotypes. Among 4,105 lines in the T1 generation, 311 displayed abnormal phenotypes. Fusion primer and nested integrated PCR was used to identify 963 independent genomic loci of T-DNA insertion sites in 1,257 T1 lines. The distribution of T-DNA insertions was non-uniform and correlated well with the predicted gene density along each chromosome. The insertions were biased toward genic regions and noncoding regions within 5 kb of a gene. Fifteen plants that showed the same phenotype as their parent with a dominant pattern in the T2 generation were chosen randomly to detect the expression levels of genes adjacent to the T-DNA integration sites by semi-quantitative RT-PCR. Fifteen candidate genes were identified. Activation was observed in 7 out of the 15 adjacent genes, including one that was located 13.1 kb away from the enhancer sequence. The activation-tagged population described in this paper will be a highly valuable resource for tobacco functional genomics research using both forward and reverse genetic approaches.

Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice

Background

Long noncoding RNAs (lncRNAs) play important roles in a wide range of biological processes in mammals and plants. However, the systematic examination of lncRNAs in plants lags behind that in mammals. Recently, lncRNAs have been identified in Arabidopsis and wheat; however, no systematic screening of potential lncRNAs has been reported for the rice genome.

Results

In this study, we perform whole transcriptome strand-specific RNA sequencing (ssRNA-seq) of samples from rice anthers, pistils, and seeds 5 days after pollination and from shoots 14 days after germination. Using these data, together with 40 available rice RNA-seq datasets, we systematically analyze rice lncRNAs and definitively identify lncRNAs that are involved in the reproductive process. The results show that rice lncRNAs have some different characteristics compared to those of Arabidopsis and mammals and are expressed in a highly tissue-specific or stage-specific manner. We further verify the functions of a set of lncRNAs that are preferentially expressed in reproductive stages and identify several lncRNAs as competing endogenous RNAs (ceRNAs), which sequester miR160 or miR164 in a type of target mimicry. More importantly, one lncRNA, XLOC_057324, is demonstrated to play a role in panicle development and fertility. We also develop a source of rice lncRNA-associated insertional mutants.

Conclusions

Genome-wide screening and functional analysis enabled the identification of a set of lncRNAs that are involved in the sexual reproduction of rice. The results also provide a source of lncRNAs and associated insertional mutants in rice.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0512-1) contains supplementary material, which is available to authorized users.

Discovery and characterization of two novel salt-tolerance genes in Puccinellia tenuiflora

Puccinellia tenuiflora is a monocotyledonous halophyte that is able to survive in extreme saline soil environments at an alkaline pH range of 9-10. In this study, we transformed full-length cDNAs of P. tenuiflora into Saccharomyces cerevisiae by using the full-length cDNA over-expressing gene-hunting system to identify novel salt-tolerance genes. In all, 32 yeast clones overexpressing P. tenuiflora cDNA were obtained by screening under NaCl stress conditions; of these, 31 clones showed stronger tolerance to NaCl and were amplified using polymerase chain reaction (PCR) and sequenced. Four novel genes encoding proteins with unknown function were identified; these genes had no homology with genes from higher plants. Of the four isolated genes, two that encoded proteins with two transmembrane domains showed the strongest resistance to 1.3 M NaCl. RT-PCR and northern blot analysis of P. tenuiflora cultured cells confirmed the endogenous NaCl-induced expression of the two proteins. Both of the proteins conferred better tolerance in yeasts to high salt, alkaline and osmotic conditions, some heavy metals and H2O2 stress. Thus, we inferred that the two novel proteins might alleviate oxidative and other stresses in P. tenuiflora.

International Consortium of Rice Mutagenesis: resources and beyond

Rice is one of the most important crops in the world. The rice community needs to cooperate and share efforts and resources so that we can understand the functions of rice genes, especially those with a role in important agronomical traits, for application in agricultural production. Mutation is a major source of genetic variation that can be used for studying gene function. We will present here the status of mutant collections affected in a random manner by physical/chemical and insertion mutageneses.As of early September 2013, a total of 447, 919 flanking sequence tags from rice mutant libraries with T-DNA, Ac/Ds, En/Spm, Tos17, nDART/aDART insertions have been collected and publicly available. From these, 336,262 sequences are precisely positioned on the japonica rice chromosomes, and 67.5% are in gene interval. We discuss the genome coverage and preference of the insertion, issues limiting the exchange and use of the current collections, as well as new and improved resources. We propose a call to renew all mutant populations as soon as possible. We also suggest that a common web portal should be established for ordering seeds.

Mutant resources for the functional analysis of the rice genome

Rice is one of the most important crops worldwide, both as a staple food and as a model system for genomic research. In order to systematically assign functions to all predicted genes in the rice genome, a large number of rice mutant lines, including those created by T-DNA insertion, Ds/dSpm tagging, Tos17 tagging, and chemical/irradiation mutagenesis, have been generated by groups around the world. In this study, we have reviewed the current status of mutant resources for functional analysis of the rice genome. A total of 246 566 flanking sequence tags from rice mutant libraries with T-DNA, Ds/dSpm, or Tos17 insertion have been collected and analyzed. The results show that, among 211 470 unique hits, inserts located in the genic region account for 68.16%, and 60.49% of nuclear genes contain at least one insertion. Currently, 57% of non-transposable-element-related genes in rice have insertional tags. In addition, chemical/irradiation-induced rice mutant libraries have contributed a lot to both gene identification and new technology for the identification of mutant sites. In this review, we summarize how these tools have been used to generate a large collection of mutants. In addition, we discuss the merits of classic mutation strategies. In order to achieve saturation of mutagenesis in rice, DNA targeting, and new resources like RiceFox for gene functional identification are reviewed from a perspective of the future generation of rice mutant resources.

Molecular biology of maize Ac/Ds elements: an overview

Maize Activator (Ac) is one of the prototype transposable elements of the hAT transposon superfamily, members of which were identified in plants, fungi, and animals. The autonomous Ac and nonautonomous Dissociation (Ds) elements are mobilized by the single transposase protein encoded by Ac. To date Ac/Ds transposons were shown to be functional in approximately 20 plant species and have become the most widely used transposable elements for gene tagging and functional genomics approaches in plants. In this chapter we review the biology, regulation, and transposition mechanism of Ac/Ds elements in maize and heterologous plants. We discuss the parameters that are known to influence the functionality and transposition efficiency of Ac/Ds transposons and need to be considered when designing Ac transposase expression constructs and Ds elements for application in heterologous plant species.

Ac-Ds solutions for rice insertion mutagenesis

Rice is the model plant for monocotyledons. Since the completion of the high-quality sequence of its genome, the international community is deploying efforts to identify the function of the 30-40,000 nontransposable element genes of rice. These efforts comprise the creation of large collections of rice mutants accessible to the international scientific community. In addition to loss of function mutants, insertion mutagenesis using Agrobacterium-mediated transformation and engineered mobile elements allows the identification of genes through enhancer or gene trapping or activation tagging. The maize transposable element Ac-Ds is known to be active in rice since the early 1990s and it does not interfere with endogenous rice transposons. This is the guaranty that induced mutation obtained with the mobility of the Ds element will be stable when the source of Ac transposase is removed from the mutated genome. In this paper, we describe single- or double-component T-DNA constructs that have been used to introduce a functional Ac-Ds system in rice and allowed the generation and selection of different type of Ds insertion mutations in the rice genome.

Genome walking in eukaryotes

Genome walking is a molecular procedure for the direct identification of nucleotide sequences from purified genomes. The only requirement is the availability of a known nucleotide sequence from which to start. Several genome walking methods have been developed in the last 20 years, with continuous improvements added to the first basic strategies, including the recent coupling with next generation sequencing technologies. This review focuses on the use of genome walking strategies in several aspects of the study of eukaryotic genomes. In a first part, the analysis of the numerous strategies available is reported. The technical aspects involved in genome walking are particularly intriguing, also because they represent the synthesis of the talent, the fantasy and the intelligence of several scientists. Applications in which genome walking can be employed are systematically examined in the second part of the review, showing the large potentiality of this technique, including not only the simple identification of nucleotide sequences but also the analysis of large collections of mutants obtained from the insertion of DNA of viral origin, transposons and transfer DNA (T-DNA) constructs. The enormous amount of data obtained indicates that genome walking, with its large range of applicability, multiplicity of strategies and recent developments, will continue to have much to offer for the rapid identification of unknown sequences in several fields of genomic research.

Rice functional genomics research: progress and implications for crop genetic improvement

Rice is a staple food crop and has become a reference of monocot plant for functional genomic research. With the availability of high quality rice genome sequence, there has been rapid accumulation of functional genomic resources, including: large mutant libraries by T-DNA insertion, transposon tagging, and chemical mutagenesis; global expression profiles of the genes in the entire life cycle of rice growth and development; full-length cDNAs for both indica and japonica rice; sequences from resequencing large numbers of diverse germplasm accessions. Such resource development has greatly accelerated gene cloning. By the end of 2010, over 600 genes had been cloned using various methods. Many of the genes control agriculturally useful traits such as yield, grain quality, resistances to biotic and abiotic stresses, and nutrient-use efficiency, thus have potential utility in crop genetic improvement. This review was aimed to provide a comprehensive summary of such progress. We also presented our perspective for future studies.

RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function

Identification of gene function is important not only for basic research but also for applied science, especially with regard to improvements in crop production. For rapid and efficient elucidation of useful traits, we developed a system named FOX hunting (Full-length cDNA Over-eXpressor gene hunting) using full-length cDNAs (fl-cDNAs). A heterologous expression approach provides a solution for the high-throughput characterization of gene functions in agricultural plant species. Since fl-cDNAs contain all the information of functional mRNAs and proteins, we introduced rice fl-cDNAs into Arabidopsis plants for systematic gain-of-function mutation. We generated >30,000 independent Arabidopsis transgenic lines expressing rice fl-cDNAs (rice FOX Arabidopsis mutant lines). These rice FOX Arabidopsis lines were screened systematically for various criteria such as morphology, photosynthesis, UV resistance, element composition, plant hormone profile, metabolite profile/fingerprinting, bacterial resistance, and heat and salt tolerance. The information obtained from these screenings was compiled into a database named 'RiceFOX'. This database contains around 18,000 records of rice FOX Arabidopsis lines and allows users to search against all the observed results, ranging from morphological to invisible traits. The number of searchable items is approximately 100; moreover, the rice FOX Arabidopsis lines can be searched by rice and Arabidopsis gene/protein identifiers, sequence similarity to the introduced rice fl-cDNA and traits. The RiceFOX database is available at http://ricefox.psc.riken.jp/.

FOX-superroots of Lotus corniculatus, overexpressing Arabidopsis full-length cDNA, show stable variations in morphological traits

Using the full-length cDNA overexpressor (FOX) gene-hunting system, we have generated 130 Arabidopsis FOX-superroot lines in bird's-foot trefoil (Lotus corniculatus) for the systematic functional analysis of genes expressed in roots and for the selection of induced mutants with interesting root growth characteristics. We used the Arabidopsis-FOX Agrobacterium library (constructed by ligating pBIG2113SF) for the Agrobacterium-mediated transformation of superroots (SR) and the subsequent selection of gain-of-function mutants with ectopically expressed Arabidopsis genes. The original superroot culture of L. corniculatus is a unique host system displaying fast root growth in vitro, allowing continuous root cloning, direct somatic embryogenesis and mass regeneration of plants under entirely hormone-free culture conditions. Several of the Arabidopsis FOX-superroot lines show interesting deviations from normal growth and morphology of roots from SR-plants, such as differences in pigmentation, growth rate, length or diameter. Some of these mutations are of potential agricultural interest. Genomic PCR analysis revealed that 100 (76.9%) out of the 130 transgenic lines showed the amplification of single fragments. Sequence analysis of the PCR fragments from these 100 lines identified full-length cDNA in 74 of them. Forty-three out of 74 full-length cDNA carried known genes. The Arabidopsis FOX-superroot lines of L. corniculatus, produced in this study, expand the FOX hunting system and provide a new tool for the genetic analysis and control of root growth in a leguminous forage plant.

Enhancer trapping in plants

Advances in sequencing technology have led to the availability of complete genome sequences of many different plant species. In order to make sense of this deluge of information, functional genomics efforts have been intensified on many fronts. With improvements in plant transformation technologies, T-DNA and/or transposon-based gene and enhancer-tagged populations in various crop species are being developed to augment functional annotation of genes and also to help clone important genes. State-of-the-art cloning and sequencing technologies, which would help identify T-DNA or transposon junction sequences in large genomes, have also been initiated. This chapter gives a brief history of enhancer trapping and then proceeds to describe gene and enhancer tagging in plants. The significance of reporter gene fusion populations in plant genomics, especially in important cereal crops, is discussed.

Transposition and target preferences of an active nonautonomous DNA transposon nDart1 and its relatives belonging to the hAT superfamily in rice

The nonautonomous nDart1 element in the hAT superfamily is one of a few active DNA transposons in rice. Its transposition can be induced by crossing with a line containing an active autonomous element, aDart1, and stabilized by segregating aDart1. No somaclonal variation should occur in nDart1-promoted gene tagging because no tissue culture is involved in nDart1 activation. By transposon display analysis, we examined the activities of nDart1-related elements in the selfed progeny of a mutable virescent pyl-v plant containing aDart1. Although various nDart1-related elements are present in the rice genome, only nDart1-3 subgroup elements, nDart1-0 and nDart1-3 in particular, were found to be transposed frequently and integrated into various sites almost all over the genome, and a fraction of the transposed elements were found to be transmitted to the next generation. More than half of the newly integrated elements were identified as nDart1-0. Analysis of the newly inserted sites revealed that the nDart1-3 subgroup elements were predominantly integrated into single-copy regions. More than 60% of the transposed elements were inserted into the genic regions that comprise putative coding regions and their 0.5-kb flanking segments, and approximately two-thirds of them were within the 0.5-kb area in front of the putative initiation codons, i.e., promoter-proximal genic regions. These characteristic features of nDart1-3 subgroup elements seem to be suitable for developing an efficient and somaclonal variation-free gene tagging system for rice functional genomics.

Assigning biological functions to rice genes by genome annotation, expression analysis and mutagenesis

Rice is the first cereal genome to be completely sequenced. Since the completion of its genome sequencing, considerable progress has been made in multiple areas including the whole genome annotation, gene expression profiling, mutant collection, etc. Here, we summarize the current status of rice genome annotation and review the methodology of assigning biological functions to hundreds of thousands of rice genes as well as discuss the major limitations and the future perspective in rice functional genomics. Available data analysis shows that the rice genome encodes around 32,000 protein-coding genes. Expression analysis revealed at least 31,000 genes with expression evidence from full-length cDNA/EST collection or other transcript profiling. In addition, we have summarized various strategies to generate mutant population including natural, physical, chemical, T-DNA, transposon/retrotransposon or gene silencing based mutagenesis. Currently, more than 1 million of mutants have been generated and 27,551 of them have their flanking sequence tags. To assign biological functions to hundreds of thousands of rice genes, global co-operations are required, various genetic resources should be more easily accessible and diverse data from transcriptomics, proteomics, epigenetics, comparative genomics and bioinformatics should be integrated to better understand the functions of these genes and their regulatory mechanisms.

Natural and artificial mutants as valuable resources for functional genomics and molecular breeding

With the completion of rice genome sequencing, large collection of expression data and the great efforts in annotating rice genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. In this study, we have reviewed currently employed tools to generate such mutant populations. These tools include natural, physical, chemical, tissue culture, T-DNA, transposon or gene silencing based mutagenesis. We also reviewed how these tools were used to generate a large collection of mutants and how these mutants can be screened and detected for functional analysis of a gene. The data suggested that the current population of mutants might be large enough to tag all predicted genes. However, the collection of flanking sequencing tags (FSTs) is limited due to the relatively higher cost. Thus, we have proposed a new strategy to generate gene-silencing mutants at the genome-wide level. Due to the large collection of insertion mutants, the next step to rice functional genomics should be focusing on functional characterization of tagged genes by detailed survey of corresponding mutants. Additionally, we also evaluated the utilization of these mutants as valuable resources for molecular breeding.

Construction and application of efficient Ac-Ds transposon tagging vectors in rice

Transposons are effective mutagens alternative to T-DNA for the generation of insertional mutants in many plant species including those whose transformation is inefficient. The current strategies of transposon tagging are usually slow and labor-intensive and yield low frequency of tagged lines. We have constructed a series of transposon tagging vectors based on three approaches: (i) AcTPase controlled by glucocorticoid binding domain/VP16 acidic activation domain/Gal4 DNA-binding domain (GVG) chemical-inducible expression system; (ii) deletion of AcTPase via Cre-lox site-specific recombination that was initially triggered by Ds excision; and (iii) suppression of early transposition events in transformed rice callus through a dual-functional hygromycin resistance gene in a novel Ds element (HPT-Ds). We tested these vectors in transgenic rice and characterized the transposition events. Our results showed that these vectors are useful resources for functional genomics of rice and other crop plants. The vectors are freely available for the community.

[Identification and genetic analysis of pale-green mutant caused by Ds insertion in rice]

Ac/Ds insertion mutation was thought to be one of the powerful tools for identifying gene function in rice. In this study, the rice mutant with pale-green leaves was isolated from the population of Ds-T-DNA and Ac-T-DNA transgenic homozygote in a japonica rice variety Zhonghua 11. The leaves of the mutant turned to be pale-green at three-leaf stage. This mutant was capable of growing slowly and maturing under low-light conditions, but, rapidly died under natural light conditions. The analysis of the photosynthetic activity characteristics by measuring chlorophyll fluorescence in vivo suggested that the mutant was a typical photo-inhibitory mutant. Genetic analysis demonstrated that the mutation was the recessive one resulted from Ds insertion.

Genetic technologies for the identification of plant genes controlling environmental stress responses

Abiotic conditions such as light, temperature, water availability and soil parameters determine plant growth and development. The adaptation of plants to extreme environments or to sudden changes in their growth conditions is controlled by a well balanced, genetically determined signalling system, which is still far from being understood. The identification and characterisation of plant genes which control responses to environmental stresses is an essential step to elucidate the complex regulatory network, which determines stress tolerance. Here, we review the genetic approaches, which have been used with success to identify plant genes which control responses to different abiotic stress factors. We describe strategies and concepts for forward and reverse genetic screens, conventional and insertion mutagenesis, TILLING, gene tagging, promoter trapping, activation mutagenesis and cDNA library transfer. The utility of the various genetic approaches in plant stress research we review is illustrated by several published examples.

Phenome analysis in plant species using loss-of-function and gain-of-function mutants

Analysis of genetic mutations is one of the most effective ways to investigate gene function. We now have methods that allow for mass production of mutant lines and cells in a variety of model species. Recently, large numbers of mutant lines have been generated by both 'loss-of-function' and 'gain-of-function' techniques. In parallel, phenotypic information covering various mutant resources has been acquired and released in web-based databases. As a result, significant progress in comprehensive phenotype analysis is being made through the use of these tools. Arabidopsis and rice are two major model plant species in which genome sequencing projects have been completed. Arabidopsis is the most widely used experimental plant, with a large number of mutant resources and several examples of systematic phenotype analysis. Rice is a major crop species and is used as a model plant, with an increasing number of mutant resources. Other plant species are also being employed in functional genetics research. In this review, the present status of mutant resources for large-scale studies of gene function in plant research and the current perspective on using loss-of-function and gain-of-function mutants in phenome research will be discussed.

Studies on rice seed quality through analysis of a large-scale T-DNA insertion population

A rice (Oryza sativa) T-DNA insertion population, which included more than 63 000 independent transgenic lines and 8 840 identified flanking sequence tags (FSTs) that were mapped onto the rice genome, was developed to systemically study the rice seed quality control. Genome-wide analysis of the FST distribution showed that T-DNA insertions were positively correlated with expressed genes, but negatively with transposable elements and small RNAs. In addition, the recovered T-DNAs were preferentially located at the untranslated region of the expressed genes. More than 11 000 putative homozygous lines were obtained through multi-generations of planting and resistance screening, and measurement of seed quality of around half of them, including the contents of starch, amylose, protein and fat, with a nondestructive near-infrared spectroscopy method, identified 551 mutants with unique or multiple altered parameters of seed quality. Analysis of the corresponding FSTs showed that genes participating in diverse functions, including metabolic processes and transcriptional regulation, were involved, indicating that seed quality is regulated by a complex network.

Systematic approaches to using the FOX hunting system to identify useful rice genes

Ectopic gene expression, or the gain-of-function approach, has the advantage that once the function of a gene is known the gene can be transferred to many different plants by transformation. We previously reported a method, called FOX hunting, that involves ectopic expression of Arabidopsis full-length cDNAs in Arabidopsis to systematically generate gain-of-function mutants. This technology is most beneficial for generating a heterologous gene resource for analysis of useful plant gene functions. As an initial model we generated more than 23,000 independent Arabidopsis transgenic lines that expressed rice fl-cDNAs (Rice FOX Arabidopsis lines). The short generation time and rapid and efficient transformation frequency of Arabidopsis enabled the functions of the rice genes to be analyzed rapidly. We screened rice FOX Arabidopsis lines for alterations in morphology, photosynthesis, element accumulation, pigment accumulation, hormone profiles, secondary metabolites, pathogen resistance, salt tolerance, UV signaling, high light tolerance, and heat stress tolerance. Some of the mutant phenotypes displayed by rice FOX Arabidopsis lines resulted from the expression of rice genes that had no homologs in Arabidopsis. This result demonstrated that rice fl-cDNAs could be used to introduce new gene functions in Arabidopsis. Furthermore, these findings showed that rice gene function could be analyzed by employing Arabidopsis as a heterologous host. This technology provides a framework for the analysis of plant gene function in a heterologous host and of plant improvement by using heterologous gene resources.

Generation of a 3D indexed Petunia insertion database for reverse genetics

BLAST searchable databases containing insertion flanking sequences have revolutionized reverse genetics in plant research. The development of such databases has so far been limited to a small number of model species and normally requires extensive labour input. Here we describe a highly efficient and widely applicable method that we adapted to identify unique transposon-flanking genomic sequences in Petunia. The procedure is based on a multi-dimensional pooling strategy for the collection of DNA samples; up to thousands of different templates are amplified from each of the DNA pools separately, and knowledge of their source is safeguarded by the use of pool-specific (sample) identification tags in one of the amplification primers. All products are combined into a single sample that is subsequently used as a template for unidirectional pyrosequencing. Computational analysis of the clustered sequence output allows automatic assignment of sequences to individual DNA sources. We have amplified and analysed transposon-flanking sequences from a Petunia transposon insertion library of 1000 individuals. Using 30 DNA isolations, 70 PCR reactions and two GS20 sequencing runs, we were able to allocate around 10 000 transposon flanking sequences to specific plants in the library. These sequences have been organized in a database that can be BLAST-searched for insertions into genes of interest. As a proof of concept, we have performed an in silico screen for insertions into members of the NAM/NAC transcription factor family. All in silico-predicted transposon insertions into members of this family could be confirmed in planta.

A versatile transposon-based activation tag vector system for functional genomics in cereals and other monocot plants

Transposon insertional mutagenesis is an effective alternative to T-DNA mutagenesis when transformation through tissue culture is inefficient as is the case for many crop species. When used as activation tags, transposons can be exploited to generate novel gain-of-function phenotypes without transformation and are of particular value in the study of polyploid plants where gene knockouts will not have phenotypes. We have developed an in cis-activation-tagging Ac-Ds transposon system in which a T-DNA vector carries a Dissociation (Ds) element containing 4x cauliflower mosaic virus enhancers along with the Activator (Ac) transposase gene. Stable Ds insertions were selected using green fluorescent protein and red fluorescent protein genes driven by promoters that are functional in maize (Zea mays) and rice (Oryza sativa). The system has been tested in rice, where 638 stable Ds insertions were selected from an initial set of 26 primary transformants. By analysis of 311 flanking sequences mapped to the rice genome, we could demonstrate the wide distribution of the elements over the rice chromosomes. Enhanced expression of rice genes adjacent to Ds insertions was detected in the insertion lines using semiquantitative reverse transcription-PCR method. The in cis-two-element vector system requires minimal number of primary transformants and eliminates the need for crossing, while the use of fluorescent markers instead of antibiotic or herbicide resistance increases the applicability to other plants and eliminates problems with escapes. Because Ac-Ds has been shown to transpose widely in the plant kingdom, the activation vector system developed in this study should be of utility more generally to other monocots.

Rice molecular breeding laboratories in the genomics era: Current status and future considerations

Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information-coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools-provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to "bridge the application gap" between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs.

The Rice Annotation Project Database (RAP-DB): 2008 update

The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

Analysis of gene-trap Ds rice populations in Korea

Insertional mutagen-mediated gene tagging populations have been essential resources for analyzing the function of plant genes. In rice, maize transposable elements have been successfully utilized to produce transposant populations. However, many generations and substantial field space are required to obtain a sufficiently sized transposant population. In rice, the japonica and indica subspecies are phenotypically and genetically divergent. Here, callus cultures with seeds carrying Ac and Ds were used to produce 89,700 lines of Dongjin, a japonica cultivar, and 6,200 lines of MGRI079, whose genome is composed of a mixture of the genetic backgrounds of japonica and indica. Of the more than 3,000 lines examined, 67% had Ds elements. Among the Ds-carrying lines, 81% of Dongjin and 63% of MGRI079 contained transposed Ds, with an average of around 2.0 copies. By examining more than 15,000 lines, it was found that 12% expressed the reporter gene GUS during the early-seedling stage. GUS was expressed in root hairs and crown root initials at estimated frequencies of 0.78% and 0.34%, respectively. The 5,271 analyzed Ds loci were found to be randomly distributed over all of the rice chromosomes.

A genome-wide gain-of function analysis of rice genes using the FOX-hunting system

The latest report has estimated the number of rice genes to be approximately 32,000. To elucidate the functions of a large population of rice genes and to search efficiently for agriculturally useful genes, we have been taking advantage of the Full-length cDNA Over-eXpresser (FOX) gene-hunting system. This system is very useful for analyzing various gain-of-function phenotypes from large populations of transgenic plants overexpressing cDNAs of interest and others with unknown or important functions. We collected the plasmid DNAs of 13,980 independent full-length cDNA (FL-cDNA) clones to produce a FOX library by placing individual cDNAs under the control of the maize Ubiquitin-1 promoter. The FOX library was transformed into rice by Agrobacterium-mediated high-speed transformation. So far, we have generated approximately 12,000 FOX-rice lines. Genomic PCR analysis indicated that the average number of FL-cDNAs introduced into individual lines was 1.04. Sequencing analysis of the PCR fragments carrying FL-cDNAs from 8615 FOX-rice lines identified FL-cDNAs in 8225 lines, and a database search classified the cDNAs into 5462 independent ones. Approximately 16.6% of FOX-rice lines examined showed altered growth or morphological characteristics. Three super-dwarf mutants overexpressed a novel gibberellin 2-oxidase gene,confirming the importance of this system. We also show here the other morphological alterations caused by individual FL-cDNA expression. These dominant phenotypes should be valuable indicators for gene discovery and functional analysis.

A rice phenomics study--phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population

With the completion of the rice genome sequencing project, the next major challenge is the large-scale determination of gene function. As an important crop and a model organism, rice provides major insights into gene functions important for crop growth or production. Phenomics with detailed information about tagged populations provides a good tool for functional genomics analysis. By a T-DNA insertional mutagenesis approach, we have generated a rice mutant population containing 55,000 promoter trap and gene activation or knockout lines. Approximately 20,000 of these lines have known integration sites. The T0 and T1 plants were grown in net "houses" for two cropping seasons each year since 2003, with the mutant phenotypes recorded. Detailed data describing growth and development of these plants, in 11 categories and 65 subcategories, over the entire four-month growing season are available in a searchable database, along with the genetic segregation information and flanking sequence data. With the detailed data from more than 20,000 T1 lines and 12 plants per line, we estimated the mutation rates of the T1 population, as well the frequency of the dominant T0 mutants. The correlations among different mutation phenotypes are also calculated. Together, the information about mutant lines, their integration sites, and the phenotypes make this collection, the Taiwan Rice Insertion Mutants (TRIM), a good resource for rice phenomics study. Ten T2 seeds per line can be distributed to researchers upon request.

Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice

Several approaches have recently been adopted to improve Agrobacterium-mediated transformation of rice, both to generate the large number of T-DNA insertion plants needed for functional analysis of the rice genome, and for production of rice with additional agronomical value. However, about 3 months of in vitro culture is still required for isolation of transgenic rice plants. Here, we report the competency of scutellum tissue from 1-day pre-cultured seeds for Agrobacterium-mediated transformation. Furthermore, early infection of rice seeds with Agrobacterium enhanced efficient selection of transformed calli. Using our system, we successfully regenerated transgenic rice plantlets within a month of the start of the aseptic culture of mature seeds. Our new system should reduce the somaclonal variation accompanying prolonged culture of rice cells in the dedifferentiated state and facilitate the molecular breeding of rice.

OryGenesDB: a database for rice reverse genetics

Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics. We have developed OryGenesDB (), a database dedicated to rice reverse genetics. Insertion mutants of rice genes are catalogued by Flanking Sequence Tag (FST) information that can be readily accessed by this database. Our database presently contains 44166 FSTs generated by most of the rice insertional mutagenesis projects. The OryGenesDB genome browser is based on the powerful Generic Genome Browser (GGB) developed in the framework of the Generic Model Organism Project (GMOD). The main interface of our web site displays search and analysis interfaces to look for insertions in any candidate gene of interest. Several starting points can be used to exhaustively retrieve the insertions positions and associated genomic information using blast, keywords or gene name search. The toolbox integrated in our database also includes an ‘anchoring’ option that allows immediate mapping and visualization of up to 50 nucleic acid sequences in the rice Genome Browser of OryGenesDB. As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors.