Study Of Natural Variation Research Articles

Gene Regulatory Networks Mediating Cold Acclimation: The CBF Pathway.

Under low nonfreezing temperature conditions, plants from temperate climates undergo physiological and biochemical adjustments that increase their tolerance to freezing temperatures. This response, termed cold acclimation, is largely regulated by changes in gene expression. Molecular and genetic studies have identified a small family of transcription factors, called C-repeat binding factors (CBFs), as key regulators of the transcriptomic rearrangement that leads to cold acclimation. The function of these proteins is tightly controlled, and an inadequate supply of CBF activity may be detrimental to the plant. Accumulated evidence has revealed an extremely intricate network of positive and negative regulators of cold acclimation that coalesce at the level of CBF promoters constituting a central hub where multiple internal and external signals are integrated. Moreover, CBF expression is also controlled at posttranscriptional and posttranslational levels further refining CBF regulation. Recently, natural variation studies in Arabidopsis have demonstrated that mutations resulting in changes in CBF expression have an adaptive value for wild populations. Intriguingly, CBF genes are also present in plant species that do not cold acclimate, which suggest that they may also have additional functions. For instance, CBFs are required for some cold-related abiotic stress responses. In addition, their involvement in plant development deserves further study. Although more studies are necessary to fully harness CBF biotechnological potential, these transcription factors are meant to be key for a rational design of crops with enhanced tolerance to abiotic stress.

Effects of seasonality and environmental gradients on Spartina alterniflora allometry and primary production.

Predictions of how salt marsh primary production and carbon storage will respond to environmental change can be improved through detailed datasets documenting responses to real‐world environmental variation. To address a shortage of detailed studies of natural variation, we examined drivers of Spartina alterniflora stem allometry and productivity in seven marshes across three regions in southern Louisiana. Live‐stem allometry varied spatially and seasonally, generally with short stems weighing more (and tall stems weighing less) in the summer and fall, differences that persist even after correcting for flowering. Strong predictive relationships exist between allometry parameters representing emergent stem mass and mass accumulation rates, suggesting that S. alterniflora populations navigate a trade‐off between larger mass at emergence and faster rates of biomass accumulation. Aboveground production and belowground production were calculated using five and four approaches, respectively. End‐of‐season aboveground biomass was a poor proxy for increment‐based production measures. Aboveground production (Smalley) ranged from 390 to 3,350 g m−2 year−1 across all marshes and years. Belowground production (max–min) was on average three times higher than aboveground; total production ranged from 1,400 to 8,500 g m−2 year−1. Above‐ and belowground production were both positively correlated with dissolved nutrient concentrations and negatively correlated to salinity. Synthesis: Interannual variation in water quality is sufficient to drive above‐ and belowground productivity. The positive relationship between nutrients and belowground production indicates that inputs of nutrients and freshwater may increase salt marsh carbon storage and ecosystem resilience to sea level rise.

History of research on C. elegans and other free-living nematodes as model organisms.

The nematode Caenorhabditis elegans is now a major model organism in biology. The choice of Sydney Brenner to adopt this species in the mid-1960s and the success of his team in raising it to a model organism status have been told (http://www.wormbook.org/toc_wormhistory.html; Brenner, 2001; Ankeny, 2001). Here we review the pre-Brenner history of the use of free-living nematodes as models for general questions in biology. We focus on the period that started in 1899 with the first publication of Emile Maupas mentioning Rhabditis elegans and ended in 1974 with the first publications by Brenner. A common thread in this period, aided by the variety in modes of reproduction of different nematode species, is found in studies of meiosis, fertilization, heredity, and sex determination. Maupas in his 1900 opus on reproduction had already chosen C. elegans as the species of reference. Hikokura Honda determined its hermaphrodite chromosomal content in 1925. C. elegans was again isolated and chosen as a main subject by Victor Nigon in the 1940-50s. Nigon mastered crosses between C. elegans hermaphrodites and males, described the meiotic behavior of chromosomes in XX hermaphrodites and X0 males and, using tetraploids, correctly inferred that sex was determined by X chromosome to autosome dosage. With Ellsworth Dougherty, Nigon isolated and studied a C. briggsae body size mutant and a C. elegans slow growth mutant. Dougherty and his team devoted most of their work to finding a defined culture medium to screen for physiological mutants, focusing on C. briggsae. With Helene Fatt, Dougherty also performed the first genetic study of natural variation in C. elegans, concerning the difference in heat resistance of the Bergerac and Bristol strains. Jean Brun, a student of Nigon, performed a long and remarkable experiment in acclimatization of C. elegans Bergerac to higher temperatures, the significance of which remains to be clarified.

A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina

The growing collection of sequenced or genotyped Arabidopsis thaliana accessions includes mostly individuals from the native Eurasian and N. African range and introduced North American populations. Here, we describe the genetic and phenotypic diversity, along with habitats and life history, of A.thaliana plants collected at the southernmost end of its worldwide distribution. Seed samples were harvested from plants growing in four sites within a ~3500-km2 -area in Patagonia, Argentina, and represent the first germplasm to be collected in South America for this species. Whole-genome resequencing revealed that plants from the four sites and a Patagonia herbarium specimen collected in 1967 formed a single haplogroup (Pat), indicating that the phenotypic variation observed in the field reflected plastic responses to the environment. admixture and principal components analyses suggest that the ancestor of the Pat haplogroup either came from Italy or the Balkan/Caucasus regions of Eurasia. In the laboratory, plants from the Pat haplogroup were hyposensitive to continuous red (Rc) and shade light, with corresponding changes in the expression of phytochrome signalling genes. Pat had higher PIF3 and PIF5 and lower HY5 expression under Rc light; and lower expression of PIL1, ATHB2 and HFR1 under shade compared to Col-0. In addition, Pat plants had a strong vernalization requirement associated with high levels of FLC expression. We conclude that including Pat in studies of natural variation and in comparison with other introduced populations will provide additional information for association studies and allow for a more detailed assessment of the demographic events following colonization.

Honorary Lifetime Membership Award: Johanna Schmitt.

Previous articleNext article FreeHonorary Lifetime Membership Award: Johanna SchmittPDFPDF PLUSFull Text Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinked InRedditEmailQR Code SectionsMoreThe American Society of Naturalists is pleased to announce that Johanna Schmitt—Annie to all of us who know her—has been named an Honorary Lifetime Member of the society. Annie received her doctorate from Stanford University, conducted a postdoctoral fellowship at Duke University, and then joined the faculty of the Ecology and Evolutionary Biology Department at Brown University. She is now a professor at the University of California, Davis, and is a past president of both the Society for the Study of Evolution and the American Society of Naturalists (ASN). Annie has received numerous awards, including election to the National Academy of Sciences and the American Academy of Arts and Sciences.Annie’s research focuses on adaptation in heterogeneous and complex environments, with a strong focus on the genetic, physiological, and ecological mechanisms underlying plant adaptation. Her areas of research inquiry include the adaptive significance of maternal effects and the shade-avoidance syndrome, phenotypic plasticity and reaction norm evolution, genetic controls on flowering time in seasonally variable settings, and most recently, the potential for adaptation under a changing climate. Her groundbreaking work in these areas provided empirical demonstrations of adaptive plasticity, shaped subsequent research on the evolution of adaptive strategies, and demonstrated the explanatory power of integrating genetic and genomic information and approaches into ecologically relevant field studies.Among many seminal studies, she performed a series of experiments providing support for functional and ecological hypotheses related to the adaptive significance of shade-avoidance responses. The shade-avoidance network enables plants to perceive light-quality cues of neighbor proximity and elicits a suite of integrated phenotypic responses, such as increased stem elongation and accelerated flowering. Based on known controls of shade-avoidance phenotypes, Annie’s studies used either genetic or environmental “engineering” to elicit diverse shade-avoidance phenotypes. She used genetic manipulations of photoreceptors in tobacco and Brassica rapa (which effectively expressed canalized elongation phenotypes) to test the functional hypothesis that elongation enhances performance under high-density settings but reduces fitness under low plant density (Schmitt et al. 1995, American Naturalist 146:937–953). This study provided rare empirical evidence that plasticity is adaptive, that is, that the expression of alternative phenotypes across divergent microsites improves fitness. Subsequent studies in her lab used elegant manipulations of light quality to either enhance or suppress stem elongation to test adaptive hypotheses within open and understory populations of Impatiens capensis. These studies showed that experimentally suppressed plants with short stature had lower fitness than elongated plants when growing at high density, but they had higher fitness at low density (Dudley and Schmitt 1996, American Naturalist 147:445–465). A related study also showed adaptive differentiation among populations in plasticity to light cues of neighbor proximity (Dudley and Schmitt 1995, Functional Ecology 9:655–666).Annie’s group has been at the forefront of recent attempts to integrate genomic information and the power of model systems such as Arabidopsis into ecological field studies. Her work spans quantitative trait loci (QTL) mapping, studies of natural variation, association mapping and genome-wide association study (GWAS), and, recently, mechanistic modeling of the environmental and genetic influences on the transition to flowering. Among other findings, her ambitious field studies in Arabidopsis’s native range have shown that alleles associated with high fitness in a common garden are at higher frequencies in those regions (Fournier-Level et al. 2011, Science 334:86–89) and upheld predictions of life-history theory on the association between mortality and selection on reproductive timing (Fournier-Level et al. 2013, Molecular Ecology 22:3552–3566).Through groundbreaking integration of mechanistic information into ecologically relevant field studies, Annie’s research will have enduring and significant impact on the field of evolutionary ecology. Her personal enthusiasm for field research and organismal biology has also inspired a generation of biologists. Finally, her focus on mechanisms ranging from genetic to whole-plant phenotypes embodies the American Society of Naturalists’ goal of enhancing the conceptual unification of the biological sciences.Cynthia Weinig and John Stinchcombe, on behalf of the ASN Executive Committee Previous articleNext article DetailsFiguresReferencesCited by The American Naturalist Volume 189, Number 4April 2017 Published for The American Society of Naturalists Article DOIhttps://doi.org/10.1086/691001 HistoryPublished online March 01, 2017 © 2017 by The University of Chicago. All rights reserved.PDF download Crossref reports no articles citing this article.

Rapid Quantification of Abscisic Acid by GC-MS/MS for Studies of Abiotic Stress Response.

Drought and low water potential induce large increases in Abscisic Acid (ABA ) content of plant tissue. This increased ABA content is essential to regulate downstream stress resistance responses; however, the mechanisms regulating ABA accumulation are incompletely known. Thus, the ability to accurately quantify ABA at high throughput and low cost is important for plant stress research. We have combined and modified several previously published protocols to establish a rapid ABA analysis protocol using gas chromatography-tandem mass spectrometry (GC-MS/MS). Derivatization of ABA is performed with (trimethylsilyl)-diazomethane rather than the harder to prepare diazomethane. Sensitivity of the analysis is sufficient that small samples of low water potential treated Arabidopsis thaliana seedlings can be routinely analyzed in reverse genetic studies of putative stress regulators as well as studies of natural variation in ABA accumulation.

Natural Variation of the Circadian Clock in Neurospora.

Most living organisms on earth experience daily and expected changes from the rotation of the earth. For an organism, the ability to predict and prepare for incoming stresses or resources is a very important skill for survival. This cellular process of measuring daily time of the day is collectively called the circadian clock. Because of its fundamental role in survival in nature, there is a great interest in studying the natural variation of the circadian clock. However, characterizing the genetic and molecular mechanisms underlying natural variation of circadian clocks remains a challenging task. In this chapter, we will summarize the progress in studying natural variation of the circadian clock in the successful eukaryotic model Neurospora, which led to discovering many design principles of the molecular mechanisms of the eukaryotic circadian clock. Despite the success of the system in revealing the molecular mechanisms of the circadian clock, Neurospora has not been utilized to extensively study natural variation. We will review the challenges that hindered the natural variation studies in Neurospora, and how they were overcome. We will also review the advantages of Neurospora for natural variation studies. Since Neurospora is the model fungal species for circadian study, it represents over 5 million species of fungi on earth. These fungi play important roles in ecosystems on earth, and as such Neurospora could serve as an important model for understanding the ecological role of natural variation in fungal circadian clocks.

Widespread natural variation of DNA methylation within angiosperms.

BackgroundDNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species.ResultsBy analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species.ConclusionsThese results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1059-0) contains supplementary material, which is available to authorized users.

Genotypes, Networks, Phenotypes: Moving Toward Plant Systems Genetics

One of the central goals in biology is to understand how and how much of the phenotype of an organism is encoded in its genome. Although many genes that are crucial for organismal processes have been identified, much less is known about the genetic bases underlying quantitative phenotypic differences in natural populations. We discuss the fundamental gap between the large body of knowledge generated over the past decades by experimental genetics in the laboratory and what is needed to understand the genotype-to-phenotype problem on a broader scale. We argue that systems genetics, a combination of systems biology and the study of natural variation using quantitative genetics, will help to address this problem. We present major advances in these two mostly disconnected areas that have increased our understanding of the developmental processes of flowering time control and root growth. We conclude by illustrating and discussing the efforts that have been made toward systems genetics specifically in plants.

Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis

Circulating blood cell counts and indices are important indicators of hematopoietic function and a number of clinical parameters, such as blood oxygen-carrying capacity, inflammation, and hemostasis. By performing whole-exome sequence association analyses of hematologic quantitative traits in 15,459 community-dwelling individuals, followed by insilico replication in up to 52,024 independent samples, we identified two previously undescribed coding variants associated with lower platelet count: a common missense variant in CPS1 (rs1047891, MAF = 0.33, discovery + replication p = 6.38× 10(-10)) and a rare synonymous variant in GFI1B (rs150813342, MAF = 0.009, discovery + replication p = 1.79× 10(-27)). By performing CRISPR/Cas9 genome editing in hematopoietic cell lines and follow-up targeted knockdown experiments in primary human hematopoietic stem and progenitor cells, we demonstrate an alternative splicing mechanism by which the GFI1B rs150813342 variant suppresses formation of a GFI1B isoform that preferentially promotes megakaryocyte differentiation and platelet production. These results demonstrate how unbiased studies of natural variation in blood cell traits can provide insight into the regulation of human hematopoiesis.

Analysis of Circadian Leaf Movements.

The circadian clock is a molecular timekeeper that controls a wide variety of biological processes. In plants, clock outputs range from the molecular level, with rhythmic gene expression and metabolite content, to physiological processes such as stomatal conductance or leaf movements. Any of these outputs can be used as markers to monitor the state of the circadian clock. In the model plant Arabidopsis thaliana, much of the current knowledge about the clock has been gained from time course experiments profiling expression of endogenous genes or reporter constructs regulated by the circadian clock. Since these methods require labor-intensive sample preparation or transformation, monitoring leaf movements is an interesting alternative, especially in non-model species and for natural variation studies. Technological improvements both in digital photography and image analysis allow cheap and easy monitoring of circadian leaf movements. In this chapter we present a protocol that uses an autonomous point and shoot camera and free software to monitor circadian leaf movements in tomato.

Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii.

We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ∼3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates conservation of genes associated with core cellular functions, while genes in large gene families and poorly characterized genes show a greater incidence of major effect mutations. De novo assembly of unmapped reads recovered genes in the field isolates that are absent from the CC-503 assembly. The laboratory reference strains show a genomic pattern of polymorphism consistent with their origin as the recombinant progeny of a diploid zygospore. Large duplications or amplifications are a prominent feature of laboratory strains and appear to have originated under laboratory culture. Extensive natural variation offers a new source of genetic diversity for studies of Chlamydomonas, including naturally occurring alleles that may prove useful in studies of gene function and the dissection of quantitative genetic traits.

The genetic architecture of sexually selected traits in two natural populations of Drosophila montana.

We investigated the genetic architecture of courtship song and cuticular hydrocarbon traits in two phygenetically distinct populations of Drosophila montana. To study natural variation in these two important traits, we analysed within-population crosses among individuals sampled from the wild. Hence, the genetic variation analysed should represent that available for natural and sexual selection to act upon. In contrast to previous between-population crosses in this species, no major quantitative trait loci (QTLs) were detected, perhaps because the between-population QTLs were due to fixed differences between the populations. Partitioning the trait variation to chromosomes suggested a broadly polygenic genetic architecture of within-population variation, although some chromosomes explained more variation in one population compared with the other. Studies of natural variation provide an important contrast to crosses between species or divergent lines, but our analysis highlights recent concerns that segregating variation within populations for important quantitative ecological traits may largely consist of small effect alleles, difficult to detect with studies of moderate power.

Peromyscus mice as a model for studying natural variation.

The deer mouse (genus Peromyscus) is the most abundant mammal in North America, and it occupies almost every type of terrestrial habitat. It is not surprising therefore that the natural history of Peromyscus is among the best studied of any small mammal. For decades, the deer mouse has contributed to our understanding of population genetics, disease ecology, longevity, endocrinology and behavior. Over a century's worth of detailed descriptive studies of Peromyscus in the wild, coupled with emerging genetic and genomic techniques, have now positioned these mice as model organisms for the study of natural variation and adaptation. Recent work, combining field observations and laboratory experiments, has lead to exciting advances in a number of fields—from evolution and genetics, to physiology and neurobiology.DOI: http://dx.doi.org/10.7554/eLife.06813.001

Microbiome/Metabolic Syndrome/Diabetes and CVD

We have carried out taxonomic profiling of gut microbiota in a population of about 100 commercially available inbred strains of mice termed the Hybrid Mouse Diversity Panel (HMDP). This panel has been developed as a systems genetics resource and can be used for high resolution association mapping of complex traits. When maintained under controlled environmental conditions, the gut microbiota composition exhibits high heritability in the HMDP as calculated using a linear mixed model assuming additive genetic effects. Genome‐wide association analysis with informative SNPs identified significant loci in the mouse genome associated with relative abundances of specific taxa. The HMDP mice have been typed for a number of cardiovascular, metabolic, and other clinical traits, allowing correlation analysis of gut microbiota composition with clinical traits. Some of these associations, such as the association between Akkermansia muciniphila levels and high fat diet response, have subsequently been confirmed in published experimental studies. A number of novel associations are presently being tested using co‐fostering of different inbred strains or experimental introduction of cultured bacterial species. A variety of diets have been studied across the HMDP. In conclusion, studies of natural variations in gut microbiota composition in mice may help identify regulatory host factors as well as providing a global view of the relationships between microbiota and clinically relevant traits.

Vascular Cambium Development.

Secondary phloem and xylem tissues are produced through the activity of vascular cambium, the cylindrical secondary meristem which arises among the primary plant tissues. Most dicotyledonous species undergo secondary development, among them Arabidopsis. Despite its small size and herbaceous nature, Arabidopsis displays prominent secondary growth in several organs, including the root, hypocotyl and shoot. Together with the vast genetic resources and molecular research methods available for it, this has made Arabidopsis a versatile and accessible model organism for studying cambial development and wood formation. In this review, we discuss and compare the development and function of the vascular cambium in the Arabidopsis root, hypocotyl, and shoot. We describe the current understanding of the molecular regulation of vascular cambium and compare it to the function of primary meristems. We conclude with a look at the future prospects of cambium research, including opportunities provided by phenotyping and modelling approaches, complemented by studies of natural variation and comparative genetic studies in perennial and woody plant species.

Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines.

Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.

QTL meta-analysis in Arabidopsis reveals an interaction between leaf senescence and resource allocation to seeds

Sequential and monocarpic senescence are observed at vegetative and reproductive stages, respectively. Both facilitate nitrogen (N) remobilization and control the duration of carbon (C) fixation. Genetic and environmental factors control N and C resource allocation to seeds. Studies of natural variation in Arabidopsis thaliana revealed differences between accessions for leaf senescence phenotypes, seed N and C contents, and N remobilization efficiency-related traits. Here, a quantitative genetics approach was used to gain a better understanding of seed filling regulation in relation to leaf senescence and resource allocation. For that purpose, three Arabidopsis recombinant inbred line populations (Ct-1×Col-0, Cvi-0×Col-0, Bur-0×Col-0) were used to map QTL (quantitative trait loci) for ten traits related to senescence, resource allocation, and seed filling. The use of common markers across the three different maps allowed direct comparisons of the positions of the detected QTL in a single consensus map. QTL meta-analysis was then used to identify interesting regions (metaQTL) where QTL for several traits co-localized. MetaQTL were compared with positions of candidate genes known to be involved in senescence processes and flowering time. Finally, investigation of the correlation between yield and seed N concentration in the three populations suggests that leaf senescence disrupts the negative correlation generally observed between these two traits.

A survey of the natural variation in biomechanical and cell wall properties in inflorescence stems reveals new insights into the utility of Arabidopsis as a wood model

The natural trait variation in Arabidopsis thaliana (L.) Heynh. accessions is an important resource for understanding many biological processes but it is underexploited for wood-related properties. Twelve A. thaliana accessions from diverse geographical locations were examined for variation in secondary growth, biomechanical properties, cell wall glycan content, cellulose microfibril angle (MFA) and flowering time. The effect of daylength was also examined. Secondary growth in rosette and inflorescence stems was observed in all accessions. Organised cellulose microfibrils in inflorescence stems were found in plants grown under long and short days. A substantial range of phenotypic variation was found in biochemical and wood-related biophysical characteristics, particularly for tensile strength, tensile stiffness, MFA and some cell wall components. The four monosaccharides galactose, arabinose, rhamnose and fucose strongly correlated with each other as well as with tensile strength and MFA, consistent with mutations in arabinogalactan protein and fucosyl- and xyloglucan galactosyl-transferase genes that result in decreases in strength. Conversely, these variables showed negative correlations with lignin content. Our data support the notion that large-scale natural variation studies of wood-related biomechanical and biochemical properties of inflorescence stems will be useful for the identification of novel genes important for wood formation and quality, and therefore biomaterial and renewable biofuel production.

OGRO: The Overview of functionally characterized Genes in Rice online database.

BackgroundThe high-quality sequence information and rich bioinformatics tools available for rice have contributed to remarkable advances in functional genomics. To facilitate the application of gene function information to the study of natural variation in rice, we comprehensively searched for articles related to rice functional genomics and extracted information on functionally characterized genes.ResultsAs of 31 March 2012, 702 functionally characterized genes were annotated. This number represents about 1.6% of the predicted loci in the Rice Annotation Project Database. The compiled gene information is organized to facilitate direct comparisons with quantitative trait locus (QTL) information in the Q-TARO database. Comparison of genomic locations between functionally characterized genes and the QTLs revealed that QTL clusters were often co-localized with high-density gene regions, and that the genes associated with the QTLs in these clusters were different genes, suggesting that these QTL clusters are likely to be explained by tightly linked but distinct genes. Information on the functionally characterized genes compiled during this study is now available in the O verview of Functionally Characterized G enes in R ice O nline database (OGRO) on the Q-TARO website (http://qtaro.abr.affrc.go.jp/ogro). The database has two interfaces: a table containing gene information, and a genome viewer that allows users to compare the locations of QTLs and functionally characterized genes.ConclusionsOGRO on Q-TARO will facilitate a candidate-gene approach to identifying the genes responsible for QTLs. Because the QTL descriptions in Q-TARO contain information on agronomic traits, such comparisons will also facilitate the annotation of functionally characterized genes in terms of their effects on traits important for rice breeding. The increasing amount of information on rice gene function being generated from mutant panels and other types of studies will make the OGRO database even more valuable in the future.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-5-26) contains supplementary material, which is available to authorized users.