From bench to bountiful harvests: a road map for the next decade of Arabidopsis research

In the face of an increasing world population and climate instability, the demands for food and fuel will continue to rise. Plant science will be crucial to help meet these exponentially increasing requirements for food and fuel supplies. Fundamental plant research will play a major role in providing key advances in our understanding of basic plant processes that can then flow into practical advances through knowledge sharing and collaborations. The model plant Arabidopsis thaliana has played a major role in our understanding of plant biology, and the Arabidopsis community has developed many tools and resources to continue building on this knowledge. Drawing from previous experience of internationally coordinated projects, The international Arabidopsis community, represented by the Multinational Arabidopsis Steering Committee (MASC), has drawn up a road map for the next decade of Arabidopsis research to inform scientists and decision makers on the future foci of Arabidopsis research within the wider plant science landscape. This article provides a summary of the MASC road map.     

Plant genomics takes root, branches out

For the past nine years, an international consortium of researchers have collaborated on a project to provide a full set of genomics tools for the model plant species Arabidopsis thaliana. Among the goals of this project were the complete sequence of the Arabidopsis genome, which may be completed in the year 2000, four years ahead of schedule. Arabidopsis was an appropriate choice as the first target of plant genomics because of its excellent genetics, outstanding research community and small genome size. Until very recently, it appeared that comprehensive high-throughput plant genomics in the public sector would largely begin and end with Arabidopsis. Over the past two years, this situation has changed completely.     

Growing weed, producing knowledge: an epistemic history of Arabidopsis thaliana

Arabidopsis is currently the most popular and well-researched model organism in plant biology. This paper documents this plant's rise to scientific fame by focusing on two interrelated aspects of Arabidopsis research. One is the extent to which the material features of the plant have constrained research directions and enabled scientific achievements. The other is the crucial role played by the international community of Arabidopsis researchers in making it possible to grow, distribute and use plant specimen that embody these material features. I argue that at least part of the explosive development of this research community is due to its successful standardisation and to the subsequent use of Arabidopsis specimen as material models of plants. I conclude that model organisms have a double identity as both samples of nature and artifacts representing nature. It is the resulting ambivalence in their representational value that makes them attractive research tools for biologists.     

Celebrating Plant Cells： A Special Issue on Plant Cell Biology

A special issue on plant cell biology is long overdue for JIPB! In the last two decades or so, the plant biology community has been thrilled by explosive discoveries regarding the molecular and genetic basis of plant growth, development, and responses to the environment, largely owing to recent maturation of model systems like Arabidopsis thaliana and the rice Oryza sativa, as well as the rapid development of high throughput technologies associated with qenomics and proteomics.     

Recent Progress in Arabidopsis Research in China： A Preface

In 2002, a workshop on Arabidopsis research in China was held in Shanghai, when a small group of Chinese plant scientists was working on this model species. Since then, we have witnessed the rapid growth of Arabidopsis research in China. This special issue of Journal of Integrative Plant Biology is dedicated exclusively to the Fourth Workshop on Arabidopsis Research in China, scheduled on November 30, 2005, in Beijing. In addition to reports collected in this special issue, the Chinese Arabidopsis community has been able to make significant contributions to many research fields. Here, I briefly summarize recent advances in Arabidopsis research in China.     

Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species

Although Arabidopsis is well established as the premiere model species in plant biology, rice (Oryza sativa) is moving up fast as the second-best model organism. In addition to the availability of large sets of genetic, molecular, and genomic resources, two features make rice attractive as a model species: it represents the taxonomically distinct monocots and is a crop species. Plant structural genomics was pioneered on a genome-scale in Arabidopsis and the lessons learned from these efforts were not lost on rice. Indeed, the sequence and annotation of the rice genome has been greatly accelerated by method improvements made in Arabidopsis. For example, the value of full-length cDNA clones and deep expressed sequence tag resources, obtained in Arabidopsis primarily after release of the complete genome, has been recognized by the rice genomics community. For rice >250,000 expressed sequence tags and 28,000 full-length cDNA sequences are available prior to the completion of the genome sequence. With respect to tools for Arabidopsis functional genomics, deep sequence-tagged lines, inexpensive spotted oligonucleotide arrays, and a near-complete whole genome Affymetrix array are publicly available. The development of similar functional genomics resources for rice is in progress that for the most part has been more streamlined based on lessons learned from Arabidopsis. Genomic resource development has been essential to set the stage for hypothesis-driven research, and Arabidopsis continues to provide paradigms for testing in rice to assess function across taxonomic divisions and in a crop species.     

Anno genominis XX: 20 years of Arabidopsis genomics

Twenty years ago, the Arabidopsis thaliana genome sequence was published. This was an important moment as it was the first sequenced plant genome and explicitly brought plant science into the genomics era. At the time, this was not only an outstanding technological achievement, but it was characterized by a superb global collaboration. The Arabidopsis genome was the seed for plant genomic research. Here, we review the development of numerous resources based on the genome that have enabled discoveries across plant species, which has enhanced our understanding of how plants function and interact with their environments.

The publication of the Arabidopsis genome sequence 20 years ago has had an enormous impact on the global plant science community.     

Chromosome landmarks as tools to study the genome of Arabidopsis thaliana

The model plant Arabidopsis thaliana has long been used for genetic, cellular and molecular studies. Whereas this plant was used as a model of genetics in the 1940's, the first cytogenetic observation of A. thaliana chromosomes was published in the beginning of the 20th century. Although Arabidopsis was not originally considered to be a good plant model for cytogenetics due to smallness of its genome, the number of published chromosome studies has expanded enormously in recent years. The advent of fluorescence in situ hybridization techniques on meiotic chromosomes together with indirect immuno-fluorescence localization of key chromosomal and nuclear proteins and wide accessibility of Arabidopsis mutants have resulted in a synergistic boost in Arabidopsis cytogenetics. In comparison to other plant species, the small genome with under-represented DNA repeats together with a small number of chromosomes makes this model plant easy to comprehend for a cytologist.     

An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community

The future bioinformatics needs of the Arabidopsis community as well as those of other scientific communities that depend on Arabidopsis resources were discussed at a pair of recent meetings held by the Multinational Arabidopsis Steering Committee and the North American Arabidopsis Steering Committee. There are extensive tools and resources for information storage, curation, and retrieval of Arabidopsis data that have been developed over recent years primarily through the activities of The Arabidopsis Information Resource, the Nottingham Arabidopsis Stock Centre, and the Arabidopsis Biological Resource Center, among others. However, the rapid expansion in many data types, the international basis of the Arabidopsis community, and changing priorities of the funding agencies all suggest the need for changes in the way informatics infrastructure is developed and maintained. We propose that there is a need for a single core resource that is integrated into a larger international consortium of investigators. We envision this to consist of a distributed system of data, tools, and resources, accessed via a single information portal and funded by a variety of sources, under shared international management of an International Arabidopsis Informatics Consortium (IAIC). This article outlines the proposal for the development, management, operations, and continued funding for the IAIC.The Multinational Arabidopsis Steering Committee (MASC) and the North American Arabidopsis Steering Committee (NAASC) hosted workshops in Nottingham, UK (April 15 to 16, 2010) and Washington DC (May 10 to 11, 2010) to consider the future bioinformatics needs of the Arabidopsis community as well as other science communities that depend vitally on Arabidopsis resources. The outcomes of both workshops were presented and discussed at the International Conference on Arabidopsis Research (ICAR) in Yokohama, Japan. The focus of the workshops was on Arabidopsis because of its unique and essential role as a reference organism for all seed plant species. The development of the highly annotated “gold standard” Arabidopsis genome sequence has been an invaluable resource for plant and crop sciences. This platform provides important information and working practices for other species and for comparative genomic and evolutionary studies. Arabidopsis tools and resources for information storage, curation, and retrieval have been developed over recent years primarily through the activities of The Arabidopsis Information Resource (TAIR), the Nottingham Arabidopsis Stock Centre (NASC), and the Arabidopsis Biological Resource Center, among others. However, the Arabidopsis community and funding agencies recognize the need for a single data management infrastructure. The key challenge is to develop and fund this resource in a sustainable and transparent manner.Global challenges surrounding food and energy security require intelligent plant breeding strategies that will be dependent on a central Arabidopsis information resource to aid our understanding of gene function and associated phenotype in many different environments. The knowledge accrued in Arabidopsis informs our understanding of the genetic basis of plant processes and crop traits. To date, this has accumulated primarily through analysis of single genes. However, gene products do not act alone but rather in complex interacting networks. Thus, the challenge for the Arabidopsis community is to understand this higher level of complexity, to a significant extent through the application of new high volume, quantitative experimental techniques. The goals of these efforts are to develop gene/protein/metabolite networks that will enable systems-level modeling of plant processes and ultimately to translate these findings to crop plants. To achieve these goals, we must develop novel approaches to data management, integration, and access.The UK workshop addressed three principal issues: the types of data generated by the Arabidopsis community, the types of data used by the community, and future needs of the community. The objective was to produce recommendations for the type of infrastructure necessary to address the challenges and opportunities associated with the application of new technologies and recommendations for a sustainable funding model to support this infrastructure. These recommendations were considered and expanded upon at the US workshop with the ultimate goal of generating solutions to the issues discussed in the first meeting. It was recognized that cohesive, cooperative, and long-term international collaboration will be critical to successfully maintain an Arabidopsis database infrastructure that is essential for plant biology research worldwide.The workshop participants concluded that there is a continued need for a central Arabidopsis information resource, based on the productivity of the Arabidopsis community and the critical importance of the findings generated by this community. For example, ∼3000 Arabidopsis publications are currently published in peer-reviewed journals each year, a nearly 10-fold increase since the early 1990s; and in 2009, TAIR was accessed by 335,692 unique visitors and had nearly 20 million page views. Furthermore, the importance of a current, well-organized, and carefully curated Arabidopsis genome to researchers studying other plants, including crops, cannot be overstated. In the future, this resource should be part of a larger infrastructure that would be dynamic and responsive to new directions in plant biology research.     

The impact of Arabidopsis research on plant biotechnology

Arabidopsis thaliana, a small annual weed belonging to the mustard family, has become a widely used model in plant genetic research. It has a small genome, short life cycle, and is easy to mutagenize. Identification of genes based on phenotype alone, often a rather difficult part of molecular genetic research, is easiest in this plant. Laboratories working on the "model" plant Arabidopsis thaliana have created a network for sharing resources and ideas, so progress has been rapid. The importance of this plant to biotechnology is that genes isolated from Arabidopsis can be used to find their homologs in crop plants. Likewise, fundamental mechanisms can be understood in a model plant, and applied in crop plants.     

Natural genetic variation in Arabidopsis: tools, traits and prospects for evolutionary ecology

BACKGROUND: The model plant Arabidopsis thaliana (Arabidopsis) shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, the potential of Arabidopsis for molecular genetic analysis of this natural variation has increased dramatically in recent years. SCOPE: Advanced genomics has accelerated molecular phylogenetic analysis and gene identification by quantitative trait loci (QTL) mapping and/or association mapping in Arabidopsis. In particular, QTL mapping utilizing natural accessions is now becoming a major strategy of gene isolation, offering an alternative to artificial mutant lines. Furthermore, the genomic information is used by researchers to uncover the signature of natural selection acting on the genes that contribute to phenotypic variation. The evolutionary significance of such genes has been evaluated in traits such as disease resistance and flowering time. However, although molecular hallmarks of selection have been found for the genes in question, a corresponding ecological scenario of adaptive evolution has been difficult to prove. Ecological strategies, including reciprocal transplant experiments and competition experiments, and utilizing near-isogenic lines of alleles of interest will be a powerful tool to measure the relative fitness of phenotypic and/or allelic variants. CONCLUSIONS: As the plant model organism, Arabidopsis provides a wealth of molecular background information for evolutionary genetics. Because genetic diversity between and within Arabidopsis populations is much higher than anticipated, combining this background information with ecological approaches might well establish Arabidopsis as a model organism for plant evolutionary ecology.     

Salinity tolerance of Arabidopsis: a good model for cereals?

Arabidopsis is a glycophyte species that is sensitive to moderate levels of NaCl. Arabidopsis offers unique benefits to genetic and molecular research and has provided much information about both Na(+) transport processes and Na(+) tolerance. A compilation of data available on Na(+) accumulation and Na(+) tolerance in Arabidopsis is presented, and comparisons are made with several crop plant species. The relationship between Na(+) tolerance and Na(+) accumulation is different in Arabidopsis and cereals, with an inverse relationship often found within cereal species that is not as evident in Arabidopsis ecotypes. Results on salinity tolerance obtained in Arabidopsis should therefore be extrapolated to cereals with caution. Arabidopsis remains a useful model to study and discover plant Na(+) transport processes.     

拟南芥——一把打开植物生命奥秘大门的钥匙

在过去的20年中,拟南芥作为模式植物广泛用于植物生命科学研究。历时10年的模式植物拟南芥的全基因组测序工作于2000年完成,通过测序获得的拟南芥基因组核苷酸序列全部公布在互联网上,有力地推动了植物生命科学研究向前发展。科学家提出的“2010计划”旨在通过全世界植物科学家的努力,到2010年能够尽可能多地了解拟南芥基因的功能。通过拟南芥研究所获得的信息将有助于人类对控制不同植物复杂生命活动机制的认识。     

Effects of jasmonic acid, ethylene, and salicylic acid signaling on the rhizosphere bacterial community of Arabidopsis thaliana

Systemically induced resistance is a promising strategy to control plant diseases, as it affects numerous pathogens. However, since induced resistance reduces one or both growth and activity of plant pathogens, the indigenous microflora may also be affected by an enhanced defensive state of the plant. The aim of this study was to elucidate how much the bacterial rhizosphere microflora of Arabidopsis is affected by induced systemic resistance (ISR) or systemic acquired resistance (SAR). Therefore, the bacterial microflora of wild-type plants and plants affected in their defense signaling was compared. Additionally, ISR was induced by application of methyl jasmonate and SAR by treatment with salicylic acid or benzothiadiazole. As a comparative model, we also used wild type and ethylene-insensitive tobacco. Some of the Arabidopsis genotypes affected in defense signaling showed altered numbers of culturable bacteria in their rhizospheres; however, effects were dependent on soil type. Effects of plant genotype on rhizosphere bacterial community structure could not be related to plant defense because chemical activation of ISR or SAR had no significant effects on density and structure of the rhizosphere bacterial community. These findings support the notion that control of plant diseases by elicitation of systemic resistance will not significantly affect the resident soil bacterial microflora.     

Arabidopsis thaliana: a model host plant to study plant-pathogen interaction using Chilean field isolates of Botrytis cinerea

One of the fungal pathogens that causes more agriculture damage is Botrytis cinerea. Botrytis is a constant threat to crops because the fungus infects a wide range of host species, both native and cultivated. Furthermore, Botrytis persists on plant debris in and on the soil. Some of the most serious diseases caused by Botrytis include gray mold on vegetables and fruits, such as grapes and strawberries. Botrytis also causes secondary soft rot of fruits and vegetables during storage, transit and at the market. In many plant-pathogen interactions, resistance often is associated with the deposition of callose, accumulation of autofluorescent compounds, the synthesis and accumulation of salicylic acid as well as pathogenesis-related proteins. Arabidopsis thaliana has been used as a plant model to study plant-pathogen interaction. The genome of Arabidopsis has been completely sequenced and this plant serves as a good genetic and molecular model. In this study, we demonstrate that Chilean field isolates infect Arabidopsis thaliana and that Arabidopsis subsequently activates several defense response mechanisms associated with a hypersensitive response. Furthermore, we propose that Arabidopsis may be used as a model host species to analyze the diversity associated with infectivity among populations of Botrytis cinerea field isolates.     

Picking out parallels: plant circadian clocks in context.

Molecular models have been described for the circadian clocks of representatives of several different taxa. Much of the work on the plant circadian system has been carried out using the thale cress, Arabidopsis thaliana, as a model. We discuss the roles of genes implicated in the plant circadian system, with special emphasis on Arabidopsis. Plants have an endogenous clock that regulates many aspects of circadian and photoperiodic behaviour. Despite the discovery of components that resemble those involved in the clocks of animals or fungi, no coherent model of the plant clock has yet been proposed. In this review, we aim to provide an overview of studies of the Arabidopsis circadian system. We shall compare these with results from different taxa and discuss them in the context of what is known about clocks in other organisms.     

Design, implementation and maintenance of a model organism database for Arabidopsis thaliana

The Arabidopsis Information Resource (TAIR) is a web-based community database for the model plant Arabidopsis thaliana. It provides an integrated view of genes, sequences, proteins, germplasms, clones, metabolic pathways, gene expression, ecotypes, polymorphisms, publications, maps and community information. TAIR is developed and maintained by collaboration between software developers and biologists. Biologists provide specification and use cases for the system, acquire, analyse and curate data, interact with users and test the software. Software developers design, implement and test the database and software. In this review, we briefly describe how TAIR was built and is being maintained.     

Root Exudates Regulate Soil Fungal Community Composition and Diversity

Plants are in constant contact with a community of soil biota that contains fungi ranging from pathogenic to symbiotic. A few studies have demonstrated a critical role of chemical communication in establishing highly specialized relationships, but the general role for root exudates in structuring the soil fungal community is poorly described. This study demonstrates that two model plant species (Arabidopsis thaliana and Medicago truncatula) are able to maintain resident soil fungal populations but unable to maintain nonresident soil fungal populations. This is mediated largely through root exudates: the effects of adding in vitro-generated root exudates to the soil fungal community were qualitatively and quantitatively similar to the results observed for plants grown in those same soils. This effect is observed for total fungal biomass, phylotype diversity, and overall community similarity to the starting community. Nonresident plants and root exudates influenced the fungal community by both positively and negatively impacting the relative abundance of individual phylotypes. A net increase in fungal biomass was observed when nonresident root exudates were added to resident plant treatments, suggesting that increases in specific carbon substrates and/or signaling compounds support an increased soil fungal population load. This study establishes root exudates as a mechanism through which a plant is able to regulate soil fungal community composition.