Randy Scholl

The Scale of Population Structure in Arabidopsis thaliana

The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.

Brachypodium as a model for the grasses: Today and the future

Over the past several years, Brachypodium distachyon (Brachypodium) has emerged as a tractable model system to study biological questions relevant to the grasses. To place its relevance in the larger context of plant biology, we outline here the expanding adoption of Brachypodium as a model grass and compare this to the early history of another plant model, Arabidopsis thaliana. In this context, Brachypodium has followed an accelerated path in which the development of genomic resources, most notably a whole genome sequence, occurred concurrently with the generation of other experimental tools (e.g. highly efficient transformation and large collections of natural accessions). This update provides a snapshot of available and upcoming Brachypodium resources and an overview of the community including the trajectory of Brachypodium as a model grass.

TAIR: a resource for integrated Arabidopsis data.

Abstract. The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) provides an integrated view of genomic data for Arabidopsis thaliana. The information is obtained from a battery of sources, including the Arabidopsis user community, the literature, and the major genome centers. Currently TAIR provides information about genes, markers, polymorphisms, maps, sequences, clones, DNA and seed stocks, gene families and proteins. In addition, users can find Arabidopsis publications and information about Arabidopsis researchers. Our emphasis is now on incorporating functional annotations of genes and gene products, genome-wide expression, and biochemical pathway data. Among the tools developed at TAIR, the most notable is the Sequence Viewer, which displays gene annotation, clones, transcripts, markers and polymorphisms on the Arabidopsis genome, and allows zooming in to the nucleotide level. A tool recently released is AraCyc, which is designed for visualization of biochemical pathways. We are also developing tools to extract information from the literature in a systematic way, and building controlled vocabularies to describe biological concepts in collaboration with other database groups. A significant new feature is the integration of the ABRC database functions and stock ordering system, which allows users to place orders for seed and DNA stocks directly from the TAIR site.

Growth of Plants and Preservation of Seeds

This chapter focuses on growth of plants on agar and soil in various environmental settings and especially in growth chambers and greenhouses. Harvesting, seed quality, and seed preservation are also considered. In addition, this chapter elaborates the conditions that are critical to the growth and development of healthy plants that produce high quality and quantity of seeds. The plant and seed management methods are discussed in the chronological order in which they would normally be utilized.

Maintaining Collections of Mutants for Plant Functional Genomics

As the plant genomics era progresses and post-genomic functional research rapidly expands, varied genetic resources of unprecedented power and scope are being developed. Partially by the mandate of public funding, these resources are being shared via stock centers and private laboratories. The successful initiation of any new research requires that advantage be taken of these stocks. Information on most plant genomic resources can be obtained through simple yet powerful. Web searches, and ordering mechanisms are linked to the information. Hence, locating and obtaining materials is rapid and simple. Currently, available genomic resources are described, and references, links for Web data, and ordering information are also included.

The Preservation of Plant Genetic Resources. Experiences with Arabidopsis

The preservation of genetic resources used to support multinational research programs in plant biology requires extensive sharing and curation of information and materials. Each sector of the community has an important role to play, from individual investigators and volunteer coordinators to

Handling Arabidopsis plants: growth, preservation of seeds, transformation, and genetic crosses.

Growing healthy plants is essential for the advancement of Arabidopsis thaliana (Arabidopsis) research. Over the last 20 years, the Arabidopsis Biological Resource Center (ABRC) has collected and developed a series of best-practice protocols, some of which are presented in this chapter. Arabidopsis can be grown in a variety of locations, growth media, and environmental conditions. Most laboratory accessions and their mutant or transgenic derivatives flower after 4-5 weeks and set seeds after 7-8 weeks, under standard growth conditions (soil, long day, 23 ºC). Some mutant genotypes, natural accessions, and Arabidopsis relatives require strict control of growth conditions best provided by growth rooms, chambers, or incubators. Other lines can be grown in less-controlled greenhouse settings. Although the majority of lines can be grown in soil, certain experimental purposes require utilization of sterile solid or liquid growth media. These include the selection of primary transformants, identification of homozygous lethal individuals in a segregating population, or bulking of a large amount of plant material. The importance of controlling, observing, and recording growth conditions is emphasized and appropriate equipment required to perform monitoring of these conditions is listed. Proper conditions for seed harvesting and preservation, as well as seed quality control, are also described. Plant transformation and genetic crosses, two of the methods that revolutionized Arabidopsis genetics, are introduced as well.

Arabidopsis Biological Resource Center

S ince their establishment two years ago, the international network of Arabidopsis resource centers, comprising the Arabidopsis Biological Resource Center (ABRC) at O ~ o State University, USA, the Nottingham Arabidopsis Stock Centre (NASC) at Nottingham University, UK, and the European DNA Resource Centre at K61n, Germany, serve Arabidopsis biological and genome researchers. The centers have released nearly seven thousand individual seed lines that cover a wide variety of stocks. These include many weUdefined lines of hormone, flowering, biochemical, form mutants, multiple marker lines, and trisomic lines. A large collection of ecotypes are also available. Seed stocks shared by NASC and ABRC include pools of 5000 T-DNA lines from Kenneth Feldmann (Tucson, AZ, USA) as well as individual mutant lines that have been identified in the initial screen of this material. In addition, the recombinant inbred mapping lines of Pablo Scolnik (Du Pont Corp.) and one hundred recombinant inbred lines donated by Caroline Dean and Clare Lister (John Innes Centre, UK) are also available. Donors of mutant stocks include Maarten Koornneef, Albert Kranz, George Redei and many others. The collaborative efforts of the Centers have facilitated the release of over one thousand new seed accessions this past year. New stocks that have been made available by ABRC include further single and multiple marker lines, 40 ecotypes donated by P. Williams, and approximately 350 lines donated by G. P. R6dei. The latest release of lines from NASC will include T-DNA lines donated by Keith Lindsey (Leicester University, UK) and Ds-transformed lines from Ian Bancroft and Caroline Dean (JICPSR, Norwich, UK). DNA stocks are preserved and distributed by the ABRC and the European DNA Resource Centre at K61n. Stocks include the mapped RFLP phage (from Elliot Meyerowitz) and cosmids (Howard Goodman and Elliot Meyerowitz), YAC Libraries produced by Erwin Grill and

Germplasm and Molecular Resources

A wide range of genetic diversity exists in various members of the Brassicaceae, notably in the genera Arabidopsis and Brassica. Comprehensive seed collections include mutants, transgenic lines, chromosomal variants, mapping populations, Targeting Induced Local Lesions in Genomes (TILLING), and natural accessions, collected from the wild. Many molecular resources have been developed and are widely utilized in research. These include expressed sequence tags (ESTs); full length, sequence-validated cDNA clones of many genes; bacterial artificial chromosome (BAC) libraries; and vectors with multiple applications. Diverse resources are maintained by numerous institutions and specialized centers. Various public and private databases with comprehensive information about the collections are also available. This chapter focuses on the resources for the members of this family, with emphasis on collections that are publicly available.

Stock Centres obtain further funding and introduce user fees

W e are pleased to announce that, based on the success of the last five years, the Stock Centres have now officially received funding to continue to provide seed, DNA, and information resources. The Nottingham Arabidopsis Stock Centre (NASC) and the Arabidopsis Biological Resource Center (ABRC) have received fiveand fouryear funding from the BBSRC and NSF, respectively. Together with the funds raised from user fees, we will be able to continue the expansion of our collections to meet the needs of the research programme.