Abstract
The analytical power of Arabidopsis thaliana genomics has turned its local varieties (accessions) from divergent habitats into important genetic resources. Variant alleles harbored in those accessions are used to identify loci controlling important plant traits with enormous benefits for analytical as well as applied purposes. We argue here that the information derived from Arabidopsis accessions can be further expanded, if a systematic effort for recording the growth conditions of new Arabidopsis accessions is rapidly implemented. The modest and feasible changes in genetic sampling practice that we propose will dramatically increase the quality and quantity of data obtained from Arabidopsis accessions. The broader data set will no longer focus solely on the genetic mechanism within the plant, but will also address the plant's interaction with its environment. We suggest (a) a modified sampling strategy involving sample size and the recording of additional growth conditions (Appendix) and (b) the establishment of a centralized and expandable database to cover all available information regarding the habitats of Arabidopsis accessions.
Key words: adaptation, Arabidopsis, ecology, evolution, genetic resources, sampling strategy
The influence of the immediate abiotic and biotic environment on the evolution of developmental, physiological, reproductive, defense-related and a variety of ecological characteristics of plants is well documented,1–3 but is rarely connected to the level of individual gene activities. This is partly because for most plants, the genetic dissection of adaptation processes at the individual, population and evolutionary levels is inherently difficult. The current and foreseeable wealth of molecular insights in the Arabidopsis model system could fill this void. With its very wide natural geographic distribution over large parts of Asia and Europe4 and it's more recent (human-induced) colonization of habitats in America, Arabidopsis thaliana provides immediate opportunities for studying adaptation processes in great molecular and genetic detail. Therefore, it is not surprising that Arabidopsis has also been used as a model system for population genetics and ecological adaptation in recent years.5–8 In a parallel dramatic development, increasing numbers of Arabidopsis accessions are currently being characterized in unprecedented molecular detail to be used as parental lines in QTL mapping studies. These two lines of research could most productively benefit from each other, if habitat information for each accession would become available.
An example of a relevant question is: how are environmental variables correlated to phenotypic or gene expression profiles of Arabidopsis accessions? An expandable list of such variables to be recorded at the sampling site would include elevation, aspect (facing north, south, east or west), soil type and soil conditions, rainfall, temperature regime, wind direction and velocity, exposure to sun irradiation, level of shade, UV level, photoperiod, snow cover, local plant communities, herbivore diversity, frequency and pressure, fire history, evidence of various disturbances and apparent diseases. We know, for instance, that various characters, such as vascular structure, fiber length and density, cuticle thickness, stomata density and pigment composition, can be subject to selection even within small, locally restricted populations.9–12 At a time when phenotypic and molecular profiles of Arabidopsis accession are being scrutinized with ever increasing precision, it would be an inexcusable loss, if the corresponding habitat data for those accessions were simply not recorded or retrievable. It seems evident that with a small, but well-coordinated additional effort, it could be possible to address a much wider array of questions and to direct the power of Arabidopsis genomics and genetics to the study of plant adaptations and evolution. Specifically, we propose that a standard list of environmental data should be provided with each accession of seeds, together with multiple deposited plants as well as electronic images of the exact site and general environment and a precise geographical position (GPS) of the sampling site (see appendix). Precise site documentation may enable re-sampling of populations to study their genetic changes over time.
Detailed recording of accession habitats and the collection of multiple plants at each location would reciprocally benefit QTL mapping efforts. First, it would firmly establish that the parental lines of a mapping cross are true natural genotypes. This is important, because any exploitation of natural alleles in breeding and biotechnology should rely in the assumption that these alleles have passed the test of natural selection and are not spontaneous mutants or propagation contaminants. Secondly, emerging correlations between habitat conditions and phenotype can guide accession choices for the establishment of new mapping populations. Phenotyping of accessions for specific cell biological or biochemical traits can be labor intensive. To keep numbers manageable, habitat properties with predictive power would be highly desirable.
In summary, we do not consider our suggestions of approximately 30 parameters (see the appendix) to be more than the beginning of a discussion. However, it seems to us that the need for organized habitat characterization and sampling is so urgent that this discussion should begin immediately.
Appendix
Proposed expanded sampling strategy.
The sampling strategy shown below should be considered only as a starting point for discussions on this matter. If the community agrees that it makes sense to spend more thinking on sampling strategies, this scheme will probably be modified. It is also conceivable that there will be more than a single sampling scheme. For example, stock centers may not want to reject accessions for which incomplete information is provided. However, it makes sense to define a good standard of data acquisition for accessions with the greatest benefits for ecological and evolutionary studies and to label such accessions accordingly. Our suggested sampling and data acquisition scheme follows.
(a) Sampling site:
A sampling site will be a GPS (global positioning system)-defined area with a maximum circular diameter of 25 m. High-resolution images of the site will help to unambiguously identify the site. This will enable repeated sampling of plants or amendment of habitat data.
(b) Sample size:
At least five plants from a given sampling site will be provided in each seed donation (samples A to E). A will be isogenized over several generations and then made available for natural-variation mapping. Lines derived from plants B to E can be requested separately for studies addressing the relationships between a local genotype and its environment. These can address, for example, the microheterogeneity of Arabidopsis genotypes in a given location, as well as communalities in their genotypes and phenotypes. Sufficient seeds from the immediate progenies of the collected plants themselves will be kept in a repository along with DNA samples from them. This material can preserve the natural origin of any important allele found in an accession.
(c) Data acquisition and management:
An expanded TAIR database will be established, to which accessions with full data sets will be added, and which will be equipped with software that allows for queries with complex combinations of properties, either of the sampling site or of the accession phenotype. The following parameters should be recorded for any submitted seed batch:
(1) Sample number. (2) Site number. (3) Collector's name. (4) Collector's e-mail. (5) Institute. (6) Date (day, month, year). (7) Taxonomic information (genus, species). (8) Confirmation of taxon required (yes, no). (9) Site information (country, province, location ____ km from ____ in a ____ direction, latitude ____ N/S, longitude ____ E/W, altitude ____ m). (10) Ecological information (topography, valley bottom, plain, undulating, hilly, terraces, summit, other—specify). (11) Drainage (excessive, free, impeded). (12) Slope (steep, moderate). (13) Aspect (north, south, east or west). (14) Bedrock (sandstone, chalk, limestone, basalt, metamorphic, granite, other—specify). (15) Stoniness (none, low, medium, high). (16) Soil texture (sand, sandy loam, loam, clay, other—specify). (17) Other notes on soil (color, pH, salinity, other—specify). (18) Habitat (forest, woodland, bush land, grassland, wooded grassland, desert, alpine, arable, wasteland, ruderal, swamp, other—specify). (19) Disturbance factors (none, moderate, severe; soil erosion, grazing, flooding, logging, cultivation, settlement, fire—recent, long ago, other—specify). (20) Population information (spatial distribution—patchy, uniform, pure stand). (21) Abundance in the site (few scattered individuals, scarce, 1–5% cover, 5–25% cover, high-more than 25% cover). (22) The dominant plant species in the site is ____. (23) The associated species are ____. (24) Extent of morphological variation (low, medium, high). (25) Characters which vary are ____. (26) Diseases and pests severity (little, moderate, severe). % population affected ____ severity ____. (27) Other notes. (28) Kind of sample (seed, vegetative). (29) Size of sample (____ plants ____ sq. meters). (30) Type of collecting (bulk, individual plants, both).
Footnotes
Previously published online as a Plant Signaling & Behavior E-publication: http://www.landesbioscience.com/journals/psb/article/9183
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