Genetic similarity among Arabidopsis thaliana ecotypes estimated by DNA sequence comparison

No apparent fitness costs associated with phytoene desaturase mutations conferred resistance to diflufenican and picolinafen in oriental mustard (Sisymbrium orientale L.)

Two mutations Leu498 and Glu425 in the PDS gene were identified as the main cause conferring resistance to diflufenican and picolinafen in two oriental mustard populations P3 and P40. As mutations are suspected to affect fitness, this study was designed to test this hypothesis using the F₂ of two crosses P3.2 (P3♂ × S♀) and P40.5 (P40♂ × S♀) of oriental mustard. The F₂ plants, which segregated for target-site point mutations of PDS gene (Leu498 and Glu425) grown in monoculture and under competition with wheat in pot-trials and evaluated for growth and fecundity. All F₂ individuals were genotyped by using Cleaved Amplified Polymorphic Sequence (CAPS) technique. Regression analysis showed no fitness cost in the resistant plants because no significant difference was identified in seed and biomass production within RR, RS and SS individuals. The absence of measurable negative effects on fitness associated mutations suggests that the frequency of the PDS resistance alleles will not decline in the absence of selection pressure of PDS-inhibitors.

Generation and identification of Arabidopsis EMS mutants

EMS mutant analysis is a routine experiment to identify new players in a specific biological process or signaling pathway using forward genetics. It begins with the generation of mutants by treating Arabidopsis seeds with EMS. A mutant with a phenotype of interest (mpi) is obtained by screening plants of the M2 generation under a specific condition. Once the phenotype of the mpi is confirmed in the next generation, map-based cloning is performed to locate the mpi mutation. During the map-based cloning, mpi plants (Arabidopsis Columbia-0 (Col-0) ecotype background) are first crossed with Arabidopsis Landsberg erecta (Ler) ecotype, and the presence or absence of the phenotype in the F1 hybrids indicates whether the mpi is recessive or dominant. F2 plants with phenotypes similar to the mpi, if the mpi is recessive, or those without the phenotype, if the mpi is dominant, are used as the mapping population. As few as 24 such plants are selected for rough mapping. After finding one marker (MA) linked to the mpi locus or mutant phenotype, more markers near MA are tested to identify recombinants. The recombinants indicate the interval in which the mpi is located. Additional recombinants and molecular markers are then required to narrow down the interval. This is an iterative process of narrowing down the mapping interval until no further recombinants or molecular markers are available. The genes in the mapping interval are then sequenced to look for the mutation. In the last step, the wild-type or mutated gene is cloned to generate binary constructs. Complementation or recapitulation provides the most convincing evidence in determining the mutation that causes the phenotype of the mpi. Here, we describe the procedures for generating mutants with EMS and analyzing EMS mutations by map-based cloning.

EVIDENCE OF LOCAL ADAPTATION TO COARSE-GRAINED ENVIRONMENTAL VARIATION IN ARABIDOPSIS THALIANA

Plants can achieve an appropriate phenotype in particular conditions either constitutively or plastically, depending in part on the grain size of the environmental conditions being considered. Coarse-grained environmental variation should result in selection for local adaptation and no selection on plasticity to novel levels of the coarse-grained environmental factors. We tested the hypotheses that natural populations of the well-studied model system Arabidopsis thaliana are locally adapted to spatially coarse-grained environmental variation, and that the photoperiodic regime per se is at least partially responsible for that local adaptation, by exposing natural populations to photoperiodic regimes characteristic of their native and foreign (novel) environments. We also tested the hypothesis that plasticity to novel photoperiodic regimes should appear random. We found that populations showed evidence of local adaptation at a spatially coarse grain, although not to photoperiodic regime per se. We also found that the plasticities to novel photoperiodic regimes appeared random and did not generally show evidence of adaptive divergence. Our study highlights the need for caution in extrapolating from the finding of local adaptation to the causes of local adaptation.

Efficient discovery of DNA polymorphisms in natural populations by Ecotilling

We have adapted the mutation detection technology used in Targeting Induced Local Lesions in Genomes (TILLING) to the discovery of polymorphisms in natural populations. The genomic DNA of a queried individual is mixed with a reference DNA and used to amplify a target 1-kbp region of DNA with asymmetrically labeled fluorescent primers. After heating and annealing, heteroduplexes are nicked at mismatched sites by the endonuclease CEL I and cut strands are visualized using Li-cor gel analyzers. Putative polymorphisms detected in one fluorescence channel can be verified by appearance of the opposite cut strand in the other channel. We demonstrated the efficiency of this technology, called Ecotilling, by the discovery in 150+ individuals of 55 haplotypes in five genes, ranging from sequences differing by a single nucleotide polymorphism to those representing complex haplotypes. The discovered polymorphisms were confirmed by sequencing and included base-pair changes, small insertions and deletions, and variation in microsatellite repeat number. Ecotilling allows the rapid detection of variation in many individuals and is cost effective because only one individual for each haplotype needs to be sequenced. The technology is applicable to any organism including those that are heterozygous and polyploid.

Naturally occurring genetic variation in Arabidopsis thaliana

Currently, genetic variation is probably the most important basic resource for plant biology. In addition to the variation artificially generated by mutants in model plants, naturally occurring genetic variation is extensively found for most species, including Arabidopsis. In many cases, natural variation present among accessions is multigenic, which has historically hampered its analysis. However, the exploitation of this resource down to the molecular level has now become feasible, especially in model species like Arabidopsis, where several genes accounting for natural variation have already been identified. Dissecting this variation requires first a quantitative trait locus (QTL) analysis, which in Arabidopsis has proven very effective by using recombinant inbred lines (RILs). Second, identifying the particular gene and the nucleotide polymorphism underlying QTL is the major challenge, and is now feasible by combining high-throughput genetics and functional genomic strategies. The analysis of Arabidopsis natural genetic variation is providing unique knowledge from functional, ecological, and evolutionary perspectives. This is illustrated by reviewing current research in two different biological fields: flowering time and plant growth. The analysis of Arabidopsis natural variation for flowering time revealed the identity of several genes, some of which correspond to genes with previously unknown function. In addition, for many other traits such as those related to primary metabolism and plant growth, Arabidopsis QTL analyses are detecting loci with small effects that are not easily amenable by mutant approaches, and which might provide new insights into the networks of gene regulation.

Genetic diversity in Arabidopsis thaliana L. Heynh. investigated by cleaved amplified polymorphic sequence (CAPS) and inter-simple sequence repeat (ISSR) markers

In this study, we investigated genetic diversity among 37 accessions in Arabidopsis thaliana from Eurasia, North Africa and North America using morphological traits and two polymerase chain reaction (PCR)-based marker systems: cleaved amplified polymorphic sequences (CAPS) and inter-simple sequence repeats (ISSR). Cluster analysis based on genetic similarities calculated from CAPS data grouped the accessions roughly according to their geographical origin: one large group contained accessions from Western, Northern and Southern Europe as well as North Africa, a second group consisted of Eastern European and Asian continental accessions. North American accessions were interspersed into these groups. Contrary to the CAPS analysis, the dendrogram obtained from the ISSR data did not reflect the geographical origin of the accessions, and the calculated genetic distances did not match the CAPS results. This could be attributable to an uneven genomic distribution of ISSR markers as substantiated by a database search for ISSR binding sites in A. thaliana genomic DNA sequence files, or to the ISSR's different mode of evolution. We recommend CAPS markers for diversity analysis in A. thaliana because a careful selection of markers can ascertain an even representation of the entire genome.

Phenotypic plasticity is the major determinant of changes in phenotypic integration in Arabidopsis

•  The way in which novel genetic variation affects the patterns of phenotypic integration in natural populations is addressed here. •  An experimental study is presented of the variability in integration caused by interpopulation hybridization and consequent genetic reshuffling, as well as by changes in the physical environment in the model system Arabidopsis thaliana (Brassicaceae). •  Our results show a basic invariance of sets of covarying traits in A. thaliana, with changes in nutrient availability as the principal factor accounting for major departures from the general pattern and where differences in the genetic background of the recombinant lines are less important. In A. thaliana, the relationships among vegetative and reproductive traits form distinct clusters in multivariate space. A high degree of congruence was found between differences in the multivariate mean phenotype and the pattern of phenotypic integration, as expected on the basis of recent theoretical models. •  This relationship might indicate strong selective constraints acting on the specialized life history of these populations, which are spring ephemerals inhabiting ruderal habitats and prone to competition avoidance.

Distribution of microsatellites in relation to coding sequences within the Arabidopsis thaliana genome

The distribution of repetitive sequences, or microsatellites, formed by either one or two base pairs and longer than eight units, has been studied in almost 1 Mb of the sequenced Arabidopsis thaliana genome. Except for those formed by only G and C residues, the repetitions are more abundant in the Arabidopsis genome than can be calculated from its nucleotide composition. They are distributed in proportions higher than expected in introns, and in the intergenic regions both proximal and distal to the coding sequences. In exons, only the TC/GA microsatellite seems to be particularly abundant. The AT/TA microsatellites produce more length variation between Arabidopsis ecotypes than the A/T repeated sequences. These two classes are more abundant per kilobase than coding sequences in the Arabidopsis genome. The results indicate not only that the presence of microsatellites is not an effect of random distribution of nucleotides, but that their resolution as molecular markers may be equivalent to the number of genes and also that they do not seem to be systematically linked to specific regulatory sequences proximal to genes.

Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you

Positional (or map-based) cloning techniques are widely used to identify the protein products of genes defined by mutation. In Arabidopsis the information generated by the Genome Initiative is giving this approach a decisive boost. A wealth of sequence polymorphisms and molecular markers is now available and can be exploited for fine mapping with technically simple and robust polymerase chain reaction-based methods. As a result it has become possible to complete positional cloning projects in a short time and with relatively little effort.

Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region

We have constructed an integrated cytogenetic map of chromosome arm 4S of Arabidopsis thaliana. The map shows the detailed positions of various multicopy and unique sequences relative to euchromatin and heterochromatin segments. A quantitative analysis of the map positions at subsequent meiotic stages revealed a striking pattern of spatial and temporal variation in chromatin condensation for euchromatin and heterochromatin. For example, the centromere region consists of three domains with distinguishable structural, molecular, and functional properties. We also characterized a conspicuous heterochromatic knob of approximately 700 kb that accommodates a tandem repeat and several dispersed pericentromere-specific repeats. Moreover, our data provide evidence for an inversion event that relocated pericentromeric sequences to an interstitial position, resulting in the heterochromatic knob.

Generation of co-dominant PCR-based markers by duplex analysis on high resolution gels

Rapid and efficient procedures for the detection of sequence polymorphisms are essential for chromosomal walking and mutation detection analyses. While DNA chip technology and denaturing high-performance liquid chromatography (DHPLC) are the methods of choice for large scale facilities, small laboratories are dependent on simple ready-to-use techniques. We show that heteroduplex analysis on high resolution gel matrices efficiently detects sequence polymorphism differing as little as a single base pair (e.g. single-nucleotide polymorphism, SNP) with standard laboratory equipment. Furthermore, the matrices also discerned differences between homoduplexes, a prerequisite for co-dominant markers. The markers thus generated are referred to as duplex analysis markers. We designed PCR primers for 36 Arabidopsis thaliana loci ranging in length from 230 bp to 1000 bp. Among three ecotypes, more than half (n = 19) of the loci examined were polymorphic; five of which contained three different alleles. This simple, high resolution technique can be used to rapidly convert sequence tagged sites into co-dominant PCR-based molecular markers for fine-scale mapping studies and chromosomal walking strategies as well as for the detection of mutations in particular genes.

dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics

PCR-based detection of single nucleotide polymorphisms is a powerful tool for the plant geneticist. Cleaved amplified polymorphic sequence analysis is the most widely used approach for the detection of single nucleotide polymorphisms. However, this technique is limited to mutations which create or disrupt a restriction enzyme recognition site. This paper presents a modification of this technique where mismatches in a PCR primer are used to create a polymorphism based on the target mutation. This technique is useful for following known mutations in segregating populations and genetic mapping of isolated DNAs used for positional based cloning of new genes. In addition, a computer program has been developed that facilitates the design of these PCR primers.

Genetic variation within and among populations of Arabidopsis thaliana

We investigated levels of nucleotide polymorphism within and among populations of the highly self-fertilizing Brassicaceous species, Arabidopsis thaliana. Four-cutter RFLP data were collected at one mitochondrial and three nuclear loci from 115 isolines representing 11 worldwide population collections, as well as from seven commonly used ecotypes. The collections include multiple populations from North America and Eurasia, as well as two pairs of collections from locally proximate sites, and thus allow a hierarchical geographic analysis of polymorphism. We found no variation at the mitochondrial locus Nad5 and very low levels of intrapopulation nucleotide diversity at Adh, Dhs1, and Gpa1. Interpopulation nucleotide diversity was also consistently low among the loci, averaging 0.0014. gst, a measure of population differentiation, was estimated to be 0.643. Interestingly, we found no association between geographical distance between populations and genetic distance. Most haplotypes have a worldwide distribution, suggesting a recent expansion of the species or long-distance gene flow. The low level of polymorphism found in this study is consistent with theoretical models of neutral mutations and background selection in highly self-fertilizing species.