Hypervariable DNA Fingerprint Loci inMicroseris pygmaea(Asteraceae, Lactuceae)

DNA fingerprinting in botany: past, present, future

Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".

Molecular markers in plant ecology

Various methods from molecular biology reveal sequence polymorphisms in organelle and nuclear DNA that can be used as highly informative markers for the structure and dynamics of genomes at the level of populations and individuals. Molecular markers that can be determined without regard to the phenotype permit an unbiased comparison of the adaptation of organisms to their environment, its genetic basis and its effect on evolution. Several marker types used in ecological research and their uses and limitations arc briefly discussed. PCR-based methods, especially arnitrary-primer-based RAPDs, are likely to be most widely used and receive most attention. The limited use of DNA markers for overall quantitative (phenetic) comparisons of 'genetic variability' and 'generic distance' is stressed and fheir power as qualitative markers for any and all relevant regions in the genome is emphasized. Specific applications relevant to plant ecology are illustrated. These are: identification of organism and genotype even where morphology is of little help, as in mycorrhiza; identification of clones in asexually-reproducing species, even when they are widespread and intermingled; determining if genetic variation in elonal populations comes from mutations within elonal lines or from independent origins of clonal lines; reconstructing the genotype phylogeny and fruit dispersal of elonal (apomicuc) and inbred selling organisms, measuring the degree of outcrossing by offspring exclusion analysis; detecting and analyzing introgression and characterizing reeombinant genotypes in hybrid zones relative to differential adaptive responses: tracing the phylogenetic origin and extent of ecologically differentiated races or species; characterizing the genetic basis, mapping and isolating the genes responsible for special adaptive responses. In a final outlook, 1 speculate about unconventional sources of genetic variation affecting the ecological characteristics of plants that will become accessible to experimental analysis with the new molecular methods. Contents Summary 403 I. Introduction 404 II. Most ecological applications concern markers in the nuclear geonome 404 III. DNA polymorphisms differ from allozyme pohmorphisms 404 IV. Types of molecular marker 405 V. The application of markers in ecology 409 VI. From marker to character 413 VII. Outlook 414 References 414.

Multilocus DNA fingerprinting and genetic relatedness in plants: a case study with banana and tomato

The technique of DNA fingerprinting is frequently used for studies of genetic diversity and relatedness in a wide range of organisms. In humans and animals, multilocus fingerprints are mainly applied to paternity and identity test cases, behavioral ecology, and the analysis of population structures. In plants and fungi, the frequent occurrence of "low-variability" fingerprint patterns additionally allows to use multilocus fingerprinting for studying taxonomical problems at an intraspecific level. In the present article, we (1) present an overview of such approaches in a series of plant species, (2) summarize our attempts to estimate genetic relationships within two cultivated plant species, banana and tomato, by band sharing data derived from oligonucleotide fingerprints, and (3) discuss the limitations and potentials of multilocus fingerprinting for the determination of genetic relatedness.

Abundance and polymorphism of simple repetitive DNA sequences in Bmssica napus L

The Brassica napus genome has been investigated by DNA fingerprinting with six synthetic oligonucleotide probes complementary to simple repetitive sequences, namely (GATA)4, (GACA)4, (GGAT)4, (CA)8, (CT)8 and (GTG)5. While all sequence motifs were found to be present in the B. napus genome, their organization and abundance varied considerably. Among the investigated probes, (GATA)4 revealed the highest level of intraspecific polymorphism and distinguishes not only between cultivars but even between different individuals belonging to the same cultivar. In contrast, (GTG)5, (GACA)4 and (GGAT)4 produced relatively homogeneous fingerprint patterns throughout different cultivars, while hybridization to (CT)8 and (CA)8 resulted in only a few weak bands superimposed on a smear. The isoschizomeric pair Hpa II and Msp I revealed the presence of methylated cytosines in the vicinity of (GATA)m repeats. The applicability of simple repetitive sequence polymorphisms as molecular markers for Brassica species is discussed.

Identification of highly polymorphic DNA regions in tomato

This paper describes the use of oligonucleotide probes to reveal highly polymorphic DNA regions in pomato. With a (GATA)4 probe the level of polymorphism detected is high enough to identify all 15 tomato cultivars used in this study. Individual plants of one cultivar all showed the same cultivar-specific DNA-finger-print. In an F2-population of self-fertilized cv. Sonatine, GATA-containing loci segregated in a Mendelian (3∶1) fashion. Experiments with in-vitro propagated plant material showed that the DNA-fingerprints are not affected by tissue-culture procedures. This indicates that changes in the genetic integrity, which often accompany in-vitro propagation (somaclonal variation), are not extended to the DNA detected with the (GATA)4 probe. The relative high stability and the Mendelian segregation of (GATA)4-derived DNA-fingerprints make them ideally suited for identification of tomato cultivars.