DNA segments mapped by reciprocal use of microsatellite primers between mouse and rat

Analysis of tetraploid Elymus species using wheat microsatellite markers and RAPD markers

An analysis of Amplification fragment polymorphism of DNA from 27 accessions of 19 tetraploid Elymus species was carried out using 18 wheat microsatellite (WMS) primer pairs and 10 decamer primers. Ten WMS primer pairs produced multiple polymorphism on all accessions tested. Two independent phenograms, one based on WMS-PCR and one on RAPDs, separated the 19 tetraploid species into two main groups, viz., the SH genome species group and the SY genome species group. The results coincide with the genomic classification of these species and hence support previous studies showing that Elymus is not a monophyletic genus. The assays indicated that accessions within a species cluster together, which concurs with the morphological classification. Interspecific and intraspecific polymorphisms were detected by the WMS-PCR and RAPD analyses. Variation was observed among accessions of Elymus caninus. The WMS-PCR detected a much higher level of polymorphism than the RAPD analysis. WMSs seem to be more efficient markers than RAPD markers for studying the population diversity of Elymus species. The potential of cross-species amplification of microsatellite markers as an additional source for genetic analysis and applications in Elymus is discussed in the context of these results.

Thirty years of Mus spretus: a promising future

Extensive genetic polymorphisms in Mus spretus have ensured its widespread use in many areas of genetics. With the recent increase in the number of single nucleotide polymorphisms available for laboratory mouse strains, M. spretus is becoming less appealing, in particular for genetic mapping. Although M. spretus mice are aggressive and poor breeders, they have a bright future because they provide phenotypes unobserved in laboratory strains, and tools are available for modifying their genome and dissecting the genetic architecture of complex traits. Furthermore, they provide information on fundamental genetic questions, such as the details of evolution of genomes and speciation. Here, we examine the use of M. spretus from these perspectives. The impending completion of the M. spretus genome sequence will synergize these advantages.

A novel set of microsatellite marker loci linkage-mapped in the house musk shrew, Suncus murinus

Ten microsatellite DNA loci developed for the white-toothed shrew (Crocidura russula) were tested for PCR amplification and for utility in linkage studies in the house musk shrew, Suncus murinus. Four primer pairs successfully yielded PCR amplicons and showed polymorphism between two mutant strains, BAN-kc,oeb and WZ. Cloning and sequencing of the PCR amplicons of all the four loci confirmed the presence of microsatellite sequences. Alleles segregating in an F2 resource population constructed from the two strains ranged between two and five. Linkage analysis of the four loci together with 18 other polymorphic markers and three mutant loci resulted in five linkage groups containing three newly mapped microsatellite loci. This study reports the first microsatellite markers being registered in this species.

Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane

The use of maize microsatellite markers as a potential cost-effective method for molecular analysis of sugarcane was evaluated. Of the 34 primer pairs obtained from maize genomic libraries, 14 showed repeatable amplifications in Saccharum species clones, commercial hybrids, and the related genera Erianthus, accounting for 41.17% cross transferability. Complex banding patterns were encountered in sugarcane with the number of amplified fragments ranging from 7 to 14 with an average of 10 per primer, indicating the high polyploidy and heterozygosity existing in sugarcane. Phenetic analysis of the SSR polymorphisms produced by nine primers could clearly differentiate the different species of Saccharum and Erianthus and revealed the relationships that existed between them. Genetic similarity co-efficient indicated low diversity existing among the S. officinarum clones (82%) and a relatively higher level of diversity in the S. spontaneum clones (69.7%). Higher level of divergence of Erianthus from Saccharum was also clearly estabilished. Five primers produced genus- and species-specific fragments for Erianthus, S. spontaneum, S. officinarum, and S. barberi. The polymorphic primers, when tested on a panel of 30 commercial sugarcane cultivars, revealed a broad range (32.4-83.3%) of pair-wise similarity values, indicating their ability to detect high levels of polymorphism. A combination of two primers could differentiate all the varieties, further emphasizing their potential in fingerprinting and varietal identification.

Chromosomal mapping of genes for epilepsy in NER: a rat strain with tonic-clonic seizures

PURPOSE

NER is a mutant rat strain that exhibits spontaneous tonic-clonic convulsions accompanied by epileptic discharges on ictal EEG and serves as a model for generalized tonic-clonic seizures in humans. Our previous experiments have suggested that a major autosomal recessive gene and several minor genes regulate the inheritance of tonic-clonic seizures in NER. The purpose of this study was to confirm the mode of inheritance and to locate the causative genes for epilepsy in NER on the rat genetic map.

METHODS

We developed F1 hybrid (F1) and reciprocal back-cross progenies of NER with a seizure-resistant strain, F344, and evaluated their seizure susceptibility under tossing-stimulated and nonstimulated conditions. Backcross animals were genotyped using simple sequence length polymorphism markers for polymerase chain reactions. Linkage between seizure susceptibility and marker loci was analyzed by chi2 statistic tests and by the computer programs MAPMAKER/EXP and MAPMAKER/QTL.

RESULTS

Under tossing-stimulating conditions, tonic-clonic seizures were provoked in 90% of NER and 66% of (F1 x NER) backcross animals, but no seizures occurred in the F344, F1, or (F1 x F344) backcross animals. Routine monitoring of nonstimulated animals revealed spontaneous tonic-clonic convulsions in 100% of NER and 64.2% of (F1 x NER) backcross animals, but no seizures in F344 or F1. Gender effect on seizure susceptibility was negligible in (F1 x NER) backcross in both conditions. Preliminary genome-wide scanning and subsequent precise location of the causative genes revealed seizure susceptibility loci, designated Ner1 and Ner2, on rat chromosomes 1 and 3, respectively.

CONCLUSIONS

Ner1 is a locus that controls the inheritance of spontaneous tonic-clonic seizures in an autosomal recessive mode, whereas Ner2 affects the occurrence of tossing-induced seizures. Orthologous genes in the vicinity of these loci may be related to epileptogenesis in other species, including humans.

Genetic analysis of inherited hypertension in the rat

Blood pressure is a quantitative trait that has a strong genetic component in humans and rats. Several selectively bred strains of rats with divergent blood pressures serve as an animal model for genetic dissection of the causes of inherited hypertension. The goal is to identify the genetic loci controlling blood pressure, i.e., the so-called quantitative trait loci (QTL). The theoretical basis for such genetic dissection and recent progress in understanding genetic hypertension are reviewed. The usual paradigm is to produce segregating populations derived from a hypertensive and normotensive strain and to seek linkage of blood pressure to genetic markers using recently developed statistical techniques for QTL analysis. This has yielded candidate QTL regions on almost every rat chromosome, and also some interactions between QTL have been defined. These statistically defined QTL regions are much too large to practice positional cloning to identify the genes involved. Most investigators are, therefore, fine mapping the QTL using congenic strains to substitute small segments of chromosome from one strain into another. Although impressive progress has been made, this process is slow due to the extensive breeding that is required. At this point, no blood pressure QTL have met stringent criteria for identification, but this should be an attainable goal given the recently developed genomic resources for the rat. Similar experiments are ongoing to look for genes that influence cardiac hypertrophy, stroke, and renal failure and that are independent of the genes for hypertension.

A radiation hybrid map of the rat genome containing 5,255 markers

A whole-genome radiation hybrid (RH) panel was used to construct a high-resolution map of the rat genome based on microsatellite and gene markers. These include 3,019 new microsatellite markers described here for the first time and 1,714 microsatellite markers with known genetic locations, allowing comparison and integration of maps from different sources. A robust RH framework map containing 1,030 positions ordered with odds of at least 1,000:1 has been defined as a tool for mapping these markers, and for future RH mapping in the rat. More than 500 genes which have been mapped in mouse and/or human were localized with respect to the rat RH framework, allowing the construction of detailed rat-mouse and rat-human comparative maps and illustrating the power of the RH approach for comparative mapping.

Microsatellite evolution: polarity of substitutions within repeats and neutrality of flanking sequences

Though extensively used in a variety of disciplines, the evolutionary pattern of microsatellite sequences is still unclear. We addressed several questions relating to microsatellite evolution by analysing historically accumulated mutation events in a large set of artiodactyl (CA)n repeats, through sequence analysis of orthologous bovine and ovine loci. The substitution rate in microsatellite flanking sequences was not different from that in intron sequences, suggesting that if intron sequences in general are selectively neutral, sequences close to microsatellites are similarly so. This observation thus does not support the idea that successful heterologous amplification of microsatellites across distantly related taxa would be due to flanking sequences generally being under some form of selection. Interestingly, the substitution rate at the first nucleotide positions flanking repeats was significantly higher than in sequences further away. Moreover, the substitution rate in repeat units in the very end of microsatellites was significantly higher than that in the middle of repeat regions. Together these observations suggest a relative instability close to the boundary between repetitive and unique sequences. We present three models that potentially could explain such a feature, all involving inefficiency of mismatch repair systems.

Comparative gene mapping: a fine-scale survey of chromosome rearrangements between ruminants and humans

A total of 202 genes were cytogenetically mapped to goat chromosomes, multiplying by five the total number of regional gene localizations in domestic ruminants (255). This map encompasses 249 and 173 common anchor loci regularly spaced along human and murine chromosomes, respectively, which makes it possible to perform a genome-wide comparison between three mammalian orders. Twice as many rearrangements as revealed by ZOO-FISH were observed. The average size of conserved fragments could be estimated at 27 and 8 cM with humans and mice, respectively. The position of evolutionary breakpoints often correspond with human chromosome sites known to be vulnerable to rearrangement in neoplasia. Furthermore, 75 microsatellite markers, 30 of which were isolated from gene-containing bacterial artificial chromosomes (BACs), were added to the previous goat genetic map, achieving 88% genome coverage. Finally, 124 microsatellites were cytogenetically mapped, which made it possible to physically anchor and orient all the linkage groups. We believe that this comprehensive map will speed up positional cloning projects in domestic ruminants and clarify some aspects of mammalian chromosomal evolution.

Extension of conserved regions in the rat and mouse genomes by chromosomal assignments of 29 rat genes

We recently constructed a comparative genetic map of the rat, mouse and human genomes based on information obtained from several databases. In this study, we performed chromosomal assignments of 29 rat genes with somatic cell hybrid clones, in order to clarify and extend the conserved regions in the rat and mouse genomes. As a result, the conserved regions were extended by 89 cM. Together with our previous report, the length of the conserved regions in the rat and mouse spans 847 cM on the mouse linkage map, indicating that 53% of the mouse genome is covered by homologous regions in the rat. In addition, four conserved regions were newly revealed. The method described in this study appears to be simple and efficient for constructing a whole genome comparative map of the rat and mouse.

Construction and extensive characterization of a goat bacterial artificial chromosome library with threefold genome coverage

A goat Bacterial Artificial Chromosome (BAC) library of 61,440 independent clones was constructed and characterized. The average size of the inserts was estimated at 153 kilobases by analyzing almost 500 clones using Not1 digestion followed by FIGE (Field Inverted Gel Electrophoresis) analysis. The library represents about three genome equivalents, which yields a theoretical probability of 0.95 of isolating a particular DNA sequence. After individual growth, the clones were arrayed in 40 superpools, which were organized in three dimension pools. A rapid technique for pool DNA preparation by microwave treatment was set up. This technique was compatible with PCR analysis. Primer pairs from 166 sequences (microsatellites, coding sequences from goat, and conserved Expressed Sequence Tags (ESTs) from humans) enabled the library to be successfully searched in 165 cases, with an average of 3.52 positive superpools. Only one sequence could not be found. The degree of chimerism was evaluated by FISH analysis with DNA from over 110 clones and was estimated at 4%. This BAC library will constitute an invaluable tool for positional cloning in ruminants, as well as for more general comparative mapping studies in mammals.

Construction of a high-resolution genetic map encompassing the hotfoot locus

Hotfoot (ho) is a mutation affecting posture and movement. We report a new allele associated with the insertion of a transgene and its high-resolution mapping. Analysis of the transgene revealed that two complete and two truncated copies are inserted at the ho locus. The ho locus cosegregated with D6Mit299 in 702 meioses and is confined to a 1.1-cM region between the markers D6Mit122 and D6Mit174. If the order and distances between markers are consistent with previously published mapping data, the position of the ho locus must be revised and placed approximately 30 cM from the centromere. This high-resolution genetic map is the first step towards the positional cloning of the ho mutation.

A non-MHC locus essential for autoimmune type I diabetes in the Komeda Diabetes-Prone rat

The Long-Evans Tokushima Lean (LETL) rat, characterized by rapid onset of insulin-dependent (type I) diabetes mellitus (IDDM), no sex difference in the incidence of IDDM, autoimmune destruction of pancreatic beta cells, and no significant T cell lymphopenia, is a desirable animal model for human IDDM. We have established a diabetes-prone substrain of the LETL rat, named Komeda Diabetes-Prone (KDP) rat, showing a 100% development of moderate to severe insulitis within 220 d of age. The cumulative frequency of IDDM was 70% at 120 d of age, and reached 82% within 220 d of age. Here, we performed the first genome-wide scan for non-MHC IDDM susceptibility genes in this strain. The analysis of three crosses has led to the revelation of a major IDDM susceptibility gene, termed Iddm/kdp1, on rat chromosome (Chr) 11. Homozygosity for the KDP allele at this locus is shown to be essential for the development of moderate to severe insulitis and the onset of IDDM. Comparative mapping suggests that the homologues of Iddm/ kdp1 are located on human Chr 3 and mouse Chr 16 and would therefore be different from previously reported IDDM susceptibility genes.

Phylogenetics of the laboratory rat Rattus norvegicus

A genealogic tree was constructed for inbred strains of the laboratory rat, including 63 strains and 214 of their substrains. Information on genetic and biochemical marker typings of these lines was collected from the literature and from the World Wide Web. Data on 995 polymorphisms were processed into a phylogenetic distance matrix, and a tree was obtained by the Fitch-Margoliash distance matrix method. The inbred strains of the laboratory rat showed an average polymorphism for pairwise comparison of 53%. Strain BN showed the highest genetic divergence from all the other ones. Comparison with the mouse phylogenetic tree indicated that laboratory rats possess a higher diversity than inbred strains of mice not derived from wild species. These results provide a phylogenetic basis in the choice of rat strains for genetic linkage experiments.

Mapping of two genetic loci, Ten-1 and Ten-2, associated with thymus enlargement in BUF/Mna rats

The thymoma-prone BUF/Mna rat is a useful model for human thymoma. Thymoma develops spontaneously in these rats at an incidence of nearly 100%. At pre-thymoma age, BUF/Mna rats have extremely large thymuses when compared with those of rats of the other strains, suggesting the presence of genes that regulate the thymus enlargement. We performed linkage study to identify the genetic loci associated with thymus enlargement in {(WKY/NCrj x BUF/Mna) F1 x BUF/Mna} backcross rats. Linkage study showed the significant associations between thymus size and markers on Chromosomes (Chrs) 1 and 13, suggesting the presence of two genes, Ten-1 and Ten-2, which regulate the thymus enlargement. Ten-1 was located between myosin light chain, muscle 2 (MYL2) and D1Mgh11 loci on Chr 1, and Ten-2 was located between synaptotagmin II (SYT2) and D13N2 loci on Chr 13.

A wide-range survey of cross-species microsatellite amplification in birds

The possibility to perform cross-species microsatellite amplification in birds was surveyed by analysing sets of primers developed from the swallow and the pied flycatcher genomes on a panel of 48 different bird species. In total, 162 cases (species/marker combinations) of heterologous amplification were recorded. Ten amplification products were sequenced and all were found to be true homologues of the original loci. There was a significant and negative relationship between microsatellite performance and evolutionary distance between the original species and the tested species. As a rough indicator of expected cross-species microsatellite performance we estimate that 50% of markers will reveal polymorphism in a species with a DNA-DNA hybridization delta T(m)H value of 5 separating it from the original species. This corresponds to a divergence time of = 11 million years before present for passerine birds. The established relationship between performance and evolutionary distance agrees very well with data obtained from some mammalian species. The proportion of polymorphic loci among those markers that amplified decreased with increasing genetic distance, suggesting that few long repeats are preserved during evolution. One of the swallow markers, HrU2, amplified a specific product in all species analyzed and will thus allow access of nuclear sequence data over a broad range of species. The only predictor of cross-species performance was the amount of non-specific amplification seen in the original species. An analysis of 10 species from within the family Hirundinidae with the swallow primers consistently revealed extensive polymorphism with average probabilities of identical genotypes ranging from 6 x 10(-4) to 6 x 10(-7). There were distinct allele frequency differences between the Hirundinidae species and we envisage that microsatellite cross-species amplification will be a useful tool in phylogeny construction and in species identification.

An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species

Microsatellites, also called sequence tagged microsatellite sites (STMSs), have become important markers for genome analysis but are currently little studied in plants. To assess the value of STMSs for analysis within the Citrus plant species, two example STMSs were isolated from an intergeneric cross between rangpur lime (Citrus x limonia Osbeck) and trifoliate orange (Poncirus trifoliata (L.) Raf.). Unique flanking primers were constructed for polymerase chain reaction amplification both within the test cross and across a broad range of citrus and related species. Both loci showed length variation between test cross parents with alleles segregating in a Mendelian fashion to progeny. Amplification across species showed the STMS flanking primers to be conserved in every genome tested. The traits of polymorphism, inheritance, and conservation across species mean that STMS markers are ideal for genome mapping within Citrus, which contains high levels of genetic variability.

Sequence conservation of microsatellites between Bos taurus (cattle), Capra hircus (goat) and related species. Examples of use in parentage testing and phylogeny analysis

A panel of 70 bovine microsatellites was tested for amplification from goat DNA. Forty-three could be successfully amplified by PCR, 20 of which were tested for polymorphism. Three were applied for parentage testing in goat families and their exclusion probability evaluated. Fourteen were cloned and sequenced from goat DNA, and goat and bovine sequences were compared to evaluate interspecific conservation. Correlation between the structure of the dinucleotide repeat and the number of alleles was studied and indicated that interruption(s) in the repeat could explain the difference in the levels of polymorphism between the two species. This study provides a valuable in vivo clue to the mechanism generating polymorphism in microsatellites. Sequence conservation was also observed for several microsatellites with two wild species of Bovidae, Nilgaï (Boselaphus tragocamelus) and Himalayan Tur (Capra cylindricornis), and with one species of Cervidae, the fallow deer (Cervus dama). This study showed that an estimated 40 per cent of the microsatellites isolated from cattle will prove useful to study the caprine genome and to characterize economically important genetic loci in this species. Moreover, bovine microsatellites were shown to constitute very useful tools for the study of genetic diversity of the Artiodactyla.

Variation of short tandem repeats within and between species belonging to the Canidae family

Frequency distribution and allele size in 20 canine microsatellite loci were analyzed in 33 flat-coated retrievers, 32 dachshunds, 10 red foxes, and 10 Arctic foxes. Overall, the major difference between the two dog breeds was the relative allele frequencies rather than the size ranges of alleles at the individual locus. The average heterozygosity within the two dog breeds was not significantly different. Since the average heterozygosity at several polymorphic loci is a relative measure of heterogeneity within the population, analysis of heterozygosity within microsatellite loci is suggested as a measure for the diversity of populations. Eighty percent (16 of 20) of the canine microsatellite primer pairs amplified corresponding loci in the two fox species. This reflects a very high sequence conservation within the Canidae family relative to findings in, for instance, the Muridae family. This indicates that it will be possible to utilize the well-characterized fox karyotype instead of the dog karyotype as a step towards physical mapping of the dog genome. Analysis of exclusion power and probabilities of genetic identity between unrelated animals by use of the seven most informative loci demonstrated that it will be possible to assemble a panel of microsatellite loci that is effective for parentage analysis in all breeds.

Simple sequences

Simple sequences (or microsatellites) are stretches of monotonous repetitions of short (1-5bp) nucleotide motifs that are distributed across the whole genome in eukaryotes. They are probably generated by slippage during replication and their primary mutation rate seems to be controlled predominantly by the efficiency of the mismatch repair system. Although most mutations in simple sequence loci appear to be neutral, some mutations in particular stretches have been implicated as having a role in human genetic diseases.