Showing papers on "Microsatellite published in 1995"

An evaluation of genetic distances for use with microsatellite loci.

Abstract: Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.

Genetic absolute dating based on microsatellites and the origin of modern humans.

Abstract: We introduce a new genetic distance for microsatellite loci, incorporating features of the stepwise mutation model, and test its performance on microsatellite polymorphisms in humans, chimpanzees, and gorillas. We find that it performs well in determining the relations among the primates, but less well than other distance measures (not based on the stepwise mutation model) in determining the relations among closely related human populations. However, the deepest split in the human phylogeny seems to be accurately reconstructed by the new distance and separates African and non-African populations. The new distance is independent of population size and therefore allows direct estimation of divergence times if the mutation rate is known. Based on 30 microsatellite polymorphisms and a recently reported average mutation rate of 5.6 x 10(-4) at 15 dinucleotide microsatellites, we estimate that the deepest split in the human phylogeny occurred about 156,000 years ago. Unlike most previous estimates, ours requires no external calibration of the rate of molecular evolution. We can use such calibrations, however, to test our estimate.

Abundance, variability and chromosomal location of microsatellites in wheat.

Abstract: The potential of microsatellite sequences as genetic markers in hexaploid wheat (Triticum aestivum) was investigated with respect to their abundance, variability, chromosomal location and usefulness in related species. By screening a lambda phage library, the total number of (GA)n blocks was estimated to be 3.6 x 104 and the number of (GT)n blocks to be 2.3 x 104 per haploid wheat genome. This results in an average distance of approximately 270 kb between these two microsatellite types combined. Based on sequence analysis data from 70 isolated microsatellites, it was found that wheat microsatellites are relatively long containing up to 40 dinucleotide repeats. Of the tested primer pairs, 36% resulted in fragments with a size corresponding to the expected length of the sequenced microsatellite clone. The variability of 15 microsatellite markers was investigated on 18 wheat accessions. Significantly, more variation was detected with the microsatellite markers than with RFLP markers with, on average, 4.6 different alleles per microsatellite. The 15 PCR-amplified microsatellites were further localized on chromosome arms using cytogenetic stocks of Chinese Spring. Finally, the primers for the 15 wheat microsatellites were used for PCR amplification with rye (Secale cereale) and barley accessions (Hordeum vulgare, H. spontaneum). Amplified fragments were observed for ten primer pairs with barley DNA and for nine primer pairs with rye DNA as template. A microsatellite was found by dot blot analysis in the PCR products of barley and rye DNA for only one primer pair.

Nonamplifying alleles at microsatellite loci: a caution for parentage and population studies.

Abstract: While genotyping wild red deer (Cervus elaphus) at microsatellite loci for paternity assignment, we found three loci (MAF65, BOVIRBP and CelJP23) with segregating nonamplifying alleles. Nonamplifying alleles were detected through mismatches between known mother-offspring pairs and by significant deviations from Hardy-Weinberg equilibria. In a wide range of molecular ecology application, and especially in parentage assignment, the possible existence of undetectable alleles must be taken into account; this may be particularly important for microsatellite data.

DNA Fingerprinting in Plants and Fungi

Abstract: Genetic Variation at the DNA Level. A Short Survey of Molecular Markers. Minisatellites and Simple Sequences: The Molecular Basis of Classical DNA Fingerprinting. Detection of DNA Polymorphisms by PCR-Based Fingerprinting. Laboratory Equipment. Methodology. Safety Precautions. DNA Isolation and Purification. DNA Fingerprinting Based on Hybridization. PCR-Based DNA Fingerprinting. Evaluation of Fragment Patterns. Applications of DNA Fingerprinting in Plants and Fungi. Development of Methods and Initial Investigations. Wild Plant Species. Cultivated Plant Species. Inheritance of DNA Fingerprints, Linkage Analysis and Genome Mapping in Plants. Fungi: Human Pathogens, Plant Pathogens, Insect Pathogens, Non-Pathogenic Fungi, and Commercially Important Fungi. Conclusions. Comparison of Methods for Detecting Genetic Variation. Morphological Characters and Allozymes vs. DNA Markers. Different Kinds of Molecular Markers. Future Prospects. Improvement of Existing Met hods. Extending the Spectrum of DNA Typing Strategies. References. Appendices. Index.

Mapping Quantitative Trait Loci Controlling Milk Production in Dairy Cattle by Exploiting Progeny Testing

Abstract: We have exploited "progeny testing" to map quantitative trait loci (QTL) underlying the genetic variation of milk production in a selected dairy cattle population. A total of 1,518 sires, with progeny tests based on the milking performances of > 150,000 daughters jointly, was genotyped for 159 autosomal microsatellites bracketing 1645 centimorgan or approximately two thirds of the bovine genome. Using a maximum likelihood multilocus linkage analysis accounting for variance heterogeneity of the phenotypes, we identified five chromosomes giving very strong evidence (LOD score > or = 3) for the presence of a QTL controlling milk production: chromosomes 1, 6, 9, 10 and 20. These findings demonstrate that loci with considerable effects on milk production are still segregating in highly selected populations and pave the way toward marker-assisted selection in dairy cattle breeding.

Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines

Abstract: Simple sequence repeats (SSRs), consisting of tandemly repeated multiple copies of mono-, di-, tri-, or tetranucleotide motifs, are ubiquitous in eukaryotic genomes and are frequently used as genetic markers, taking advantage of their length polymorphism. We have examined the polymorphism of such sequences in the chloroplast genomes of plants, by using a PCR-based assay. GenBank searches identified the presence of several (dA)n.(dT)n mononucleotide stretches in chloroplast genomes. A chloroplast (cp) SSR was identified in three pine species (Pinus contorta, Pinus sylvestris, and Pinus thunbergii) 312 bp upstream of the psbA gene. DNA amplification of this repeated region from 11 pine species identified nine length variants. The polymorphic amplified fragments were isolated and the DNA sequence was determined, confirming that the length polymorphism was caused by variation in the length of the repeated region. In the pines, the chloroplast genome is transmitted through pollen and this PCR assay may be used to monitor gene flow in this genus. Analysis of 305 individuals from seven populations of Pinus leucodermis Ant. revealed the presence of four variants with intrapopulational diversities ranging from 0.000 to 0.629 and an average of 0.320. Restriction fragment length polymorphism analysis of cpDNA on the same populations previously failed to detect any variation. Population subdivision based on cpSSR was higher (Gst = 0.22, where Gst is coefficient of gene differentiation) than that revealed in a previous isozyme study (Gst = 0.05). We anticipate that SSR loci within the chloroplast genome should provide a highly informative assay for the analysis of the genetic structure of plant populations.

Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models

Abstract: Samples from nine populations belonging to three African (intermissa, scutellata and capensis) and four European (mellifera, ligustica, carnica and cecropia) Apis mellifera subspecies were scored for seven microsatellite loci. A large amount of genetic variation (between seven and 30 alleles per locus) was detected. Average heterozygosity and average number of alleles were significantly higher in African than in European subspecies, in agreement with larger effective population sizes in Africa. Microsatellite analyses confirmed that A. mellifera evolved in three distinct and deeply differentiated lineages previously detected by morphological and mitochondrial DNA studies. Dendrogram analysis of workers from a given population indicated that super-sisters cluster together when using a sufficient number of microsatellite data whereas half-sisters do not. An index of classification was derived to summarize the clustering of different taxonomic levels in large phylogenetic trees based on individual genotypes. Finally, individual population x loci data were used to test the adequacy of the two alternative mutation models, the infinite allele model (IAM) and the stepwise mutation models. The better fit overall of the IAM probably results from the majority of the microsatellites used including repeats of two or three different length motifs (compound microsatellites).

The PiGMaP consortium linkage map of the pig (Sus scrofa).

Abstract: A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). As 69 of the markers on the linkage map have also been mapped physically (by others), there is significant integration of linkage and physical map data. Six informative markers failed to show linkage to these maps. As in other species, the genetic map of the heterogametic sex (male) was significantly shorter (∼16.5 Morgans) than the genetic map of the homogametic sex (female) (∼21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be ∼18 Morgans in length. Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping. Because the linkage map incorporates both highly polymorphic Type II loci, predominantly microsatellites, and Type I loci, it will be useful both for large experiments to map quantitative trait loci and for the subsequent isolation of trait genes following a comparative and candidate gene approach.

Conservation and dynamics of microsatellite loci over 300 million years of marine turtle evolution.

Abstract: Microsatellite loci consisting of (CA)(n) repetitive arrays were obtained from three species of marine turtle, and primers were designed to test for polymorphism within species and the persistence of microsatellites across species. Homologous loci were found in each test of six marine species within two families (Cheloniidae and Dermochelyidae), as well as in a freshwater species (Emydidae, Trachemys, scripta), which indicates a conservation of flanking sequences spanning approximately 300 million years of divergent evolution. The persistence of homologous microsatellites across marine turtles was confirmed by direct sequencing of loci across species and by the discovery of polymorphism in 24 of 30 cross species tests. The conservation of flanking sequences could be due to a slow rate of base substitution in turtle nuclear DNA, as previously reported for mtDNA. In contrast, the presence of up to 25 alleles per locus per species indicates that the replication slippage events responsible for changes in allele length operate as in mammals. Comparisons of alleles among species revealed that alleles of the same length may not be homologous due to mutations within the flanking sequences. Levels of heterozygosity were consistently higher in species from which the primers were designed, which suggests problems with cross-species comparisons of variability. Within species, microsatellite variation between divergent populations was consistent with results from previous mtDNA studies indicating the usefulness of microsatellites for comparing male- versus female-mediated gene flow.

An autosomal genetic-linkage map of the sheep genome

Abstract: We report the first extensive ovine genetic linkage map covering 2070 cM of the sheep genome. The map was generated from the linkage analysis of 246 polymorphic markers, in nine three-generation full-sib pedigrees, which make up the AgResearch International Mapping Flock. We have exploited many markers from cattle so that valuable comparisons between these two ruminant linkage maps can be made. The markers, used in the segregation analyses, comprised 86 anonymous microsatellite markers derived from the sheep genome, 126 anonymous microsatellites from cattle, one from deer, and 33 polymorphic markers of various types associated with known genes. The maximum number of informative meioses within the mapping flock was 222. The average number of informative meioses per marker was 140 (range 18-209). Linkage groups have been assigned to all 26 sheep autosomes.

The use of microsatellite DNA markers for soybean genotype identification

Abstract: Conventional morphological and pigementation traits, as well as disease resistance, have been used to distinguish the uniqueness of new soybean cultivars for purposes of plant variety protection. With increasing numbers of cultivars and a finite number of conventional characters, it has become apparent that such traits will not suffice to establish uniqueness. The objective of this work was to provide an initial evaluation of microsatellite or simple-sequence-repeat (SSR) DNA markers to develop unique DNA profiles of soybean genotypes. Microsatellites are DNA sequences such as (AT)n/(TA)n and (ATT)n/(TAA)n that are composed of tandemly repeated 2–5-basepair DNA core sequences. The DNA sequences flanking microsatellites are generally conserved allowing the selection of polymerase chain reaction (PCR) primers that will amplify the intervening SSR. Variation in the number of tandem repeats, “n”, results in PCR product length differences. The SSR alleles present at three (AT)n/(TA)n and four (ATT)n/(TAA)n loci were determined in each of 96 diverse soybean genotypes. Between 11 and 26 alleles were found at each of the seven loci. Only two genotypes had identical SSR allelic profiles and these had very similar pedigrees. The gene diversity for the seven markers averaged 0.87 for all 96 genotypes and 0.74 for a subset of 26 North American cultivars. These are much higher than soybean gene diversity values obtained using RFLP markers, and are similar to the average values obtained for human microsatellite markers. SSR markers provide an excellent complement to the conventional markers that are currently used to characterize soybean genotypes.

Validation of mitochondrial DNA sequencing for forensic casework analysis.

Abstract: Two sets of studies were performed to evaluate the forensic utility of sequencing human mitochondrial DNA (mtDNA) derived from various tissues and amplified by the polymerase chain reaction (PCR). Sequencing was performed on a Perkin-Elmer/Applied Biosystems Division (PE/ABD) automated DNA sequencer (model 373A). The first set of experiments included typical validation studies that had previously been conducted on forensic DNA markers, such as: chemical contaminant effects on DNA from blood and semen and the effect of typing DNA extracted from body fluid samples deposited on various substrates. A second set of experiments was performed strictly on human hair shafts. These studies included typing mtDNA from hairs that were: (1) from different body areas, (2) chemically treated, (3) from deceased individuals, and (4) deliberately contaminated with various body fluids. The data confirm that PCR-based mtDNA typing by direct automated sequencing is a valid and reliable means of forensic identification.

Microsatellite evolution — evidence for directionality and variation in rate between species

Abstract: Microsatellite DNA sequences are rapidly becoming the dominant source of nuclear genetic markers for a wide range of applications, from genome mapping to forensic testing to population studies. If misinterpretation is to be avoided, it is vital that we understand fully the way in which microsatellite sequences evolve. We have therefore compared allele length distributions for 42 microsatellites in humans with their homologues in a range of related primates. We find a highly significant trend for the loci to be longer in humans, showing that microsatellites can evolve directionally and at different rates in closely related species.

A novel measure of genetic distance for highly polymorphic tandem repeat loci

Abstract: Genetic distance measures are indicators of relatedness among populations or species and are useful for reconstructing the historic and phylogenetic relationships among such groups. Classical measures of genetic distance were developed to analyze biochemical and serological polymorphisms, systems which generally show limited variability. However, these traditional measures of genetic distance are inadequate for the analysis of certain classes of variable number tandem repeat (VNTR) loci, which have a larger number of alleles and higher levels of heterozygosity than traditional genetic markers. At the higher levels of heterozygosity observed at these loci, the standard measures of genetic distance are nonlinear and do not account for the mutational mechanisms of hypervariable loci. We have developed a measure of genetic distance, DSW, which is appropriate for the analysis of highly polymorphic DNA loci. Using computer simulations of diverging populations, we show that DSW conforms to linearity and that the variance is similar in magnitude to traditional measures of genetic distance. Comparisons of phylogenetic trees derived from the simulated divergence of human racial groups demonstrate that the branch lengths of trees prepared using DSW are more similar to the model tree than those generated using other measures. Finally, we demonstrate the applicability of DSW to evolutionary analysis by reconstructing the relationships among eight human populations using 14 microsatellite and STR loci. The phylogenetic trees generated using DSW are different from trees constructed with traditional measures and better reflect the well-documented ancient divergence of African and non-African populations.

Barley microsatellites: allele variation and mapping.

Abstract: Microsatellites have developed into a powerful tool for mapping mammalian genomes and first reports about their use in plants have been published. A database search of 228 barley sequences from GenBank and EMBL was made to determine which simple sequence repeat (SSR) motif prevails in barley. Nearly all types of SSRs were found. The (A)n and (T)n SSRs occurred more often than (C)n and (G)n for n≥10. Among the dinucleotide repeats, the (CG)n SSRs occurred least often. Trinucleotide repeats did not occur with n>7 and there is no correlation between the GC content in the trinucleotide motifs and the number of observed SSRs. Analysing 15 different microsatellites with 11 barleys yielded 2.1 alleles per microsatellite. Sequencing 25 putative microsatellites showed that the resolution capacity of highquality agarose gels was sufficient to determine differences of only three base paris. Five microsatellites were mapped on three different chromosomes of a barley RFLP map.

Integration of Simple Sequence Repeat DNA Markers into a Soybean Linkage Map

Abstract: A total of 40 simple sequence repeat (SSR) or microsatellite DNA markers were mapped in a soybean [Glycine max (L.) Merrill] mapping population that consisted of 60 F 2 plants from a cross between near isogenic lines of the cultivars Clark and Harosoy. The first objective of study was to determine the map location of SSR loci in relation to 13 classical loci controlling pigmentation and morphological traits, seven isozyme loci, and a total of 118 RFLP and RAPD markers. The second objective was to determine if the microsatellite loci were randomly distributed in the soybean genome. Linkage analysis with MAPMAKER 3.0b yielded 29 linkage groups with a total map length of 1486 centimorgans (cM). This compares with a map length of 1056 cM if the SSR markers were removed from the data set. Thirty-four of the microsatellite loci were placed in linkage groups. SSR loci were linked to loci controlling nine of the 13 classical traits, and two of seven isozyme loci. Eighteen of the 29 linkage groups contained at least one SSR locus. While this result suggested that the microsatellite loci were randomly distributed throughout the soybean genome, two clusters of five and four SSR loci, spanning 23.4 and 33.6 cM, respectively, were detected. These results indicated a relatively limited amount of clustering of soybean SSR loci, and demonstrated that microsatellite genetic markers should provide an excellent complement to RFLP and RAPD markers for use in soybean molecular biology, genetics, and breeding research. Because SSR markers detect only single genetic loci and are highly polymorphic, they can be extremely informative in pedigree tracing studies, in the analysis of progeny from multiparent matings, in a wide range of mapping applications, and in genotype identification.

Assessment of genetic diversity in dent and popcorn (Zea mays L.) inbred lines using inter-simple sequence repeat (ISSR) amplification

Abstract: Popcorn (Zea mays L.) hybrids grown in the United States are derived from narrow-based germplasm, and standard RFLP analysis detects relatively little polymorphism. Inter-simple sequence repeat (ISSR) amplification, a novel technique based on PCR amplification of inter-microsatellite sequences to target multiple loci in the genome, was employed to investigate its potential for detection of polymorphism among nineteen popcorn and eight dent corn inbred lines. ISSR yielded an average of 54 bands/primer/inbred line, with over 98% of the bands repeatable across DNA extractions and separate PCR runs. Ten primers based on di- and tri-nucleotide tandem repeats revealed 73% and 87% polymorphism among popcorn and dent corn lines, respectively, with an overall 95% polymorphism rate. Principal component and cluster analyses resulted in grouping of dent and popcorn lines corresponding to their heterotic breeding pools. ISSR amplification, in addition to being both simple and cost and time efficient, provides for rapid production of highly polymorphic markers which appear to correspond to known pedigree information. Therefore, the ISSR technique may have great potential for identifying polymorphism in species with narrow-based germplasm, and for use in DNA marker-assisted breeding approaches.

Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living bonobos (Pan paniscus)

Abstract: We show that nuclear DNA extracted from faeces of free living bonobos (Pan paniscus) can be used to amplify hypervariable simple sequence repeats, which can be used for paternity analysis and kinship studies. Of 130 DNA extractions of samples from 33 different animals, about two-thirds yielded PCR products at the first attempt. For several samples only a second extraction resulted in positive amplifications. Consistency tests revealed that in some cases only one of the two alleles was amplified. Presumably this is due to a very limited amount of bonobo DNA in the sample and we suggest therefore that a sample found to be homozygous at a given locus should be typed repeatedly for verification.

Specific microsatellite loci for brook charr reveal strong population subdivision on a microgeographic scale

Abstract: We have isolated specific microsatellite loci from a partial genomic library of brook charr Salvelinus fontinalis. Their usefulness was investigated by measuring intra- and inter-population genetic diversity at four loci among 20 individuals from each of five lakes located 3 to 22 km apart in La Mauricie national park (Canada). These markers were moderately to highly polymorphic. A total of five, six, 16 and 18 alleles per locus were detected, and their overall expected heterozygosity was 0.53, 0.58, 0.86 and 0.87. Strong inter-population diversity was detected. Highly significant differences in allelic frequencies were found in all but two pairwise χ2 permutation tests between populations at all loci. Numerous population unique alleles were observed in all five lakes. Consequently, a highly significant component of total genetic diversity was due to interpopulation variance, as exemplified by GST values of 0.33, 0.42, 0.47 and 0.84 for each individual locus. Altogether, the results indicated that these loci should be valuable in addressing fine scale population genetics questions in brook charr. To our knowledge, they also represent the first available microsatellites developed in the genus Salvelinus.

Characterization of highly variable (GA/CT) n microsatellites in the bur oak, Quercus macrocarpa

Abstract: The objective of this study was to ascertain the usefulness of polymerase chain reaction (PCR)-based microsatellite analysis for studying pollination and parentage in a wind-pollinated temperate tree. A small insert genomic library of the bur oak (Quercus macrocarpa) was constructed and screened for the presence of (CA/GT) n and (GA/CT) n repeats. The proportion of positive clones yielded estimates of 3×105 such dinucleotide repeats per genome, roughly comparable to abundances reported in other eukaryotic genomes. Thirteen positive clones were sequenced. In contrast to mammalian genomes, the (GA/CT) n motif was more abundant than the (CA/GT) n motif in these clones. The (GA/CT) n repeats also showed longer average repeat length (mean n=16.2 versus 7.3), suggesting that they are better candidates for yielding polymorphic genetic markers in oak genomes. Indeed, a survey of adult bur oaks and offspring in a small stand in northern Illinois at 3 of these (GA/CT) n microsatellite loci revealed Mendelian inheritance and extremely high levels of polymorphism, with the number of alleles at each locus ranging from 11–20 and heterozygosity ranging from 0.66 to 0.75. These results, indicating that (GA/CT) n microsatellites are both abundant and highly polymorphic in the bur oak genome, suggest that such genetic markers have tremendous potential for applications for studies of parentage, pollination and dispersal in temperate trees.

The molecular basis and evolutionary history of a microsatellite null allele in bears.

Abstract: Non-amplifying, or ’null’ alleles at microsatellite loci have been found to be common in humans (Callen et nl. 1993) and deer (Pemberton et al. 1995), and consideration must be given to the existence of such alleles in any microsatellite data set. The presence of segregating null alleles in populations is presumably the result of sequence polymorphisms that affect the binding site of one of the oligonucleotide primers used for amplification. In one case a null allele was found to result from an &bp deletion that prevented binding of one primer (Callen et al. 1993). Redesigning the primers used for amplification has allowed the collection of complete genotypic data at this and other loci. We have been using eight microsatellite markers for population studies in the three North American ursids (Paetkau & Strobeck 1994; Paetkau et al. 1995; Craighead et al. 1995), and for pedigree analysis in other species of bears. Null alleles were detected at locus GlOP in both Asiatic black bears (Ursus thibetanus) through the absence of a match between a father and two of his offspring (Fig. 1) and in North American black bears (U. americanus) through the detection of s ighcant heterozygote defiaencies in population samples from three Canadian National Parks (Table 1). To permit collection of complete genotypic data, and to investigate the phylogenetic distribution of the null alleles, a new GT-strand primer was designed with a binding site 10 bases distal to that of the original primer (5’-AGllTTACATAGGAGGAAGAAA-3’). This primer was used to survey all the black bears previously typed at locus GlOP (methods described in Paetkau et ul. 1995). The resulting pedigree (Fig. 1) and population data (Table 1) suggest that the new primer produced complete genotypic data. Within populations the null alleles vary in size in accordance with the variation normally seen at dinucleotide repeat loci suggesting that the mutation underlying the null alleles has existed for a reasonably long time. The molecular basis and phylogenetic origin of the null alleles was investigated by sequencing alleles of locus GlOP in each of the eight speaes of bears two alleles from each species except for four alleles, including two null alleles, from each of U. nmericanus and U. thibetanus. The primers were a chimera of an M13 sequence primer and a microsatellite primer a device which allowed collection of sequence data from the first base after the primer-binding site, as the start of the sequence reaction was moved back from the 3’ end of the primer (AC-strand,

Linkage disequilibrium mapping of a type 1 diabetes susceptibility gene (IDDM7) to chromosome 2q31-q33.

Abstract: The role of human chromosome 2 in type 1 diabetes was evaluated by analysing linkage and linkage disequilibrium at 21 microsatellite marker loci, using 348 affected sibpair families and 107 simplex families. The microsatellite D2S152 was linked to, and associated with, disease in families from three different populations. Our evidence localizes a new diabetes susceptibility gene, IDDM7, to within two centiMorgans of D2S152. This places it in a region of chromosome 2q that shows conserved synteny with the region of mouse chromosome 1 containing the murine type 1 diabetes gene, Idd5. These results demonstrate the utility of polymorphic microsatellites for linkage disequilibrium mapping of genes for complex diseases.

Application of two microsatellite sequences in wheat storage proteins as molecular markers.

Abstract: In eukaryotes, tandem arrays of simple-sequence repeat sequences can find applications as highly variable and multi-allelic PCR-based genetic markers. In hexaploid bread wheat, a large-genome inbreeding species with low levels of RFLP, di- and trinucleotide tandem repeats were found in 22 published gene sequences, two of which were converted to PCR-based markers. These were shown to be genome-specific and displayed high levels of variation. These characteristics make them especially suitable for intervarietal breeding applications.

Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations

Abstract: Atlantic salmon populations show low levels of genetic differentiation relative to other salmonid species, when surveyed by allozymes, and with mitochondrial DNA and nuclear ribosomal DNA markers. Here we report the application of three novel microsatellite VNTR loci to population differentiation in Atlantic salmon. A total of 232 microsatellites, cloned from Atlantic salmon, were classified as perfect, imperfect, and compound repeats. Microsatellite length, as in other teleosts, was significantly larger than published mammalian microsatellites. Primers for PCR amplification of three salmon microsatellites were designed. Allele frequencies, degree of polymorphism, and heterozygosity were estimated for five populations from Nova Scotia, Canada, and from Europe. Nei's genetic distances of 0.02–0.9 were observed among populations. There was a clear discrimination between Canadian and European fish based on unique alleles present at two loci. These Atlantic salmon primers also amplify presumably homologous lo...

Resolving genetic relationships with microsatellite markers: a parentage testing system for the swallow Hirundo rustica.

Abstract: Eight polymorphic microsatellite markers from the swallow were isolated and characterized. Extraordinary variability was revealed at the HrU6 locus with 45 different alleles scored among 46 unrelated individuals. The probability that the same genotype combination would occur in two random and unrelated individuals at six selected loci was as low as 1.3 x 10(-8) and the combined exclusion probability was 0.9996. Stable Mendelian inheritance was observed in about 1000 meioses. No significant linkage was revealed and for almost all combinations of marker-pairs, linkage closer than 5 cM could be excluded. At two loci, null (nonamplifying) alleles were encountered. Thirteen (30%) extra-pair offspring were identified in 5 (56%) broods when applying the marker set on a nearly complete swallow colony. We were able to identify a single male from the other families in the colony as the most likely father for nine of the 13 extra-pair offspring.