ANIMAL CONSERVATION, Issue 3 2000
Juliann L. Waits
Although capture,recapture techniques are often used to estimate population size, these approaches are difficult to implement for a wide variety of species. Highly polymorphic microsatellite markers are useful in individual identification, and these ,molecular tags' can be collected without having to capture or trap the individual. However, several sources of error associated with molecular identification techniques, including failure to identify individuals with the same genotype for these markers as being different, and incorrect assignment of individual genotypes, could bias population estimates. Simulations of populations sampled for the purpose of estimating population size were used to assess the extent of these potential biases. Population estimates tended to be biased downward as the likelihood of individuals sharing the same genotype increased (as measured by the probability of identity (PI) of the multi-locus genotype); this bias increased with population size. Populations of 1000 individuals were underestimated by ,5% when the PI was as small as 1.4 × 10,7. A similar-sized bias did not occur for populations of 50 individuals until the PI had increased to approximately 2.5 × 10,5. Errors in genotype assignment resulted in overestimates of population size; this problem increased with the number of samples and loci that were genotyped. Population estimates were often >200% the size of the simulated populations when the probability of making a genotyping error was 0.05/locus and 7,10 loci were used to identify individuals. This bias was substantially reduced by decreasing genotyping error rate to 0.005. If possible, only highly polymorphic loci that are critical for the identification of the individual should be used in molecular tagging, and considerable efforts should be made to minimize errors in genotype determination. [source]

Microsatellites from Clarias batrachus and their polymorphism in seven additional catfish species

MOLECULAR ECOLOGY RESOURCES, Issue 3 2003
G. H. Yue
Abstract We isolated 18 novel microsatellite loci from the walking catfish (Clarias batrachus), and examined their cross-amplification in seven additional catfish species from three families. Sixteen of the 18 microsatellites were polymorphic in the source species (allele number: 2,10/locus and expected heterozygosity: 0.30,0.87). Moreover, nine of these 18 primer pairs cross-amplified specific and polymorphic products from the genome of at least six of the seven other catfish species tested. However, the success rate of cross-species amplification varied from locus to locus, indicating that cross-species amplification of microsatellites is locus-dependent. [source]

Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation

MOLECULAR ECOLOGY, Issue 4 2001
T. L. King
Abstract Atlantic salmon (n = 1682) from 27 anadromous river populations and two nonanadromous strains ranging from south-central Maine, USA to northern Spain were genotyped at 12 microsatellite DNA loci. This suite of moderate to highly polymorphic loci revealed 266 alleles (5,37/locus) range-wide. Statistically significant allelic and genotypic heterogeneity was observed across loci between all but one pairwise comparison. Significant isolation by distance was found within and between North American and European populations, indicating reduced gene flow at all geographical scales examined. North American Atlantic salmon populations had fewer alleles, fewer unique alleles (though at a higher frequency) and a shallower phylogenetic structure than European Atlantic salmon populations. We believe these characteristics result from the differing glacial histories of the two continents, as the North American range of Atlantic salmon was glaciated more recently and more uniformly than the European range. Genotypic assignment tests based on maximum-likelihood provided 100% correct classification to continent of origin and averaged nearly 83% correct classification to province of origin across continents. This multilocus method, which may be enhanced with additional polymorphic loci, provides fishery managers the highest degree of correct assignment to management unit of any technique currently available. [source]

INTEGRATING EVOLUTIONARY AND FUNCTIONAL APPROACHES TO INFER ADAPTATION AT SPECIFIC LOCI

EVOLUTION, Issue 9 2010
Jay F. Storz
Inferences about adaptation at specific loci are often exclusively based on the static analysis of DNA sequence variation. Ideally, population-genetic evidence for positive selection serves as a stepping-off point for experimental studies to elucidate the functional significance of the putatively adaptive variation. We argue that inferences about adaptation at specific loci are best achieved by integrating the indirect, retrospective insights provided by population-genetic analyses with the more direct, mechanistic insights provided by functional experiments. Integrative studies of adaptive genetic variation may sometimes be motivated by experimental insights into molecular function, which then provide the impetus to perform population genetic tests to evaluate whether the functional variation is of adaptive significance. In other cases, studies may be initiated by genome scans of DNA variation to identify candidate loci for recent adaptation. Results of such analyses can then motivate experimental efforts to test whether the identified candidate loci do in fact contribute to functional variation in some fitness-related phenotype. Functional studies can provide corroborative evidence for positive selection at particular loci, and can potentially reveal specific molecular mechanisms of adaptation. [source]

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

EVOLUTION, Issue 9 2008
David L. Stern
Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis -regulatory, rather than the coding, regions of developmental genes. This "cis -regulatory hypothesis" has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis -regulatory hypothesis. We then test the empirical support for the cis -regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis -regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis -regulatory changes published annually is rapidly increasing. Above the species level, cis -regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis -regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question "Do coding or cis -regulatory mutations cause more phenotypic evolution?" hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics. [source]

THE ADDITIVE GENETIC VARIANCE AFTER BOTTLENECKS IS AFFECTED BY THE NUMBER OF LOCI INVOLVED IN EPISTATIC INTERACTIONS

EVOLUTION, Issue 4 2003
Yamama Naciri-Graven
Abstract We investigated the role of the number of loci coding for a neutral trait on the release of additive variance for this trait after population bottlenecks. Different bottleneck sizes and durations were tested for various matrices of genotypic values, with initial conditions covering the allele frequency space. We used three different types of matrices. First, we extended Cheverud and Routman's model by defining matrices of "pure" epistasis for three and four independent loci; second, we used genotypic values drawn randomly from uniform, normal, and exponential distributions; and third we used two models of simple metabolic pathways leading to physiological epistasis. For all these matrices of genotypic values except the dominant metabolic pathway, we find that, as the number of loci increases from two to three and four, an increase in the release of additive variance is occurring. The amount of additive variance released for a given set of genotypic values is a function of the inbreeding coefficient, independently of the size and duration of the bottleneck. The level of inbreeding necessary to achieve maximum release in additive variance increases with the number of loci. We find that additive-by-additive epistasis is the type of epistasis most easily converted into additive variance. For a wide range of models, our results show that epistasis, rather than dominance, plays a significant role in the increase of additive variance following bottlenecks. [source]

PATHOGEN RESISTANCE AND GENETIC VARIATION AT MHC LOCI

EVOLUTION, Issue 10 2002
Philip W. Hedrick
Abstract., Balancing selection in the form of heterozygote advantage, frequency-dependent selection, or selection that varies in time and/or space, has been proposed to explain the high variation at major histocompatibility complex (MHC) genes. Here the effect of variation of the presence and absence of pathogens over time on genetic variation at multiallelic loci is examined. In the basic model, resistance to each pathogen is conferred by a given allele, and this allele is assumed to be dominant. Given that s is the selective disadvantage for homozygotes (and heterozygotes) without the resistance allele and the proportion of generations, which a pathogen is present, is e, fitnesses for homozygotes become (1 ,s)(n-1)e and the fitnesses for heterozygotes become (1 ,s)(n-2)e, where n is the number of alleles. In this situation, the conditions for a stable, multiallelic polymorphism are met even though there is no intrinsic heterozygote advantage. The distribution of allele frequencies and consequently heterozygosity are a function of the autocorrelation of the presence of the pathogen in subsequent generations. When there is a positive autocorrelation over generations, the observed heterozygosity is reduced. In addition, the effects of lower levels of selection and dominance and the influence of genetic drift were examined. These effects were compared to the observed heterozygosity for two MHC genes in several South American Indian samples. Overall, resistance conferred by specific alleles to temporally variable pathogens may contribute to the observed polymorphism at MHC genes and other similar host defense loci. [source]

THE HISTORICAL BIOGEOGRAPHY OF TWO CARIBBEAN BUTTERFLIES (LEPIDOPTERA: HELICONIIDAE) AS INFERRED FROM GENETIC VARIATION AT MULTIPLE LOCI

EVOLUTION, Issue 3 2002
Neil Davies
Abstract Mitochondrial DNA and allozyme variation was examined in populations of two Neotropical butterflies, Heliconius charithonia and Dryas iulia. On the mainland, both species showed evidence of considerable gene flow over huge distances. The island populations, however, revealed significant genetic divergence across some, but not all, ocean passages. Despite the phylogenetic relatedness and broadly similar ecologies of these two butterflies, their intraspecific biogeography clearly differed. Phylogenetic analyses of mitochondrial DNA sequences revealed that populations of D. iulia north of St. Vincent are monophyletic and were probably derived from South America. By contrast, the Jamaican subspecies of H. charithonia rendered West Indian H. charithonia polyphyletic with respect to the mainland populations; thus, H. charithonia seems to have colonized the Greater Antilles on at least two separate occasions from Central America. Colonization velocity does not correlate with subsequent levels of gene flow in either species. Even where range expansion seems to have been instantaneous on a geological timescale, significant allele frequency differences at allozyme loci demonstrate that gene flow is severely curtailed across narrow ocean passages. Stochastic extinction, rapid (re)colonization, but low gene flow probably explain why, in the same species, some islands support genetically distinct and nonexpanding populations, while nearby a single lineage is distributed across several islands. Despite the differences, some common biogeographic patterns were evident between these butterflies and other West Indian taxa; such congruence suggests that intraspecific evolution in the West Indies has been somewhat constrained by earth history events, such as changes in sea level. [source]

A FAMILY WITH AUTOSOMAL DOMINANT MUTILATING NEUROPATHY NOT LINKED TO EITHER 3q13-q22 OR 9q22 LOCI

JOURNAL OF THE PERIPHERAL NERVOUS SYSTEM, Issue 1 2000
E. Bellone
The clinical separation of CMT2 from HSAN I may be difficult in some kindreds in which the sensory and motor symptoms and deficits are approximately alike. The genetic studies of CMT2 families are also controversial: one form of CMT2 was shown to map on chromosome 3q13-q22 and named CMT2B; the HSAN I locus was mapped to 9q22.1. We describe a family with an autosomal dominant inheritance in which at least three members, belonging to three generations, developed a progressive neuropathy that combined limb weakness, wasting, and severe distal sensory loss leading to prominent mutilating changes. The onset was in late childhood, with progressive weakness in the lower limbs and later in the hands, resulting in a severe paralysis in the feet in one patient. Sensory disturbances were pronounced in 2 patients, and led to poorly healing ulcerations with osteomyelitis and amputations in one foot and mutilating lesions of both hands. Electrophysiological investigation revealed an axonopaty with consistent motor damage. Sural nerve biopsy showed a reduction in the density of both myelinated and unmyelinated fibers, with regenerating clusters. Linkage analysis using 5 microsatellite markers within to the critical 9q22 region was performed. Lod scores of this family calculated by LINKAGE package excluded association to this locus. We also performed linkage studies with chr. 3q13-q22 markers associated to the CMT2b locus. Lod scores excluded this locus as well as responsiblity of the familial phenotype. The severity of motor involvement would suggest classifying the disorder of this family as a form of HSMN II rather than HSAN, indicating that a new locus is involved in the pathogenesis of this disorder. [source]

THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION

EVOLUTION, Issue 5 2007
Hopi E. Hoekstra
An important tenet of evolutionary developmental biology ("evo devo") is that adaptive mutations affecting morphology are more likely to occur in the cis -regulatory regions than in the protein-coding regions of genes. This argument rests on two claims: (1) the modular nature of cis -regulatory elements largely frees them from deleterious pleiotropic effects, and (2) a growing body of empirical evidence appears to support the predominant role of gene regulatory change in adaptation, especially morphological adaptation. Here we discuss and critique these assertions. We first show that there is no theoretical or empirical basis for the evo devo contention that adaptations involving morphology evolve by genetic mechanisms different from those involving physiology and other traits. In addition, some forms of protein evolution can avoid the negative consequences of pleiotropy, most notably via gene duplication. In light of evo devo claims, we then examine the substantial data on the genetic basis of adaptation from both genome-wide surveys and single-locus studies. Genomic studies lend little support to the cis -regulatory theory: many of these have detected adaptation in protein-coding regions, including transcription factors, whereas few have examined regulatory regions. Turning to single-locus studies, we note that the most widely cited examples of adaptive cis -regulatory mutations focus on trait loss rather than gain, and none have yet pinpointed an evolved regulatory site. In contrast, there are many studies that have both identified structural mutations and functionally verified their contribution to adaptation and speciation. Neither the theoretical arguments nor the data from nature, then, support the claim for a predominance of cis -regulatory mutations in evolution. Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis -regulatory and structural mutations, with a substantial contribution of the latter. [source]

NATURAL SELECTION ON A POLYMORPHIC DISEASE-RESISTANCE LOCUS IN IPOMOEA PURPUREA

EVOLUTION, Issue 2 2007
Joel M. Kniskern
Although disease-resistance polymorphisms are common in natural plant populations, the mechanisms responsible for this variation are not well understood. Theoretical models predict that balancing selection can maintain polymorphism within a population if the fitness effects of a resistance allele vary from a net cost to a net benefit, depending upon the extent of pathogen damage. However, there have been a few attempts to determine how commonly this mechanism operates in natural plant,pathogen interactions. Ipomoea purpurea populations are often polymorphic for resistance and susceptibility alleles at a locus that influences resistance to the fungal pathogen, Coleosporium ipomoeae. We measured the fitness effects of resistance over three consecutive years at natural and manipulated levels of damage to characterize the type of selection acting on this locus. Costs of resistance varied in magnitude from undetectable to 15.5%, whereas benefits of resistance sometimes equaled, but never exceeded, these costs. In the absence of net benefits of resistance at natural or elevated levels of disease, we conclude that selection within individual populations of I. purpurea probably does not account completely for maintenance of this polymorphism. Rather, the persistence of this polymorphism is probably best explained by a combination of variable selection and meta-population processes. [source]

MOLECULAR AND PHYLOGENETIC CHARACTERIZATION OF PHORMIDIUM SPECIES (CYANOPROKARYOTA) USING THE CPCB-IGS-CPCA LOCUS,

JOURNAL OF PHYCOLOGY, Issue 1 2005
Ivanka Teneva
The accurate determination of species of Cyanoprokaryota/Cyanophyceae has many important applications. These include the assessment of risk with regard to blooms in water reservoirs as well as the identification of species capable of producing valuable bioactive compounds. Commonly, Cyanoprokaryota are classified based on their morphology. However, morphological criteria are not always reliable because they may change, for example, due to environmental factors. Thus, genetic and molecular analyses are a promising additional approach, but their application has so far been limited to relatively few genera. In light of this, we present here the first characterization of species and strains of the genus Phormidium Kütz. based on the cpcB-IGS-cpcA locus of the phycocyanin operon. In phylogenetic analyses using deduced amino acid sequences of the cpcB-cpcA regions, Phormidium was found to be polyphyletic. This analysis appeared to be dominated by the cpcB region, which is characterized by a relatively high percentage of informative substitutions. The percentage of variable positions within the cpcB-IGS-cpcA locus overall was 16.5%, thereby indicating a level of divergence remarkably higher than that reported for Nodularia and Arthrospira in previous studies relying on cpcB-IGS-cpcA. Further, alignment of informative nucleotide substitutions in the cpcB-IGS-cpcA sequences revealed a mosaic distribution, which may be indicative of genetic recombination events. Finally, the length and sequences of the IGS region alone proved useful as markers to differentiate the cyanobacterial genus Phormidium. However, whether the IGS region per se is sufficiently discriminatory to differentiate between Phormidium species or even strains requires further investigation using newly identified Phormidium sequence data. [source]

IDENTIFICATION AND CLONING OF AMPLIFIED FRAGMENT LENGTH POLYMORPHISM MARKERS LINKED TO THE MATING TYPE LOCUS OF CHLAMYDOMONAS REINHARDTII (CHLOROPHYTA)

JOURNAL OF PHYCOLOGY, Issue 3 2001
Ralf Werner
Amplified fragment length polymorphism (AFLP) markers have been widely used to generate molecular maps of plant species, including crops and cereals. We report on a useful protocol to identify AFLPs from Chlamydomonas reinhardtii Dangeard with digoxigenin labeled primers. Although Chlamydomonas has a small genome with a high GC content, we could detect polymorphic bands that led to the identification of several AFLP markers linked to the mating type locus of Chlamydomonas. Three of these markers were isolated from the gel, reamplified, and cloned. The clones were sequenced, and the insertion of the correct fragment was verified in AFLP gels and in Southern blots. One marker showed sequence identity to parts of the fus1 gene, known to be unique in the plus mating type. We also converted some of the AFLP markers into sequence tagged site markers, which allows a fast and convenient screening of progeny of crosses. This procedure will be a useful and fast alternative to the conventional generation of maps for the positional cloning of genes from Chlamydomonas. [source]

Fine mapping and detection of the causative mutation underlying Quantitative Trait Loci

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2010
E. Uleberg
Summary The effect on power and precision of including the causative SNP amongst the investigated markers in Quantitative Trait Loci (QTL) mapping experiments was investigated. Three fine mapping methods were tested to see which was most efficient in finding the causative mutation: combined linkage and linkage disequilibrium mapping (LLD); association mapping (MARK); a combination of LLD and association mapping (LLDMARK). Two simulated data sets were analysed: in one set, the causative SNP was included amongst the markers, while in the other set the causative SNP was masked between markers. Including the causative SNP amongst the markers increased both precision and power in the analyses. For the LLD method the number of correctly positioned QTL increased from 17 for the analysis without the causative SNP to 77 for the analysis including the causative SNP. The likelihood of the data analysis increased from 3.4 to 13.3 likelihood units for the MARK method when the causative SNP was included. When the causative SNP was masked between the analysed markers, the LLD method was most efficient in detecting the correct QTL position, while the MARK method was most efficient when the causative SNP was included as a marker in the analysis. The LLDMARK method, combining association mapping and LLD, assumes a QTL as the null hypothesis (using LLD method) and tests whether the ,putative causative SNP' explains significantly more variance than a QTL in the region. Thus, if the putative causative SNP does not only give an Identical-By-Descent (IBD) signal, but also an Alike-In-State (AIS) signal, LLDMARK gives a positive likelihood ratio. LLDMARK detected less than half as many causative SNPs as the other methods, and also had a relatively high false discovery rate when the QTL effect was large. LLDMARK may however be more robust against spurious associations, because the regional IBD is largely corrected for by fitting a QTL effect in the null hypothesis model. [source]

Linkage and QTL mapping for Sus scrofa chromosome 11

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2003
M. Dragos-Wendrich
Summary Linkage and QTL maps of Sus scrofa chromosome 11 (SSC11) have been produced based on four microsatellite markers genotyped in three F2 families from Wild Boar (W), Meishan (M) and Pietrain (P) crosses. The maps were similar across the families and in agreement with already published maps. Quantitative Trait Loci (QTLs) were identified in the W × M family and not in the M × P and W × P families. The QTLs affected live weight, loin and neck meat weight, back-fat depth and food consumption, and explained up to 4.7% of the F2 phenotypic variance. Additive and dominance effects were similar in size. The Wild Boar QTL alleles led to higher trait values in comparison with Meishan alleles. Zusammenfassung Kopplungskarten für Chromosom 11 (SSC11), die durch Analyse von vier Mikrosatelliten-Markern in drei F2 -Familien aus Kreuzungen von Wildschwein (W), Meishan (M) und Pietrain (P) erstellt wurden, zeigten eine gute Übereinstimmung zwischen den Familien sowie mit Literaturergebnissen. Quantitative Trait Loci (QTLs) waren in der Familie W × M nachzuweisen, jedoch nicht in den Familien M × P und W × P. Sie beeinflussten Lebendgewicht, Kotelettstranggewicht, Rückenspeckdicke und Futteraufnahme und erklärten bis zu 4,7% der phänotypischen Varianz in der F2 -Generation. Additiv- und Dominanzeffekte waren ähnlich groß. Wildschwein-QTL-Allele führten im Vergleich zu Meishan-Allelen zu höheren Merkmalswerten. [source]

Linkage and QTL mapping for Sus scrofa chromosome 12

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2003
G. Yue
Summary The SSC12 (Sus scrofa chromosome 12) linkage and QTL maps were generated using 11 markers, of which seven to 10 have been used in the three F2 families based on Wild Boar (W), Meishan (M) and Pietrain (P) crosses. Linkage maps showed identical marker order among the families, but differed in total lengths. They were in agreement with the already published maps, except for the order SWR1021,SW605. Most quantitative trait loci (QTLs) affected fat or meat content in carcass, but were also found for some other traits (heart weight, CK20 values and teat number). They explained up to 5.4% of F2 phenotypic variance. Meishan alleles had stimulating effects on fat deposition and decreasing effects on lean content and CK20 value. The QTL profiles differed between families, with QTL effects in the vicinity of the GH1 locus found solely in the M × P family. Zusammenfassung Auf der Basis von elf Markern wurden Kopplungs- und QTL-Karten für Chromosom 12 (SSC12) in drei F2 -Familien aus Kreuzungen von Wildschwein (W), Meishan (M) und Pietrain (P) erstellt. Hierbei wurden sieben bis zehn Marker pro F2 -Familie benutzt. Die Kopplungskarten zeigten eine gleichartige Anordnung der Loci für alle Familien, jedoch mit verschiedenen Kartenlängen. Sie stimmen, außer in der Anordnung SWR1021,SW605, mit bereits publizierten Karten überein. Quantitative Trait Loci (QTLs) waren hauptsächlich für Merkmale des Fett-oder Fleischanteils im Schlachtkörper festzustellen, daneben aber auch für weitere Merkmale (Herzgewicht, CK20 -Wert, Zitzenzahl). Sie erklärten bis zu 5,4% der phänotypischen Varianz in der F2 -Generation. Meishan-Allele waren assoziiert mit einer Steigerung des Fettansatzes sowie einer Reduktion der Anteile wertvoller Teilstücke und der CK20 -Werte. Die QTL-Profile unterschieden sich zwischen den Familien und ließen Assoziationen mit dem GH1 -Locus nur in der Familie M × P erkennen. [source]

Generalized marker regression and interval QTL mapping methods for binary traits in half-sib family designs

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2001
H. N. Kadarmideen
A Generalized Marker Regression Mapping (GMR) approach was developed for mapping Quantitative Trait Loci (QTL) affecting binary polygenic traits in a single-family half-sib design. The GMR is based on threshold-liability model theory and regression of offspring phenotype on expected marker genotypes at flanking marker loci. Using simulation, statistical power and bias of QTL mapping for binary traits by GMR was compared with full QTL interval mapping based on a threshold model (GIM) and with a linear marker regression mapping method (LMR). Empirical significance threshold values, power and estimates of QTL location and effect were identical for GIM and GMR when QTL mapping was restricted to within the marker interval. These results show that the theory of the marker regression method for QTL mapping is also applicable to binary traits and possibly for traits with other non-normal distributions. The linear and threshold models based on marker regression (LMR and GMR) also resulted in similar estimates and power for large progeny group sizes, indicating that LMR can be used for binary data for balanced designs with large families, as this method is computationally simpler than GMR. GMR may have a greater potential than LMR for QTL mapping for binary traits in complex situations such as QTL mapping with complex pedigrees, random models and models with interactions. Generalisierte Marker Regression und Intervall QTL Kartierungsmethoden für binäre Merkmale in einem Halbgeschwisterdesign Es wurde ein Ansatz zur generalisierten Marker Regressions Kartierung (GMR) entwickelt, um quantitative Merkmalsloci (QTL) zu kartieren, die binäre polygenetische Merkmale in einem Einfamilien-Halbgeschwisterdesign beeinflussen. Das GMR basiert auf der Theorie eines Schwellenwertmodells und auf der Regression des Nachkommenphänotyps auf den erwarteten Markergenotyp der flankierenden Markerloci. Mittels Simulation wurde die statistische Power und Schiefe der QTL Kartierung für binäre Merkmale nach GMR verglichen mit vollständiger QTL Intervallkartierung, die auf einem Schwellenmodell (GIM) basiert, und mit einer Methode zur linearen Marker Regressions Kartierung (LMR). Empirische Signifikanzschwellenwerte, Power und Schätzer für die QTL Lokation und der Effekt waren für GIM und GMR identisch, so lange die QTL Kartierung innerhalb des Markerintervalls definiert war. Diese Ergebnisse zeigen, dass die Theorie der Marker Regressions-Methode zur QTL Kartierung auch für binäre Merkmale und möglicherweise auch für Merkmale, die keiner Normalverteilung folgen, geeignet ist. Die linearen und Schwellenmodelle, die auf Marker Regression (LMR und GMR) basieren, ergaben ebenfalls ähnliche Schätzer und Power bei großen Nachkommengruppen, was schlussfolgern lässt, dass LMR für binäre Daten in einem balancierten Design mit großen Familien genutzt werden kann. Schließlich ist diese Methode computertechnisch einfacher als GMR. GMR mag für die QTL Kartierung bei binären Merkmalen in komplexen Situationen ein größeres Potential haben als LMR. Ein Beispiel dafür ist die QTL Kartierung mit komplexen Pedigrees, zufälligen Modellen und Interaktionsmodellen. [source]

The Influence of Perceived Loci of Control and Causality in the Theory of Planned Behavior in a Leisure-Time Exercise Context

JOURNAL OF APPLIED BIOBEHAVIORAL RESEARCH, Issue 1 2004
Martin S. Hagger
The contribution that generalized locus of control and perceived locus of causality made to adolescents' intentions to participate in leisure-time physical activity was examined. A mediational model included constructs from three theoretical approaches: locus of control, self-determination theory (SDT), and the theory of planned behavior. A structural equation model revealed that the effects of generalized locus of control on attitudes, subjective norms, and intentions to participate in physical activity were mediated by intrinsic motives from SDT. Findings provide evidence in support of a motivational sequence in which locus of control influences situation-specific attitudes, subjective norms, and intentions mediated by the context-specific motives from SDT. [source]

Quantitative Trait Loci for BMD in an SM/J by NZB/BlNJ Intercross Population and Identification of Trps1 as a Probable Candidate Gene,,

JOURNAL OF BONE AND MINERAL RESEARCH, Issue 9 2008
Naoki Ishimori
Abstract Identification of genes that regulate BMD will enhance our understanding of osteoporosis and could provide novel molecular targets for treatment or prevention. We generated a mouse intercross population and carried out a quantitative trait locus (QTL) analysis of 143 female and 124 male F2 progeny from progenitor strains SM/J and NZB/BlNJ using whole body and vertebral areal BMD (aBMD) as measured by DXA. We found that both whole body and vertebral aBMD was affected by two loci on chromosome 9: one with a significant epistatic interaction on distal chromosome 8 and the other with a sex-specific effect. Two additional significant QTLs were identified on chromosome 12, and several suggestive ones were identified on chromosomes 5, 8, 15, and 19. The chromosome 9, 12, and 15 loci have been previously identified in other crosses. SNP-based haplotype analysis of the progenitor strains identified blocks within the QTL region that distinguish the low allele strains from the high allele strains, significantly narrowing the QTL region and reducing the possible candidate genes to 98 for chromosome 9, 31 for chromosome 12, and only 2 for chromosome 15. Trps1 is the most probable candidate gene for the chromosome 15 QTL. The sex-specific effects may help to elucidate the BMD differences between males and females. This study shows the power of statistical modeling to resolve linked QTLs and the use of haplotype analysis in narrowing the list of candidates. [source]

Multiple Genetic Loci From CAST/EiJ Chromosome 1 Affect vBMD Either Positively or Negatively in a C57BL/6J Background,

JOURNAL OF BONE AND MINERAL RESEARCH, Issue 1 2006
Bouchra Edderkaoui
Abstract Skeletal phenotype analyses of 10 B6.CAST-1 congenic sublines of mice have revealed evidence for the presence of three closely linked QTLs in Chr 1 that influence femoral vBMD both positively and negatively. Introduction: BMD is an important component of bone strength and a recognized predictor of risk for osteoporotic fracture. Our goal in this study was to fine map the chromosomal location of volumetric BMD (vBMD) quantitative trait loci (QTLs) in mouse distal chromosome 1 (Chr 1). Materials and Methods: After several backcrosses of the B6.CAST-1T congenic strain, which carried the initial BMD QTL in Chr 1 with B6 mice, the N10F1 generation mice were intercrossed to obtain recombinations that yielded different regions of the QTL. Thirty-eight polymorphic markers were used to fine map the initial 1T QTL region (100-192 Mb). Different skeletal parameters were compared between the 10 sublines and B6 female mice at 16 weeks of age. A t -test was used to determine the significant difference between sublines and B6 control mice, whereas one-way ANOVA and posthoc (Newman-Keuls) tests were performed to compare the phenotype between the sublines. Results: Significantly higher femur vBMD was found in sublines that carried cast alleles from 100 to 169 and 172 to 185 Mb of the centromere compared with the B6 control mice (10-12%, p < 0.001). However, sublines that carried cast alleles from 185 to 192 Mb showed significantly lower femur vBMD compared with the control mice (,6%, p < 0.05). Furthermore, femur vBMD phenotype showed a negative correlation with endosteal circumference (r = ,0.8, p = 0.003), and a strong correlation with cortical thickness for combined data from the 10 sublines (r = 0.97, p < 0.001). Moreover, a high correlation was found between body weight and both periosteal and endosteal circumferences for sublines carrying cast alleles from 167 to 175, 168 to 185, and 169 to 185 Mb, whereas no significant correlation was found between these parameters for sublines carrying cast alleles from 172 to 185 Mb. Conclusions: Genetic analysis using congenic sublines revealed that the initial BMD QTL on Chr 1 is a complex site with multiple loci affecting bone phenotypes, showing the value of the congenic approach in clearly identifying loci that control specific traits. [source]

Mapping Quantitative Trait Loci for Vertebral Trabecular Bone Volume Fraction and Microarchitecture in Mice,

JOURNAL OF BONE AND MINERAL RESEARCH, Issue 4 2004
Mary L Bouxsein
Abstract BMD, which reflects both cortical and cancellous bone, has been shown to be highly heritable; however, little is known about the specific genetic factors regulating trabecular bone. Genome-wide linkage analysis of vertebral trabecular bone traits in 914 adult female mice from the F2 intercross of C57BL/6J and C3H/HeJ inbred strains revealed a pattern of genetic regulation derived from 13 autosomes, with 5,13 QTLs associated with each of the traits. Ultimately, identification of genes that regulate trabecular bone traits may yield important information regarding mechanisms that regulate mechanical integrity of the skeleton. Introduction: Both cortical and cancellous bone influence the mechanical integrity of the skeleton, with the relative contribution of each varying with skeletal site. Whereas areal BMD, which reflects both cortical and cancellous bone, has been shown to be highly heritable, little is known about the genetic determinants of trabecular bone density and architecture. Materials and Methods: To identify heritable determinants of vertebral trabecular bone traits, we evaluated the fifth lumbar vertebra from 914 adult female mice from the F2 intercross of C57BL/6J (B6) and C3H/HeJ (C3H) progenitor strains. High-resolution ,CT was used to assess total volume (TV), bone volume (BV), bone volume fraction (BV/TV), trabecular thickness (Tb.Th), separation (Tb.Sp), and number (Tb.N) of the trabecular bone in the vertebral body in the progenitors (n = 8/strain) and female B6C3H-F2 progeny (n = 914). Genomic DNA from F2 progeny was screened for 118 PCR-based markers discriminating B6 and C3H alleles on all 19 autosomes. Results and Conclusions: Despite having a slightly larger trabecular bone compartment, C3H progenitors had dramatically lower vertebral trabecular BV/TV (,53%) and Tb.N (,40%) and higher Tb.Sp (71%) compared with B6 progenitors (p < 0.001 for all). Genome-wide quantitative trait analysis revealed a pattern of genetic regulation derived from 13 autosomes, with 5,13 quantitative trait loci (QTLs) associated with each of the vertebral trabecular bone traits, exhibiting adjusted LOD scores ranging from 3.1 to 14.4. The variance explained in the F2 population by each of the individual QTL after adjusting for contributions from other QTLs ranged from 0.8% to 5.9%. Taken together, the QTLs explained 22,33% of the variance of the vertebral traits in the F2 population. In conclusion, we observed a complex pattern of genetic regulation for vertebral trabecular bone volume fraction and microarchitecture using the F2 intercross of the C57BL/6J and C3H/HeJ inbred mouse strains and identified a number of QTLs, some of which are distinct from those that were previously identified for total femoral and vertebral BMD. Identification of genes that regulate trabecular bone traits may ultimately yield important information regarding the mechanisms that regulate the acquisition and maintenance of mechanical integrity of the skeleton. [source]

Quantitative Trait Loci on Chromosomes 2p, 4p, and 13q Influence Bone Mineral Density of the Forearm and Hip in Mexican Americans,

JOURNAL OF BONE AND MINERAL RESEARCH, Issue 12 2003
Candace M Kammerer
Abstract We performed a genome scan using BMD data of the forearm and hip on 664 individuals in 29 Mexican-American families. We obtained evidence for QTL on chromosome 4p, affecting forearm BMD overall, and on chromosomes 2p and 13q, affecting hip BMD in men. Introduction: The San Antonio Family Osteoporosis Study (SAFOS) was designed to identify genes and environmental factors that influence bone mineral density (BMD) using data from large Mexican-American families. Materials and Methods: We performed a genome-wide linkage analysis using 416 highly polymorphic microsatellite markers spaced approximately 9.5 cM apart to locate and identify quantitative trait loci (QTL) that affect BMD of the forearm and hip. Multipoint variance components linkage analyses were done using data on all 664 subjects, as well as two subgroups of 259 men and 261 premenopausal women, from 29 families for which genotypic and phenotypic data were available. Results: We obtained significant evidence for a QTL affecting forearm (radius midpoint) BMD in men and women combined on chromosome 4p near D4S2639 (maximum LOD = 4.33, genomic p = 0.006) and suggestive evidence for a QTL on chromosome 12q near locus D12S2070 (maximum conditional LOD = 2.35). We found suggestive evidence for a QTL influencing trochanter BMD on chromosome 6 (maximum LOD = 2.27), but no evidence for QTL affecting the femoral neck in men and women combined. In men, we obtained evidence for QTL affecting neck and trochanter BMD on chromosomes 2p near D2S1780 (maximum LOD = 3.98, genomic p = 0.013) and 13q near D13S788 (maximum LOD = 3.46, genomic p = 0.039), respectively. We found no evidence for QTL affecting forearm or hip BMD in premenopausal women. Conclusion: These results provide strong evidence that a QTL on chromosome 4p affects radius BMD in Mexican-American men and women, as well as evidence that QTL on chromosomes 2p and 13q affect hip BMD in men. Our results are consistent with some reports in humans and mice. [source]

Congenic Strains of Mice for Verification and Genetic Decomposition of Quantitative Trait Loci for Femoral Bone Mineral Density,

JOURNAL OF BONE AND MINERAL RESEARCH, Issue 2 2003
Kathryn L Shultz
Abstract Peak femoral volumetric bone mineral density (femoral bone mineral density) in C57BL/6J (B6) 4-month-old female mice is 50% lower than in C3H/HeJ (C3H) and 34% lower than in CAST/EiJ (CAST) females. Genome-wide analyses of (B6 × C3H)F2 and (B6 × CAST)F2 4-month-old female progeny demonstrated that peak femoral bone mineral density is a complex quantitative trait associated with genetic loci (QTL) on numerous chromosomes (Chrs) and with trait heritabilities of 83% (C3H) and 57% (CAST). To test the effect of each QTL on femoral bone mineral density, two sets of loci (six each from C3H and CAST) were selected to make congenic strains by repeated backcrossing of donor mice carrying a given QTL-containing chromosomal region to recipient mice of the B6 progenitor strain. At the N6F1 generation, each B6.C3H and B6.CAST congenic strain (statistically 98% B6-like in genomic composition) was intercrossed to obtain N6F2 progeny for testing the effect of each QTL on femoral bone mineral density. In addition, the femoral bone mineral density QTL region on Chr 1 of C3H was selected for congenic subline development to facilitate fine mapping of this strong femoral bone mineral density locus. In 11 of 12 congenic strains, 6 B6.C3H and 5 B6.CAST, femoral bone mineral density in mice carrying c3h or cast alleles in the QTL regions was significantly different from that of littermates carrying b6 alleles. Differences also were observed in body weight, femoral length, and mid-diaphyseal periosteal circumference among these 11 congenic strains when compared with control littermates; however, these latter three phenotypes were not consistently correlated with femoral bone mineral density. Analyses of eight sublines derived from the B6.C3H-1T congenic region revealed two QTLs: one located between 36.9 and 49.7 centiMorgans (cM) and the other located between 73.2 and 100.0 cM distal to the centromere. In conclusion, these congenic strains provide proof of principle that many QTLs identified in the F2 analyses for femoral bone mineral density exert independent effects when transferred and expressed in a common genetic background. Furthermore, significant differences in femoral bone mineral density among the congenic strains were not consistently accompanied by changes in body weight, femur length, or periosteal circumference. Finally, decomposition of QTL regions by congenic sublines can reveal additional loci for phenotypes assigned to a QTL region and can markedly refine genomic locations of quantitative trait loci, providing the opportunity for candidate gene testing. [source]

Allele Frequencies of 15 STR Loci in the Population of the City of Quito, Ecuador

JOURNAL OF FORENSIC SCIENCES, Issue 2 2008
María Atilia Gómez Ph.D.
Population: Quito City Population (Ecuador, South America, n = 116,207). [source]

Haplotype Frequencies of Eight Y-Chromosome Short Tandem Repeats Loci in Four Amerindian Populations (State of Hidalgo, Mexico)

JOURNAL OF FORENSIC SCIENCES, Issue 2 2007
Carme Barrot Ph.D.
POPULATION: Amerindian populations: Huastecos (n=97), Otomies de la Sierra (n=41), Otomies del Valle (n=40), and Tepehuas (n=13). [source]

Allele Frequencies of 20 Y-Chromosomal Short Tandem Repeat Loci in a Tribal Population of Deccan Plateau, India

JOURNAL OF FORENSIC SCIENCES, Issue 2 2007
G. Hima Bindu M.Sc.
POPULATION: Eighty male individuals from a nomadic tribal population belonging to Dravidian and Indo-Caucasian ethnicities from Deccan Plateau, Andhra Pradesh, India (1), were analyzed in the present study. [source]

Allele Frequencies for Two Short Tandem Repeat Loci in the Chinese Han Population from Chengdu, China, and a Thai Population from Thailand

JOURNAL OF FORENSIC SCIENCES, Issue 1 2007
Yanyun Wang M.D.
POPULATION: Chinese Han and Thai. [source]

Southwest China Han Population Data for Nine Y-STR Loci by Multiplex Polymerase Chain Reaction

JOURNAL OF FORENSIC SCIENCES, Issue 1 2007
Meisen Shi Ph.D.
POPULATION: One hundred and twenty unrelated Han ethnic individuals from Chengdu, southwest China. [source]

Analysis of Y-STR Loci in a Population Sample from Northeast China

JOURNAL OF FORENSIC SCIENCES, Issue 1 2006
Xiuling Wang Ph.D.
POPULATION: A total of 141 unrelated Chinese Han male individuals living in Liaoning in northeast China. [source]

Quantitative Trait Loci for Panicle Layer Uniformity Identified in Doubled Haploid Lines of Rice in Two Environments

JOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 9 2009
Liangyong Ma
Abstract Uniformity of stem height in rice directly affects crop yield potential and appearance, and has become a vital index for rice improvement. In the present study, a doubled haploid (DH) population, derived from a cross between japonica rice Chunjiang 06 and indica rice TN1 was used to analyze the quantitative trait locus (QTL) for three related traits of panicle-layer-uniformity; that is, the tallest panicle height, the lowest panicle height and panicle layer disuniformity in two locations: Hangzhou (HZ) and Hainan (HN). A total of 16 QTLs for three traits distributed on eight chromosomes were detected in two different environments. Two QTLs, qTPH -4 and qTPH -8 were co-located with the QTLs for qLPH -4 and qLPH -8, which were only significant in the HZ environment, whereas the qTPH -6 and qLPH -6 located at the same interval were only significant in the HN environment. Two QTLs, qPLD -10-1 and qPLD -10-2, were closely linked to qTPH-10, and they might have been at the same locus. One QTL, qPLD -3, was detected in both environments, explaining more than 23% of the phenotypic variations. The CJ06 allele of qPLD -3 could increase the panicle layer disuniformity by 9.23 and 4.74 cm in the HZ and HN environments. Except for qPLD -3, almost all other QTLs for the same trait were detected only in one environment, indicating that these three traits were dramatically affected by environmental factors. The results may be useful for elucidation of the molecular mechanism of panicle-layer-uniformity and marker assisted breeding for super-rice. [source]