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Marker Interval (marker + interval)

Distribution by Scientific Domains

Life Sciences	57%

Selected Abstracts

Rapid haplotype reconstruction in pedigrees with dense marker maps

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2004
J. J. Windig
Summary Reconstruction of marker phases is not straightforward when parents are untyped. In these cases information from other relatives has to be used. In dense marker maps, however, the space of possible haplotype configurations tends to be too large for procedures such as Monte Carlo Markov chains (MCMC) to be finished within a reasonable time. We developed an algorithm that is fast and generally finds the most probable haplotype. The basic idea is to use, the smallest informative marker brackets in offspring, for each marker interval. By using only information from the offspring and analysing each marker interval separately, the lengthy analysis of large numbers of different haplotype configurations is avoided. Nevertheless the most probable haplotype can be found quickly provided the marker map is dense and enough offspring are available. Simulations are provided to indicate how well the algorithm works at different combinations of marker density, number of offspring and number of alleles per marker. In situations where the algorithm reconstruction of the most probable haplotype is not guaranteed, the algorithm may still provide a haplotype close to the optimum, i.e. a suitable starting point for numeric optimization algorithms. Zusammenfassung Die Rekonstruktion der Kopplungsphasen von Markern ist nicht unkompliziert, wenn die Typisierung der Eltern fehlt. In derartigen Fällen müssen Informationen von Verwandten genutzt werden. In dichten Markerkarten tendiert der Bereich für mögliche Haplotypenkonfigurationen jedoch dazu, zu groß zu werden, um Verfahren wie Monte Carlo Markov Chains (MCMC) in einem angemessenen Zeitrahmen anzuwenden. Wir entwickelten einen Algorithmus, der schnell ist und im Allgemeinen die wahrscheinlichsten Haplotypen findet. Die grundlegende Idee dabei bestand darin, für jeden Markerintervall erstfolgende informative Markern am linker und rechter Zeite in den Nachkommen zu nutzen. Durch die ausschließliche Nutzung von Nachkommeninformationen und durch die separate Analyse von Markerintervallen, wird die langatmige Analyse großer Anzahlen unterschiedlicher Haplotypenkonfigurationen umgangen. Dennoch kann der wahrscheinlichste Haplotyp schnell gefunden werden, vorausgesetzt die Markerkarte ist dicht und ausreichend Nachkommen sind verfügbar. Simulationen werden zur Verfügung gestellt, um zu zeigen wie gut der Algorithmus bei unterschiedlichen Kombinationen von Markerdichte, Anzahl von Nachkommen und Allelen pro Marker arbeitet. In Situationen, wo die algorithmische Rekonstruktion des wahrscheinlichsten Haplotypen nicht garantiert werden kann, kann der Algorithmus dennoch einen Haplotypen nahe des Optimums bereitstellen, z.B. einen geeigneten Startpunkt für numerische Optimierungsalgorithmen. [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]

Logistic regression approach to modelling the variability of recombination rate

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2000
By J. Szyda
The objective of the paper is to quantify the relationship between recombination rate and factors such as ,sex of sperm', paternal halfsib family, and individual, using logistic regression modelling. The analysed data set consists of 2214 single bovine sperm cell samples. Haplotypes at each single sperm were determined at eleven marker loci forming eight intervals located on chromosomes 6, 23 and X/Y. The experimental design comprises six paternal halfsib families. Six logistic regression models are fitted to the data from each interval. Departure from commonly assumed homogenous recombination is detected for one marker interval on chromosome 23 , influence of individual and ,sex of sperm' by family interaction, and for both intervals mapped to sex chromosomes , influence of ,sex of sperm' and paternal halfsib family. [source]

Genetic linkage map construction and location of QTLs for fruit-related traits in cucumber

PLANT BREEDING, Issue 2 2008
X. J. Yuan
Abstract A 173-point genetic linkage map of cucumber (Cucumis sativus L.), consisting of 116 SRAPs, 33 RAPDs, 11 SSRs, 9 SCARs, 3 ISSRs, and 1 STS, was constructed using 130 F2 progeny derived from a narrow cross between line S94 (Northern China open-field type) and line S06 (greenhouse European type). The seven linkage groups spanned 1016 cM with a mean marker interval of 5.9 cM. Using the F2 population and its F3 derived families, a total of 38 QTLs were detected on five linkage groups with an LOD threshold of 3.0 for nine fruit-related traits: fruit weight, length, and diameter, fruit flesh thickness, seed-cavity diameter, fruit-stalk length, fruit pedicel length, length/diameter and length/stalk ratio. Of the identified QTLs, fsl4.3 for fruit-stalk length explained the largest portion of phenotypic variation (r2 = ,30%). Several QTLs were detected in the same linkage region in different generations and different seasons. Additionally, several QTLs for various fruit traits were mapped to the same or neighbouring marker intervals, suggesting they are possible character associations for controlling cucumber fruit development. [source]

Confirmation and refinement of a QTL on BTA5 affecting milk production traits in the Fleckvieh dual purpose cattle breed

ANIMAL GENETICS, Issue 1 2010
A. Awad
Summary We analysed a QTL affecting milk yield (MY), milk protein yield (PY) and milk fat yield (FY) in the dual purpose cattle breed Fleckvieh on BTA5. Twenty-six microsatellite markers covering 135 cM were selected to analyse nine half-sib families containing 605 sons in a granddaughter design. We thereby assigned two new markers to the public linkage map using the CRI-MAP program. Phenotypic records were daughter yield deviations (DYD) originating from the routinely performed genetic evaluations of breeding animals. To determine the position of the QTL, three different approaches were applied: interval mapping (IM), linkage analysis by variance component analysis (LAVC), and combined linkage disequilibrium (LD) and linkage (LDL) analysis. All three methods mapped the QTL in the same marker interval (BM2830-ETH152) with the greatest test-statistic value at 118, 119.33 and 119.33 cM respectively. The positive QTL allele simultaneously increases DYD in the first lactation by 272 kg milk, 7.1 kg milk protein and 7.0 kg milk fat. Although the mapping accuracy and the significance of a QTL effect increased from IM over LAVC to LDL, the confidence interval was large (13, 20 and 24 cM for FY, MY and PY respectively) for the positional cloning of the causal gene. The estimated averages of pair wise marker LD with a distance <5 cM were low (0.107) and reflect the large effective population size of the Fleckvieh subpopulation analysed. This low level of LD suggests a need for increase in marker density in following fine mapping steps. [source]

Identification of quantitative trait loci for drought tolerance at seedling stage by screening a large number of introgression lines in maize

PLANT BREEDING, Issue 4 2009
Z. Hao
Abstract The maize genome hosts tremendous phenotypic and molecular diversity. Introgression lines (ILs), developed by continuous backcrossing to recurrent parents, could provide a unique genetic stock for quantitative trait locus (QTL) mapping. Using maize lines from six heterotic groups of different ecological zones, we developed >500 BC2F2 IL sets by crossing 11 inbred lines (as recurrent parents) with >200 local maize inbred lines (as donor parents). Of them, 34 IL sets were selected as a subset for drought tolerance screening and a total of 417 ILs survived under severe water stress at seedling stage. One set of 32 surviving ILs, derived from Chang7-2/DHuang212, was used for QTL mapping with simple sequence repeat markers covering the whole genome, with seven QTL detected. Furthermore, investigating all surviving ILs, we identified two common regions in bin 3.04, corresponding to marker intervals bnlg1904,umc1772 and umc1223,bnlg1957, respectively, which shared high genetic variation in three IL sets. Our results indicated that selective genotyping can be used to identify genetic loci for complex traits. The ILs, highly selected for drought tolerance in this study, provide a unique set of materials for both genomic studies and development of enhanced germplasm resources. [source]