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Pedigree Information (pedigree + information)
Selected AbstractsCase-control association testing in the presence of unknown relationshipsGENETIC EPIDEMIOLOGY, Issue 8 2009Yoonha Choi Abstract Genome-wide association studies result in inflated false-positive results when unrecognized cryptic relatedness exists. A number of methods have been proposed for testing association between markers and disease with a correction for known pedigree-based relationships. However, in most case-control studies, relationships are generally unknown, yet the design is predicated on the assumption of at least ancestral relatedness among cases. Here, we focus on adjusting cryptic relatedness when the genealogy of the sample is unknown, particularly in the context of samples from isolated populations where cryptic relatedness may be problematic. We estimate cryptic relatedness using maximum-likelihood methods and use a corrected ,2 test with estimated kinship coefficients for testing in the context of unknown cryptic relatedness. Estimated kinship coefficients characterize precisely the relatedness between truly related people, but are biased for unrelated pairs. The proposed test substantially reduces spurious positive results, producing a uniform null distribution of P -values. Especially with missing pedigree information, estimated kinship coefficients can still be used to correct non-independence among individuals. The corrected test was applied to real data sets from genetic isolates and created a distribution of P -value that was close to uniform. Thus, the proposed test corrects the non-uniform distribution of P -values obtained with the uncorrected test and illustrates the advantage of the approach on real data. Genet. Epidemiol. 33:668,678, 2009. © 2009 Wiley-Liss, Inc. [source] Epistatic kinship a new measure of genetic diversity for short-term phylogenetic structures , theoretical investigationsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 3 2006C. Flury Summary The epistatic kinship describes the probability that chromosomal segments of length x in Morgan are identical by descent. It is an extension from the single locus consideration of the kinship coefficient to chromosomal segments. The parameter reflects the number of meioses separating individuals or populations. Hence it is suggested as a measure to quantify the genetic distance of subpopulations that have been separated only few generations ago. Algorithms for the epistatic kinship and the extension of the rules to set up the rectangular relationship matrix are presented. The properties of the epistatic kinship based on pedigree information were investigated theoretically. Pedigree data are often missing for small livestock populations. Therefore, an approach to estimate epistatic kinship based on molecular marker data are suggested. For the epistatic kinship based on marker information haplotypes are relevant. An easy and fast method that derives haplotypes and the respective frequencies without pedigree information was derived based on sampled full-sib pairs. Different parameters of the sampling scheme were tested in a simulation study. The power of the method decreases with increasing segment length and with increasing number of segments genotyped. Further, it is shown that the efficiency of the approach is influenced by the number of animals genotyped and the polymorphism of the markers. It is discussed that the suggested method has a considerable potential to allow a phylogenetic differentiation between close populations, where small sample size can be balanced by the number, the length, and the degree of polymorphism of the chromosome segments considered. [source] Using pedigree information to monitor genetic variability of endangered populations: the Xalda sheep breed of Asturias as an exampleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2 2003F. Goyache Summary The aim of this work is to highlight the need of monitoring small populations to conserve their genetic variability by using a set of parameters to characterize both the structure of populations and management practices. As a representative example we analyse the pedigree information of the endangered Xalda sheep breed of Asturias. The herdbook of Xalda sheep included a total of 805 animals and 62 herds. The number of founders was 329. Nowadays, there are 562 live animals and 26 active herds. The breed is in risk of losing genetic diversity because of the abusive use of certain individuals as parents. The effective number of founder animals is 81.1. The effective number of founder herds is 9.9. The average value of inbreeding in the whole Xalda population was 1.5%. The average relatedness (AR) coefficient reached 1.8% in the whole pedigree. The genetic representation of the lines of founders is unbalanced. Inbreeding trends and effective size do not provide realistic information concerning the risk of loss of diversity as a result of the shallowness of the genealogical information. We suggest the monitoring of the breed using AR to unbalance the genetic contributions of specific individuals, equalizing the genetic representation of the founders and lines in the population. In addition, AR can suggest the introduction of new, under-represented animals in herds showing high average AR values relative to the population. Our results can be useful to improve the development of conservation initiatives involving open herdbooks to avoid the risk of loss of genetic diversity caused by incorrect management practices. Zusammenfassung Verwendung von Pedigree Informationen zur Konservierung genetischer Variabilität in gefährdeten Populationen: Das asturische Xalda Schaf als Beispiel Das Ziel dieser Arbeit ist es, die Notwendigkeit hervorzuheben, Pedigree Informationen in kleinen Populationen durch Verwendung bestimmter Parameter zu analysieren, um sowohl die Struktur der Populationen als auch Managementmaßnahmen zu charakterisieren. Als repräsentatives Beispiel analysieren wir Pedigree Informationen des gefährdeten Xalda Schafes in Asturien. Das Herdbuch des Xalda Schafes umfasst 805 Tiere in 62 Herden. Die Population ging aus 329 Tieren hervor. Zur Zeit beträgt die Population 562 lebende Tiere und 26 aktive Herden. Die Rasse ist aufgrund der starken Nutzung weniger Individuen als Elterntiere in Gefahr, genetische Variabilität zu verlieren. Die effektive Zahl an Gründertieren ist 81,1, die an Herden 9,9. Der durchschnittliche Inzuchtkoeffizient in der gesamten Xalda Population war 1,5%. Der durchschnittliche Verwandtschaftskoeffizient (AR) erreichte 1,8% im gesamten Pedigree. Die genetische Repräsentation der Ausgangslinien ist nicht ausgewogen. Der Inzuchtzuwachs und die effektive Größe bringen aufgrund unzureichender genealogischer Daten keine realistischen Informationen bezüglich Gefährdungsstatus. Wir empfehlen eine Untersuchung der Rasse unter Verwendung von AR, um die genetischen Anteile spezifischer Individuen auszugleichen und um die unausgewogene genetische Repräsentation der Gründer und Basislinien in der Population auszugleichen. Die Verwendung von AR legt die Nutzung neuer, unterrepräsentierter Tiere in den Herden nahe, die hohe durchschnittliche AR Werte im Vergleich zur Gesamtpopulation aufweisen. Unsere Ergebnisse können für die Weiterentwicklungen von Konservierungsmaßnahmen wie offene Herdbücher nützlich sein, um das Risiko eines Verlustes genetischer Diversität durch fehlerhafte Zuchtmaßnahmen zu vermeiden. [source] Effects of nonrandom parental selection on estimation of variance componentsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 4 2000F.S. Schenkel Summary Bayesian estimation via Gibbs sampling, REML, and Method R were compared for their empirical sampling properties in estimating genetic parameters from data subject to parental selection using an infinitesimal animal model. Models with and without contemporary groups, random or nonrandom parental selection, two levels of heritability, and none or 15% randomly missing pedigree information were considered. Nonrandom parental selection caused similar effects on estimates of variance components from all three methods. When pedigree information was complete, REML and Bayesian estimation were not biased by nonrandom parental selection for models with or without contemporary groups. Method R estimates, however, were strongly biased by nonrandom parental selection when contemporary groups were in the model. The bias was empirically shown to be a consequence of not fully accounting for gametic phase disequilibrium in the subsamples. The joint effects of nonrandom parental selection and missing pedigree information caused estimates from all methods to be highly biased. Missing pedigree information did not cause biased estimates in random mating populations. Method R estimates usually had greater mean square errors than did REML and Bayesian estimates. Zusammenfassung Bayes Schätzungen über Gibbs Stichproben, REML und Methode R wurden hinsichtlich ihrer empirischen Stichprobeneigenschaften für die Schätzung genetischer Parameter aus Daten unter Elternselektion bei Annahme eines unfinitesimalen Tiermodells verglichen. Es wurden Modelle mit und ohne Zeitgefährtimen Gruppen, zwei Stufen von Heritabilitäten, zufälliger und Elternselektion und komplette oder 15 % fehlende Ahnen verglichen. Bei vollständiger Ahneninformation waren Bayes und REML Schätzungen nicht verzerrt, Methode R aber bei Elternselektion und Zeitgefährtinnenstruktur der Daten stark verzerrt. Dies konnte empirisch auf Nichtberücksichtigung des gametischen Phasen-Ungleichgewichtes zurückgeführt werden. Die gemeinsame Wirkung fehlender Abstammungen und Elternselektion verursachte bei allen Methoden starke Verzerrungen außer bei niedrigen Heritabilitätswerten und einheitlicher Population (keine Zeitgefährten Gruppen). Unvollständige Abstammungen verursachten in zufallsgepaarten Populationen keine Verzerrung. Methode R führte i.a. zu größeren mittleren Fehlerquadraten als REML oder Bayes Methoden. [source] Epilepsy in Border Collies: Clinical Manifestation, Outcome, and Mode of InheritanceJOURNAL OF VETERINARY INTERNAL MEDICINE, Issue 1 2010V. Hülsmeyer Background: There is a lack of data on idiopathic epilepsy (IE) in Border Collies (BCs) in the veterinary literature. Hypothesis: Genetic epilepsy occurs in BCs and is frequently characterized by a severe clinical course and poor response to medical treatment. Animals: Forty-nine BCs diagnosed with IE. Methods: Medical records, seizure data, treatment data, and pedigree information of affected dogs were collected. Cases were classified phenotypically as affected or not affected; mild, moderate, or severe clinical course; active epilepsy (AE) or remission; and drug resistant or not drug resistant. Results: Clinical manifestations were classified as having a moderate (33%) or severe clinical course (49%), characterized by a high prevalence of cluster seizures and status epilepticus. Survival time was significantly decreased in dogs <2 years of age at seizure onset, and in dogs with a severe clinical course. Drug resistance was apparent in 71% of 24 dogs treated with ,2 antiepileptic drugs. The epilepsy remission rate was 18%. Median age at onset was significantly higher and initial seizure frequency was significantly lower in dogs with remission compared with dogs with AE. Pedigree analyses indicated a strong genetic founder effect in the appearance of epilepsy, resembling autosomal recessive inheritance. Conclusion and Clinical Importance: The present study confirms the occurrence of genetically mediated epilepsy with a frequent severe clinical course and drug resistance in BCs. The results provide information about the long-term prognosis of IE in BCs for veterinarians and concerned owners, and may benefit breeders as well. [source] Characterization of novel sugarcane expressed sequence tag microsatellites and their comparison with genomic SSRsPLANT BREEDING, Issue 4 2006L. R. Pinto Abstract Microsatellites or simple sequence repeats (SSRs) are one of the most suitable markers for genome analysis as they have great potential to aid breeders to develop new improved sugarcane varieties. The development of SSR derived from expressed sequence tags (EST) opens new opportunities for genetic investigations at a functional level. In the present work, the polymorphism obtained with a subset of 51 EST,SSRs derived from sucest was compared with those generated by 50 genomic SSRs (gSSR) in terms of number of alleles, polymorphism information content, discrimination power and their ability to establish genetic relationships among 18 sugarcane clones including three Saccharum species (S. officinarum, S. barberi, S. sinense). The majority of EST,SSRs loci had four to six alleles in contrast to the seven to nine observed for the gSSRs loci. Approximately, 35% of the gSSRs had PIC values around 0.90 in contrast to 15% of the EST,SSRs. However, the mean discrimination power of the two types of SSR did not differ significantly as much as the average genetic similarity (GS) based on Dice coefficient. The correlation between GS of the two types of SSRs was high (r = 0.71/P = 0.99) and significant. Although differences were observed between dendrograms obtained with each SSR type, both were in good agreement with pedigree information. The S. officinarum clone IJ76-314 was grouped apart from the other clones evaluated. The results here demonstrate that EST,SSRs can be successfully used for genetic relationship analysis, extending the knowledge of genetic diversity of sugarcane to a functional level. [source] Does Late Reproduction Extend the Life Span?POPULATION AND DEVELOPMENT REVIEW, Issue 3 2004Findings from European Royalty Statistical associations between late reproduction and female longevity led to speculations that a late birth increases a mother's life span. The database used here includes all descendants of King George I of England (1660,1727) and his wife, Sophie Dorothea (1666,1726), born in the royal dynasties in Europe up to 1939 (n=1,672). In the era of British world supremacy, these descendants formed the uppermost layer of the European aristocracy, occupying all royal thrones from 1850 onward. Novel in this study is the use of pedigree information. In pairs of ever-married full sisters (brothers), both surviving to 45 (50) years, both having at least one child, the study examines whether the sibling with the first,or last,child born later in life also lived a longer life. This design controls for genetics, socioeconomic status, parity, social support, child mortality, birth cohort, and various environmental factors. In the 157 pairs of sisters and 191 pairs of brothers, later reproduction did not extend the life span. [source] Genetic diversity in a collection of old and new bread wheat cultivars from Iran as revealed by simple sequence repeat-based analysisANNALS OF APPLIED BIOLOGY, Issue 1 2009S.A. Mohammadi Abstract Genetic diversity in a collection of 70 bread wheat (Triticum aestivum) genotypes was studied using 73 microsatellite [simple sequence repeat (SSR)] loci evenly spaced on wheat chromosomes. A total of 592 alleles with an average of 8.53 allele/locus were detected, of which 185 (31.25%) occurred only in a specific group of genotypes. A set of SSR markers consisted of 22 loci with polymorphic information content values of 0.80 or higher were selected for rapid fingerprinting of many genotypes. Average of gene diversity was 0.74 ± 0.017, and significant difference between observed and maximum theoretical values of gene diversity in the analysed SSR loci was obtained using a paired t -test. Genetic distance-based clustering methods including unweighted pair group method with arithmetic average and neighbour joining (NJ) were used for grouping of genotypes. The resulted dendrogram based on NJ and number of differences coefficient hinted of the existence of three groups. This grouping was in agreement with the pedigree information and confirmed by high within-group bootstrap value. A comparatively higher genetic diversity in the studied wheat collection as revealed by presence of high allelic diversity and large number of specific alleles could be utilised in development of new cultivars with desired characteristics. [source] Parentage assignment in Haliotis midae L.: a precursor to future genetic enhancement programmes for South African abaloneAQUACULTURE RESEARCH, Issue 9 2010Nicol-Candice Van Den Bergb Abstract The establishment and evaluation of family lines using pedigree information provides an advanced understanding of the variability that exists for complex, economically valuable traits and is a necessary step in the execution of an effective breeding programme. The aim of this study was to assign parentage to mass-spawned Haliotis midae juveniles using species-specific microsatellite markers. Screening of wild abalone individuals revealed that the nine loci selected complied with the minimum requirements for parentage analyses: a null allele frequency <5% as well as a high number and frequency of alleles per locus. A total of 598 individuals were genotyped (198 breeding individuals and 400 F1 progeny) from two farms, with parentage results yielding 91% and 90% successful assignment for Farms A and B respectively. This study, therefore, provided the necessary pedigree information required for controlled breeding of individual adult abalone and indicated the usefulness of the panel of microsatellite markers selected for parentage assignment. [source] | |||||||||||||