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Unlinked Loci (unlinked + locus)
Selected AbstractsLinked vs. unlinked markers: multilocus microsatellite haplotype-sharing as a tool to estimate gene flow and introgressionMOLECULAR ECOLOGY, Issue 2 2007WIM J. M. KOOPMAN Abstract We have explored the use of multilocus microsatellite haplotypes to study introgression from cultivated (Malus domestica) into wild apple (Malus sylvestris), and to study gene flow among remnant populations of M. sylvestris. A haplotype consisted of alleles at microsatellite loci along one chromosome. As destruction of haplotypes through recombination occurs much faster than loss of alleles due to genetic drift, the lifespan of a multilocus haplotype is much shorter than that of the underlying alleles. When different populations share the same haplotype, this may indicate recent gene flow between populations. Similarly, haplotypes shared between two species would be a strong signal for introgression. As the expected lifespan of a haplotype depends on the strength of the linkage, the length [in centiMorgans (cM)] of the haplotype shared contains information on the number of generations passed. This application of shared haplotypes is distinct from using haplotype-sharing to detect association between markers and a certain trait. We inferred haplotypes for four to eight microsatellite loci on Linkage Group 10 of apple from genotype data using the program phase, and then identified those haplotypes shared between populations and species. Compared with a Bayesian analysis of unlinked microsatellite loci using the program structure, haplotype-sharing detected a partially different set of putative hybrids. Cultivated haplotypes present in M. sylvestris were short (< 1.5 cM), indicating that introgression had taken place many generations ago, except for two Belgian plants that contained a haplotype of 47.1 cM, indicating recent introgression. In the estimation of gene flow, FST based on unlinked loci indicated small (0.032,0.058) but statistically significant differentiation between some populations only. However, various M. sylvestris haplotypes were shared in nearly all pairwise comparisons of populations, and their length indicated recent gene flow. Hence, all Dutch populations should be considered as one conservation unit. The added value of using sharing of multilocus microsatellite haplotypes as a source of population genetic information is discussed. [source] Isolation and characterization of microsatellite markers for paternity assessment in the golden whistler (Pachycephala pectoralis: Aves)MOLECULAR ECOLOGY RESOURCES, Issue 1 2005W. F. D. VAN DONGEN Abstract We isolated and characterized six novel microsatellite markers for paternity analysis in the golden whistler Pachycephala pectoralis, by screening an enriched genomic library using nonradioactive PCR techniques. The six loci exhibited little or no evidence of null alleles and showed high levels of polymorphism (mean HE = 0.85, mean number of alleles = 15.2), making them suitable for paternity assessment in this species (exclusion probability of six unlinked loci = 0.9997). [source] Novel polymorphic microsatellite markers for paternity analysis in the red-capped robin (Petroica goodenovii: Aves)MOLECULAR ECOLOGY RESOURCES, Issue 4 2003D. K. Dowling Abstract Seven microsatellite loci were isolated and characterized from the red-capped robin Petroica goodenovii, using nonradioactive polymerase chain reaction (PCR)-based techniques to screen an enriched genomic library. Five loci showed no evidence of null alleles and were variable [mean heterozygosity (HE) = 0.440, mean number of alleles = 8]. Cross-amplification using primers for microsatellites in Phylloscopus occipitalis and Emberiza schoeniclus yielded another two polymorphic loci. The combined set of five red-capped robin and two cross-amplified loci are suitable for paternity assignment (exclusion probability for seven unlinked loci = 0.9760). [source] Testing Association with Interactions by Partitioning Chi-SquaresANNALS OF HUMAN GENETICS, Issue 1 2009Y. Yang Summary Gene-gene interaction plays an important role in association studies for complex diseases. There have been different approaches to incorporating gene-gene interactions in candidate gene or genome-wide association studies, especially for those genes with no marginal effects but with interaction effects. However, there is no general agreement on how interaction should be tested and how main effects and interaction effects act on a significance signal. In this paper, we propose a test of the null hypothesis of no association in terms of interaction effects for two unlinked loci, which is a 4 degrees of freedom (df) chi-square for two SNPs. The test, derived by contrasting inter-locus disequilibrium measures between cases and controls, can be viewed as the interaction component of the total Pearson chi-square. The remaining portion of the total chi-square can also be used for association analysis, which emphasizes main effects. Simulation studies show that in most situations our interaction test is similar in power to the test based on a logistic regression model but has more power when the genes have no marginal effects. Results also show that single-locus marginal tests can lose much power if interaction effects dominate main effects. For some specific genetic models, the interaction test may be further partitioned into four 1-df chi-squares for individual interaction effect. The interaction pattern can best be demonstrated by the 1-df chi-square components. Simulation results show that there is substantial power gain if interaction patterns are properly incorporated in association analysis. [source] | ||||||||||