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Observed Polymorphisms (observed + polymorphism)
Selected AbstractsPATHOGEN RESISTANCE AND GENETIC VARIATION AT MHC LOCIEVOLUTION, Issue 10 2002Philip 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] Automated Alignment and Nomenclature for Consistent Treatment of Polymorphisms in the Human Mitochondrial DNA Control RegionJOURNAL OF FORENSIC SCIENCES, Issue 5 2010Bruce Budowle Ph.D. Abstract:, Naming mtDNA sequences by listing only those sites that differ from a reference sequence is the standard practice for describing the observed variations. Consistency in nomenclature is desirable so that all sequences in a database that are concordant with an evidentiary sequence will be found for estimating the rarity of that profile. The operational alignment and nomenclature rules, i.e., "Wilson Rules," suggested for this purpose do not always guarantee a single consistent sequence description for all observed polymorphisms. In this work, the operational alignment/nomenclature rules were reconfigured to better reflect traditional user preferences. The rules for selecting alignments are described. In addition, to avoid human error and to more efficiently name mtDNA sequence variants, a computer-facilitated method of aligning mtDNA sample sequences with a reference sequence was developed. There were 33 differences between these hierarchical rules and the data in SWGDAM, which translates into a 99.92% consistency between the new rules and the manual historical nomenclature approach. The data support the reliability of the current SWGDAM database. As the few discrepancies were changed in favor of the new hierarchical rules, the quality of the SWGDAM database is further improved. [source] Characterization of microsatellite loci in silver carp (Hypophthalmichthys molitrix), and cross-amplification in other cyprinid speciesMOLECULAR ECOLOGY RESOURCES, Issue 3 2006A. A. GHEYAS Abstract Captive populations of silver carp (Hypophthalmichthys molitrix), a major aquaculture species in Asia, would undoubtedly benefit from genetic monitoring and improvement programs. We report the isolation and preliminary characterization of 16 microsatellite loci derived from both conventional and microsatellite-enriched libraries. Inheritance studies confirmed the allelic nature of observed polymorphisms at all loci, while identifying null alleles at two loci. These loci, having varying degrees of polymorphism, should provide useful markers for applied genetic studies. A high degree of cross-amplification among 10 other cyprinid species suggests that these loci may have more widespread utility. [source] Use of cDNA-AFLP for transcript profiling in narrow genetic pools; for example, cucumber (Cucumis sativus L.)PLANT BREEDING, Issue 5 2006K. M. Bae Abstract A cDNA-AFLP transcript profiling was employed to examine three representative tissues (seedling, ovary and leaf) of nine Korean cucumber (Cucumis sativus L.) F1 hybrids. Differential accumulation of transcript-derived fragments (TDFs) was detected in 92 profiles. Genetic distance-based cluster analysis partitioned these hybrids into four main groupings, consistent with their phenotypic relationships. Although several polymorphic profiles were confirmed by reverse transcriptase polymerase chain reaction (RT-PCR) analysis, many were not reproducible, indicating that a large portion of the observed polymorphisms were based on sequence variation of transcripts rather than expression of variation. Thus, it is proposed that cDNA-AFLP profiling be based on a dual descriptor system (sequence and expression). Data indicate that such a system would provide an efficient genetic marker system for identifying polymorphisms in narrow genetic pools. [source] | ||||||||||