Effects Of Molecular Markers Consequences On Genotyping Errors

Abstract

Genotype error can greatly reduce the power of a genetic study. For family data, genotype error can be assessed by examining marker data for non-Mendelian inconsistencies, closely linked markers for double recombination events, and consistency of duplicate genotypes. Genetic markers are widely used to determine the parentage of individuals in studies of mating systems, reproductive success, dispersals, quantitative genetic parameters and in the management of conservation populations. These markers are, however, imperfect for parentage analyses because of the presence of genotyping errors and undetectable alleles, which may cause incompatible genotypes (mismatches) between parents and offspring and thus result in false exclusions of true parentage. Highly polymorphic markers widely used in parentage analyses, such as microsatellites, are especially prone to genotyping errors. Molecular markers based on a hybridization reaction or PCR stage that detect DNA polymorphism are currently used in various fields of biology, including the study and preservation of genetic diversity, identification of individuals, phylogenetic, mapping of useful traits of quality and resistance to stress factors. , in the breeding process, biotechnology, etc. Before starting the experiment, researchers must determine what type of markers to use based on the following criteria: the variability and number of required markers, the need for their codominance, the corresponding requirements for the extracted DNA; practical - efficiency, reproducibility of analysis, the necessary appropriate technical support and cost. For a correct interpretation of the results of genotyping, one should take into account the fact that the use of any type of molecular markers is associated with a number of genotyping errors, the main ones being the loss of larger alleles, “zero” alleles, “stutter” alleles due to the peculiarities of Tag polymerase, and non-homology of amplified sequences of the same size (homoplasia). Researchers formulate defining conditions to reduce genotyping errors and reduce their impact on the final analysis. These include the quality and quantity of analyzed DNA, the level of technical capabilities and professionalism of the staff, since the human factor is defined as one of the main reasons for incorrect results; conducting pilot experiments for a comparative assessment of the theoretical and real error rate. The minimization of errors is achieved by assessing the capabilities of a particular type and screening markers; optimization of experimental methods, proper use of controls, replicates, and development of statistical approaches to identify errors. The trade-off between culling error-generating loci and increasing the potential of the retained loci to amplify the genetic signal can be different in different studies, but the main thing is that this signal is not lost for the sake of an “acceptable” level of error and the researchers develop empirical approaches to achieve the desired compromise.so that this signal is not lost for the sake of an "acceptable" level of error and researchers develop empirical approaches to achieve the desired compromise.so that this signal is not lost for the sake of an "acceptable" level of error and researchers develop empirical approaches to achieve the desired compromise.