In diploids, the frequencies of codominant alleles can be obtained by simply counting different genotypes in the sample. Failure to use estimates of high precision can lead to the calculation of incorrect profile probabilities and hence unreliable probabilistic conclusions. Generally, allele frequency estimates are obtained from existing databases. Irrespective of the application, the use of DNA profiling to identify individuals requires reliable estimates of allele frequencies at the selected marker loci. More recently there has been interest in applying the same DNA technology for identification of plant varieties ( Mihalov et al, 2000 Henry, 2001). The theory underlying application of DNA profiling-based evidence in forensic science for resolving parentage disputes and alleged suspects of crime is well documented ( Evett and Weir, 1998). Markers, such as microsatellites, with their high degree of polymorphism and codominant inheritance provide more information, often sufficient to distinguish individuals within a population. In more recent years the scope of such studies has increased several fold by the use of polymorphic molecular markers. We also discuss the nature of some of the additional problems that may be encountered with estimating allele frequencies in polyploids for which other solutions still need to be developed.Īllele frequency data have been used in the past for analysis of phylogeny and population structure of species and of distinct populations of the same species. The method will be demonstrated on simulated data. We will discuss the implications of these factors and present an EM-type algorithm for estimating allele frequencies of a polyploid population under certain patterns of inheritance. Furthermore, some polyploids can be cryptic exhibiting disomy, instead of the polysomic inheritance. Furthermore ‘null’ individuals are rarely detected in polyploids. For example, in a tetraploid, with four alleles at a locus showing polysomic inheritance, although 35 genotypes are possible, these will fall into only 15 marker phenotypic classes. Estimating allele frequencies in a polyploid population is, therefore, complicated because of some marker genotypes being phenotypically indistinguishable. Polyploidy is common amongst horticultural plants. However, such markers do not reveal the dosage of alleles in a polyploid. Microsatellites are the markers of choice for this fingerprinting. It is becoming evident that accurate identification of these accessions through DNA fingerprinting is essential for effective utilisation and maintenance of this germplasm. HortResearch maintains a large germplasm of horticultural plant species. There is now interest in applying the same DNA profiling technology to identification of plant varieties. More recently, with the application of molecular markers in human DNA profiling we have also seen the need for reliable population allele frequency estimates for making probabilistic inferences. Allele frequencies have long been studied by biologists interested in evolution and speciation.
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