Estimation of allele frequencies in polyploids under certain patterns of inheritance

Abstract

Allele frequencies have long been studied by biologists interested in evolution and speciation. 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. There is now interest in applying the same DNA profiling technology to identification of plant varieties. HortResearch maintains a large germplasm of horticultural plant species. It is becoming evident that accurate identification of these accessions through DNA fingerprinting is essential for effective utilisation and maintenance of this germplasm. Microsatellites are the markers of choice for this fingerprinting. However, such markers do not reveal the dosage of alleles in a polyploid. Polyploidy is common amongst horticultural plants. Estimating allele frequencies in a polyploid population is, therefore, complicated because of some marker genotypes being phenotypically indistinguishable. 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. Furthermore 'null' individuals are rarely detected in polyploids. Furthermore, some polyploids can be cryptic exhibiting disomy, instead of the polysomic inheritance. 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. The method will be demonstrated on simulated data. 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. Heredity (2005) 95, 327-334.

Different patterns of colonization of Oxalis alpina in the Sky Islands of the Sonoran desert via pollen and seed flow

“…The allele dosage in this method is inferred based on the ratio of the allele peak areas from the microsatellite electropherograms for each individual at every locus. We estimated the average frequency of null alleles in 17 populations of O. alpina based on De Silva method (De Silva, Hall, Rikkerink, McNeilage, & Fraser, 2005) implemented in POLYSAT (Clark & Jasieniuk, 2011). We found average null allele frequencies of 0.16, 0.02, 0.001, 0.02, 0.13, 0.10, 0.09, and 0.02 for loci Oxa17, 25, 41, 43, 63, 81, 84, and 88, respectively.…”

Using principle component analysis to compare genetic diversity across polyploidy levels within plant complexes: an example from British Restharrows (Ononis spinosa and Ononis repens)

“…While the situation for pure allopolyploids is usually relatively simple with disomic inheritance, the situation in segmental allopolyploids or autopolyploids is more complex, ranging from mild to complete polysomic inheritance, depending on the degree of chromosomal homology present between the chromosome sets in the polyploid. A number of groups have presented theoretical treatments for dealing with polysomic inheritance in autopolyploids (for example, Glendinning, 1989;Moody et al, 1993;Ronfort et al, 1998;DeSilva et al, 2005) often based around a proposed cytological analysis of bivalent/multivalent ratios in meiosis or on marker inheritance. The development of mapping strategies for autotetraploids has also taken the study of inheritance in such species further (Hackett and Luo, 2003;Luo et al, 2004).…”

Sidik Jari DNA 88 Plasma Nutfah Ubi Jalar di Indonesia Berdasarkan Delapan Penanda SSR

“…Frekuensi alel per lokus dalam kasus lokus multialelik tidak dapat dihitung meskipun penanda yang digunakan bersifat kodominan, karena dosis setiap alel tidak dapat ditentukan (De Silva et al, 2005;Zhang et al, 2000). Karena keterbatasan tersebut, Zhang et al (2000) menghitung heterosigositas aktual sebagai persentase aksesi yang heterosigot dari seluruh aksesi yang diteliti pada tiap-tiap lokus.…”