Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting—peak ratios) method

Abstract

Polysomic inheritance frequently results in the simultaneous occurrence of several microsatellite DNA alleles on a single locus. The MAC-PR (microsatellite DNA allele counting-peak ratios) method was recently developed for the analysis of polyploid plants and makes use of the quantitative values for microsatellite allele peak areas. To date, this approach has only been used in plants with known genetic relationships. We report here the application of MAC-PR for the first time to random samples of unknown pedigrees. We analysed six microsatellite loci using a set of tetraploid ornamental rose ( Rosa x hybrida L.) varieties. For each locus, all alleles were analysed in pairwise combinations in order to determine their copy number in the individual samples. This was accomplished by calculating the ratios between the peak areas for two alleles in all of the samples where these two alleles occurred together. The allele peak ratios observed were plotted in a histogram, and those histograms that produced at least two well-separated groups were selected for further analysis. Mean allelic peak ratio values for these groups were compared to the relationships expected between alleles in hypothetical configurations of the locus investigated. Using this approach, we were able to assign precise allelic configurations (the actual genotype) to almost all of the varieties analysed for five of the six loci investigated. MAC-PR also appears to be a very effective tool for detecting 'null' alleles in polyploid species.

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

“…Genemapper version 4.0 (Applied Biosystems) was used to genotype all individuals across eight microsatellite loci. Genotypic configurations (for each of the four allele copies for tetraploids) were determined using the microsatellite DNA allele counting‐peak ratios (MAC‐PR) method (Esselink, Nybom, & Vosman, 2004). 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.…”

Relative strength of fine-scale spatial genetic structure in paternally vs biparentally inherited DNA in a dioecious plant depends on both sex proportions and pollen-to-seed dispersal ratio

“…Detailed studies are needed, however, to reveal the potential to produce heteroplasmy in wild yew populations. MAC-PR (microsatellite DNA allele counting based on peak ratios; Esselink et al, 2004) or similar quantitative techniques can be used for this purpose. Adopting the theory of genetic drift to the results of controlled crossing enabled us to predict that the contribution of maternal mtDNA to a zygote should not exceed ∼ 5%, but could be as low as o0.1%.…”

Multilocus half-tetrad analysis and centromere mapping in citrus: evidence of SDR mechanism for 2n megagametophyte production and partial chiasma interference in mandarin cv ‘Fortune’

“…2n gamete allelic structure inference from triploid hybrid genotypes For a locus bearing totally different parental allelic configurations (A 1 A 2 Â A 3 A 4 ), the genotype of the 2n gamete was directly read from the triploid hybrid structure. When the male and female genitor shared one allele (A 1 A 2 Â A 2 A 2 and A 1 A 2 Â A 2 A 3 ), the inference of the 2n female gamete structure was carried out from the measured allele dosage by the microsatellite DNA allele counting-peak ratio method (MAC-PR; Esselink et al, 2004), for the triploid hybrids that have inherited the common allele from the male genitor. The validation Half-tetrad analysis and centromere mapping in citrus J Cuenca et al of the MAC-PR method for the analysed loci and populations is given as Supplementary Information.…”