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Inference of individual ploidy level using codominant markers.

Baoguo LiDerek W DunnZhong-Hu LiPei ZhangYu DaiBao-Guo Li
Published in: Molecular ecology resources (2019)
A significant portion of plant species are polyploids, with ploidy levels sometimes varying among individuals and/or populations. Current techniques to determine the individual ploidy, e.g., flow cytometry, chromosome counting or genotyping-by-sequencing, are often cumbersome. Based on the genotypic probabilities for polysomic inheritance under double-reduction, we developed a model to estimate allele frequency and infer the ploidy status of individuals from the allelic phenotypes of codominant genetic markers. The allele frequencies are estimated by an expectation-maximization algorithm in the presence of null alleles, false alleles, negative amplifications and self-fertilization, and the posterior probabilities are used to assign individuals into different levels of ploidy. The accuracy of this method under different conditions is evaluated. Our methods are freely available in a new software package, ploidyinfer, for use by other researchers which can be downloaded from http://github.com/huangkang1987/ploidyinfer.
Keyphrases
  • flow cytometry
  • single cell
  • copy number
  • machine learning
  • mitochondrial dna
  • high throughput
  • genetic diversity