Genotypic Frequencies at Equilibrium for Polysomic Inheritance Under Double-Reduction

Huang, Kang; Wang, Tongcheng; Dunn, Derek W.; Zhang, Pei; Cao, Xiaoxiao; Liu, Rucong; Li, Baoguo

doi:10.1534/g3.119.400132

Cited by 24 publications

(51 citation statements)

References 54 publications

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“…These inheritance models determine the a priori probabilities of the genotypic frequencies, based on the genotypic and phenotypic frequencies under each model (Huang, Wang, et al, ). We are able to calculate the posterior probabilities of the genotypes hidden behind the phenotypes and these genotypes are weighted by their posterior probabilities.…”

Section: Methodsmentioning

confidence: 99%

“…The genotypes at 20 tetra‐allelic loci for these individuals were generated under the PRCS model (Datasets A‐D) or the RCS/disomic model (Dataset E‐G) and then converted into phenotypes. The true values of the compared statistics were derived using the methods of Huang, Dunn, Li, et al (), Huang, Wang, et al (), and are shown in Table .…”

Section: Simulations and Comparisonsmentioning

confidence: 99%

“…polygene improves on existing packages and also includes four polysomic inheritance models, that is, random chromosome segregation (RCS) (Muller, 1914), pure random chromatid segregation (PRCS) (Haldane, 1930), complete equational segregation (Mather, 1935) and partial equational segregation (Huang, Wang, et al, 2019). A brief description of these models can be found in the Supporting Information S1 (section double reduction models).…”

Section: Materials S and Me Thodsmentioning

confidence: 99%

“…These inheritance models determine the a priori probabilities of the genotypic frequencies, based on the genotypic and phenotypic frequencies under each model (Huang, Wang, et al, 2019).…”

Section: Materials S and Me Thodsmentioning

confidence: 99%

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polygene: Population genetics analyses for autopolyploids based on allelic phenotypes

et al. 2019

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Polyploidy has appeared in almost every ancestral plant lineage, and in extant species, occurs frequently. When present, polyploidy presents problems for genetic data analysis, which are caused by both genotypic ambiguities and double‐reduction. To address these problems, we developed a new software package, polygene, which enables the estimation of genotypic frequencies for a number of polysomic inheritance models. Specifically, polygene obtains posterior probabilities for genotypes hidden within allelic phenotypes. Comprehensive modes of genetic analyses are provided by polygene, which include genetic diversity analysis, tests for allelic phenotypic or genotypic distributions, linkage disequilibrium and genetic differentiation, genetic distance analysis, principal coordinates analysis, hierarchical clustering analysis, individual inbreeding coefficient estimation, individual heterozygosity index estimation, population assignment, pairwise relatedness estimation, parentage analysis, analysis of molecular variance and Bayesian clustering. polygene enables easy and convenient allelic phenotype‐ or genotype‐based analysis for both autopolyploids and diploids. polygene will thus facilitate molecular ecology research involving autopolyploids.

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Section: Methodsmentioning

confidence: 99%

Section: Simulations and Comparisonsmentioning

confidence: 99%

Section: Materials S and Me Thodsmentioning

confidence: 99%

“…These inheritance models determine the a priori probabilities of the genotypic frequencies, based on the genotypic and phenotypic frequencies under each model (Huang, Wang, et al, 2019).…”

Section: Materials S and Me Thodsmentioning

confidence: 99%

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polygene: Population genetics analyses for autopolyploids based on allelic phenotypes

et al. 2019

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“…We therefore used an alternative method to obtain an approximate solution, using the inbreeding coefficient F as an intermediate variable and by assuming that inbreeding is only caused by selfing. The value of F at the equilibrium state under double‐reduction and self‐fertilization has been derived previously (Huang et al, ):

F = \frac{8 α + s v}{8 α + v (s + v - s v)},

where

α = \underset{i}{false\sum} i α_{i}

, and α i denotes the probability that a gamete carries i pairs of identical‐by‐double‐reduction (IBDR) alleles.…”

Section: Methodsmentioning

confidence: 99%

Inference of individual ploidy level using codominant markers

Huang

Dunn

et al. 2019

Molecular Ecology Resources

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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.

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Development of simple sequence repeat markers for Chamerion angustifolium (Onagraceae)

Wang

Dunn

et al. 2019

Appl Plant Sci

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Premise Rosebay willowherb, or fireweed (Chamerion angustifolium: Onagraceae), has diploid, tetraploid, and hexaploid cytotypes. There are known physiological and ecological differences among the three cytotypes, but genetic differences remain undetermined. We developed simple sequence repeat (SSR) markers for this species. Methods and Results Leaf samples were collected from three hexaploid C. angustifolium populations. We successfully amplified 16 SSR loci, which were found to be highly polymorphic. The number of alleles, the observed heterozygosity levels, and the expected heterozygosity levels ranged from four to 13, 0.286–0.899, and 0.372–0.871, respectively. Most primers could also be amplified successfully in C. conspersum and the closely related species Epilobium palustre. Conclusions The 16 polymorphic SSR markers developed here will be useful for genetic studies in C. angustifolium and related species.

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Genotypic Frequencies at Equilibrium for Polysomic Inheritance Under Double-Reduction

Cited by 24 publications

References 54 publications

polygene: Population genetics analyses for autopolyploids based on allelic phenotypes

polygene: Population genetics analyses for autopolyploids based on allelic phenotypes

Inference of individual ploidy level using codominant markers

Development of simple sequence repeat markers for Chamerion angustifolium (Onagraceae)

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