Inference of individual ploidy level using codominant markers

Huang, Kang; Dunn, Derek W.; Li, Zhong Hu; Zhang, Pei; Dai, Yu Cheng; Li, Bao Guo

doi:10.1111/1755-0998.13032

Cited by 6 publications

(3 citation statements)

References 52 publications

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“…Polyploids are a group of plants with great importance in plant evolutionary studies and plant breeding. Although there is a rich body of literature on quantitative genetic dissection of complex traits based on artificial crosses [ 23 , 24 , 25 ], only a few studies have investigated the population genetic diversity of polyploids [ 4 , 15 , 16 , 26 , 27 ]. There are few methodological studies that describe analytical models for population and evolutionary genetics in polyploids by considering the structural and organizational complexities of polyploid genomes [ 28 ].…”

Section: Discussionmentioning

confidence: 99%

Asymptotic tests for Hardy–Weinberg equilibrium in hexaploids

Wang

et al. 2022

Horticulture Research

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Hexaploids, a group of organisms containing three complete sets of chromosomes in a single nucleus, are of utmost importance to evolutionary studies and breeding programs. Many studies have focused on hexaploid linkage analysis and QTL mapping in controlled crosses, but little methodology has been developed to reveal how hexaploids diversify and evolve in natural populations. We formulate a general framework for studying the pattern of genetic variation in autohexaploid populations through testing deviation from Hardy–Weinberg equilibrium (HWE) at individual molecular markers. We confirm that hexaploids cannot reach exact HWE, but can approach asymptotic HWE at 8–9 generations of random mating. We derive a statistical algorithm for testing HWE and the occurrence of double reduction for autopolyploids, a phenomenon that affects population variation during long evolutionary processes. We perform computer simulation to validate the statistical behavior of our test procedure and demonstrate its usefulness by analyzing a real data set for autohexaploid chrysanthemum. By extending it to allothexaploids, our test procedure will provide a generic tool for illustrating the genome structure of hexaploids in the quest to infer their evolutionary status and design association studies of complex traits.

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Section: Discussionmentioning

confidence: 99%

Asymptotic tests for Hardy–Weinberg equilibrium in hexaploids

Wang

et al. 2022

Horticulture Research

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“…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: 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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“…Nevertheless, flow cytometry is still limited by the quality and age of the material and requires bringing material to the lab. Similar restrictions apply to other methods that generate ploidy information parallel to genotyping, such as microsatellite analyses (Huang et al, 2019) or genotyping-by-sequencing (Gompert and Mock, 2017;Siadjeu et al, 2018).…”

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confidence: 99%

Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens

Buono

Albach

2023

Appl Plant Sci

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Premise: Polyploidy has become a central factor in plant evolutionary biological research in recent decades. Methods such as flow cytometry have revealed the widespread occurrence of polyploidy; however, its inference relies on expensive lab equipment and is largely restricted to fresh or recently dried material. Methods: Here, we assess the applicability of infrared spectroscopy to infer ploidy in two related species of Veronica (Plantaginaceae). Infrared spectroscopy relies on differences in the absorbance of tissues, which could be affected by primary and secondary metabolites related to polyploidy. We sampled 33 living plants from the greenhouse and 74 herbarium specimens with ploidy known through flow cytometrical measurements and analyzed the resulting spectra using discriminant analysis of principal components (DAPC) and neural network (NNET) classifiers. Results: Living material of both species combined was classified with 70% (DAPC) to 75% (NNET) accuracy, whereas herbarium material was classified with 84% (DAPC) to 85% (NNET) accuracy. Analyzing both species separately resulted in less clear results. Discussion: Infrared spectroscopy is quite reliable but is not a certain method for assessing intraspecific ploidy level differences in two species of Veronica. More accurate inferences rely on large training data sets and herbarium material. This study demonstrates an important way to expand the field of polyploid research to herbaria.K E Y W O R D S discriminant analysis of principal components (DAPC), herbaria, infrared spectroscopy, neural network, polyploidy, Veronica Appl. Plant Sci.

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Inference of individual ploidy level using codominant markers

Cited by 6 publications

References 52 publications

Asymptotic tests for Hardy–Weinberg equilibrium in hexaploids

Asymptotic tests for Hardy–Weinberg equilibrium in hexaploids

polygene: Population genetics analyses for autopolyploids based on allelic phenotypes

Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens

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