Recursive Test of Hardy-Weinberg Equilibrium in Tetraploids

Sun, Lidan; Gan, Jingwen; Jiang, Libo; Wu, Rongling

doi:10.1016/j.tig.2020.11.006

Cited by 17 publications

(49 citation statements)

References 52 publications

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“…One clarifying example is that in an S1 population (one generation of selfing), the random mating hypothesis is satisfied, since the distribution of offspring genotypes is a convolution of the gamete probabilities within a single individual, but hardly any researcher would claim that the population is at equilibrium. However, Sun et al [2020] conflated these hypotheses: they use null hypothesis (1) in tetraploids and claim that their resulting test is one against the null of equilibrium, when theirs in actuality is a test against the null of random mating.…”

Section: Methodsmentioning

confidence: 99%

“…In this section, we will generalize the likelihood framework of Sun et al [2020] from tetraploids to general ploidy levels. Though Sun et al [2020] claim that their likelihood approach is a test for equilibrium, as we have shown in Section 2.1, this is really a test for random mating. However, testing this hypothesis might be useful in its own right to clarify the mating behavior in a system.…”

Section: Likelihood Inference For Random Matingmentioning

confidence: 99%

“…There also exists a point of confusion in the literature on the difference between random mating and equilibrium. For example, Sun et al [2020] develop a likelihood framework that they claim tests for equilibrium in tetraploids, but we would say actually tests for random mating (Section 2.2). In brief, we propose that random mating implies that genotype frequencies of the current generation are a convolution of the genotype frequencies of the gametes created by the parental generation, while equilibrium implies a steady state of genotype frequencies given a meiotic process and other population forces.…”

Section: Introductionmentioning

confidence: 99%

“…We clarify this distinction in Section 2.1, and show that distinguishing between these hypotheses is rather subtle, particularly for tetraploids. The random mating hypothesis might be of interest, and so in Section 2.2 we generalize the approach of Sun et al [2020] to higher ploidy levels.…”

Section: Introductionmentioning

confidence: 99%

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Double reduction estimation and equilibrium tests in natural autopolyploid populations

Gerard

2021

Preprint

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Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the co-migration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate double reduction given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U-statistic minimization approach that we show generalizes the classical equilibrium χ2 test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U-statistic to test for equilibrium. Finally, we highlight the difficulty in distinguishing between random mating and equilibrium in tetraploids at biallelic loci. Our methods are implemented in the hwep R package on GitHub (https://github.com/dcgerard/hwep).

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Section: Methodsmentioning

confidence: 99%

Section: Likelihood Inference For Random Matingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Double reduction estimation and equilibrium tests in natural autopolyploid populations

Gerard

2021

Preprint

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“…The polyqtlR R package is a reliable tool for QTL analysis using identity-by-descent (IBD) probabilities in F 1 populations of outcrossing in heterozygous polyploid species. With the continual analysis of polyploid genetic model systems (Jiang et al, 2020;Sun et al, 2020), the software tools for polyploid genetic research will also provide a better understanding of polyploid inheritance.…”

Section: Tools For Genetic Studies In Polyploidsmentioning

confidence: 99%

Identification and QTL Analysis of Flavonoids and Carotenoids in Tetraploid Roses Based on an Ultra-High-Density Genetic Map

et al. 2021

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Roses are highly valuable within the flower industry. The metabolites of anthocyanins, flavonols, and carotenoids in rose petals are not only responsible for the various visible petal colors but also important bioactive compounds that are important for human health. In this study, we performed a QTL analysis on pigment contents to locate major loci that determine the flower color traits. An F1 population of tetraploid roses segregating for flower color was used to construct an ultra-high-density genetic linkage map using whole-genome resequencing technology to detect genome-wide SNPs. Previously developed SSR and SNP markers were also utilized to increase the marker density. Thus, a total of 9,259 markers were mapped onto seven linkage groups (LGs). The final length of the integrated map was 1285.11 cM, with an average distance of 0.14 cM between adjacent markers. The contents of anthocyanins, flavonols and carotenoids of the population were assayed to enable QTL analysis. Across the 33 components, 46 QTLs were detected, explaining 11.85–47.72% of the phenotypic variation. The mapped QTLs were physically clustered and primarily distributed on four linkage groups, namely LG2, LG4, LG6, and LG7. These results improve the basis for flower color marker-assisted breeding of tetraploid roses and guide the development of rose products.

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Modeling of Hardy-Weinberg Equilibrium Using Dynamic Random Networks in an ABM Framework

Tarantino

Panunzi

Romano

2023

Complex Networks and Their Applications XI

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Recursive Test of Hardy-Weinberg Equilibrium in Tetraploids

Cited by 17 publications

References 52 publications

Double reduction estimation and equilibrium tests in natural autopolyploid populations

Double reduction estimation and equilibrium tests in natural autopolyploid populations

Identification and QTL Analysis of Flavonoids and Carotenoids in Tetraploid Roses Based on an Ultra-High-Density Genetic Map

Modeling of Hardy-Weinberg Equilibrium Using Dynamic Random Networks in an ABM Framework

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