Estimation of double reduction and genetic parameters of autotetraploids

Tai, G. C. C.

doi:10.1038/hdy.1982.65

Cited by 14 publications

(4 citation statements)

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“…Most work on estimating the double reduction rate has been done in experimental populations with known pedigrees (Bourke et al., 2015; Haynes & Douches, 1993; Stift et al., 2008; Tai, 1982a, 1982b; Wu et al., 2001). To evaluate which method produces better estimates of the double reduction rate, we implemented a likelihood approach to estimate the double reduction rate in F1 populations, and ran a simulation study in Web Appendix L comparing estimates from F1 and natural populations.…”

Section: Discussionmentioning

confidence: 99%

“…Since experimental populations only require modeling a finite number of meioses for each offspring, this makes modeling much simpler. Using experimental populations, researchers have estimated the double reduction rate either using segregation frequencies (Bourke et al, 2015;Haynes & Douches, 1993;Stift et al, 2008;Tai, 1982aTai, , 1982bWu et al, 2001), or they obtain estimates as a byproduct of haplotype reconstruction (Zheng et al, 2016(Zheng et al, , 2021. For natural populations, the only manuscript we could find that claims to estimate the double reduction rate is that of Jiang et al (2021).…”

Section: Introductionmentioning

confidence: 99%

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Double Reduction Estimation and Equilibrium Tests in Natural Autopolyploid Populations

Gerard

2022

Biometrics

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Double Reduction Estimation and Equilibrium Tests in Natural Autopolyploid Populations

Gerard

2022

Biometrics

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“…Let 7r be the probability, associated to a meiosis pattern R, of having two nonidentical alleles in a 2n gamete. Among FDR gametes, 7r equals 1 -b/2 and among SDR gametes 7r = b, where b is the frequency of single exchanging tetrads (TAI 1982). Then the R value, RY g, can be written in terms of the value of the individuals:…”

Section: A General Model For Interpopulation Crosses Between Diploid and Tetraploid Populationsmentioning

confidence: 99%

Quantitative genetics of 4x-2x hybrid populations with first-division restitution and second-division restitution 2n gametes produced by diploid parents.

David¹,

Galláis²

1995

Genetics

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A model is proposed to describe the genetic value of 4x-2x hybrids resulting from crosses between tetraploid genitors and diploid genitors that produce 2n gametes. The model takes into account the genetic consequences of the First Division Restitution (FDR) and Second Division Restitution (SDR) meiosis, particularly on the homozygosity level that 2n gametes contribute to 4x-2x hybrids. As genes can be identical by descent, numerous parameters are needed in the classical approach to describe the inbreeding effects on the mean and variance of 4x-2x hybrids. Using the concept of test value, the model allows a large decrease in the number of required parameters. The model gives the components of genetic variance and usual covariances between relatives using these synthetic parameters. The model is then used to study the efficiency of a recurrent breeding scheme to improve diploid genitors for their combining ability with tetraploid genitors. It appears that, in presence of dominance, ignoring the meiosis pattern will lead to an overestimation of additive variance and then of genetic advance. Some genetic considerations on the differences between FDR and SDR mechanisms lead us to suggest an experimental comparison of their respective advantages and disadvantages for the type of considered recurrent selection. An experimental crossing design is proposed to obtain estimates of the genetic parameters needed for this comparison.

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“…Since experimental populations only require modeling a finite number of meioses for each offspring, this makes modeling much simpler. Using experimental populations, researchers have estimated double reduction either using segregation frequencies [Tai, 1982a,b, Haynes and Douches, 1993, Wu et al, 2001, Stift et al, 2008, Bourke et al, 2015], or they obtain estimates as a byproduct of haplotype reconstruction [Zheng et al, 2016, 2021]. For natural populations, the only manuscript we could find that claims to estimate double reduction is that of Jiang et al [2021].…”

Section: Introductionmentioning

confidence: 99%

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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Estimation of double reduction and genetic parameters of autotetraploids

Cited by 14 publications

References 14 publications

Double Reduction Estimation and Equilibrium Tests in Natural Autopolyploid Populations

Double Reduction Estimation and Equilibrium Tests in Natural Autopolyploid Populations

Quantitative genetics of 4x-2x hybrid populations with first-division restitution and second-division restitution 2n gametes produced by diploid parents.

Double reduction estimation and equilibrium tests in natural autopolyploid populations

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