Modeling Population Genetic Data in Autotetraploid Species

Luo, Zewei; Zhang, Ze; Zhang, R. M.; Pandey, Madhav; Gailing, Oliver; Hattemer, H. H.; Finkeldey, Reiner

doi:10.1534/genetics.105.044974

Cited by 22 publications

(26 citation statements)

References 24 publications

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“…Given that the upper limit is much greater than the rate cited above, we may anticipate that double reduction is effective in eliminating lethal alleles along autotetraploid chromosomes. On the other hand, the recombination frequency in autotetraploids could be as high as 3 4 , as opposed to the upper limit of 1 2 in diploids, supporting the observation that the evolution of polyploid genomes was an extremely dynamic process compared to that of diploids (Song et al 1995;Luo et al 2006).…”

Section: Discussionsupporting

confidence: 62%

Constructing Genetic Linkage Maps Under a Tetrasomic Model

et al. 2006

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An international consortium has launched the whole-genome sequencing of potato, the fourth most important food crop in the world. Construction of genetic linkage maps is an inevitable step for taking advantage of the genome projects for the development of novel cultivars in the autotetraploid crop species. However, linkage analysis in autopolyploids, the kernel of linkage map construction, is theoretically challenging and methodologically unavailable in the current literature. We present here a theoretical analysis and a statistical method for tetrasomic linkage analysis with dominant and/or codominant molecular markers. The analysis reveals some essential properties of the tetrasomic model. The method accounts properly for double reduction and incomplete information of marker phenotype in regard to the corresponding phenotype in estimating the coefficients of double reduction and recombination frequency and in testing their significance by using the marker phenotype data. Computer simulation was developed to validate the analysis and the method and a case study with 201 AFLP and SSR markers scored on 228 full-sib individuals of autotetraploid potato is used to illustrate the utility of the method in map construction in autotetraploid species.

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Section: Discussionsupporting

confidence: 62%

Constructing Genetic Linkage Maps Under a Tetrasomic Model

et al. 2006

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“…This leads to tetrasomic inheritance; i.e., all possible allelic combinations are produced in equal frequencies (Muller 1914), which is generally considered indicative of autotetraploidy . Approaches have been developed to account for the complexities of tetrasomic inheritance in population genetic analyses (Moody et al 1993;Ronfort et al 1998;Luo et al 2006b) and linkage mapping (e.g., Luo et al 2004Luo et al , 2006a.…”

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confidence: 99%

Segregation Models for Disomic, Tetrasomic and Intermediate Inheritance in Tetraploids: A General Procedure Applied to Rorippa (Yellow Cress) Microsatellite Data

Bérénos²,

et al. 2008

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Tetraploid inheritance has two extremes: disomic in allotetraploids and tetrasomic in autotetraploids. The possibility of mixed, or intermediate, inheritance models has generally been neglected. These could well apply to newly formed hybrids or to diploidizing (auto)tetraploids. We present a simple likelihood-based approach that is able to incorporate disomic, tetrasomic, and intermediate inheritance models and estimates the double-reduction rate. Our model shows that inheritance of microsatellite markers in natural tetraploids of Rorippa amphibia and R. sylvestris is tetrasomic, confirming their autotetraploid origin. However, in F 1 hybrids inheritance was intermediate to disomic and tetrasomic inheritance. Apparently, in meiosis, chromosomes paired preferentially with the homolog from the same parental species, but not strictly so. Detected double-reduction rates were low. We tested the general applicability of our model, using published segregation data. In two cases, an intermediate inheritance model gave a better fit to the data than the tetrasomic model advocated by the authors. The existence of inheritance intermediate to disomic and tetrasomic has important implications for linkage mapping and population genetics and hence breeding programs of tetraploids. Methods that have been developed for either disomic or tetrasomic tetraploids may not be generally applicable, particularly in systems where hybridization is common.

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“…The authors argued that the rate of heterozygosity losses in polyploid species due to selfing and mating among relatives is much slower than for diploids, which would slow down the development of SGS in polyploids. The argument is relevant to the low level of significant genetic structure observed in sycamore maple, which is also an autotetraploid tree species with tetrasomic inheritance (Luo et al 2006). However, the effects of polyploidization may differ depending on the pre-existing systems of incompatibility or self-sterility.…”

Section: Discussionmentioning

confidence: 99%

Fine-scale spatial genetic structure of sycamore maple (Acer pseudoplatanus L.)

et al. 2011

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Knowledge of SGS in plants is vital to understand the ecological and evolutionary dynamics of populations and to plan conservation strategies. Some of the major factors that can affect spatial genetic structure (SGS) in plants are the level of gene flow, spatial arrangement and life stages of individuals within populations. Applying six highly variable microsatellite markers, we investigated the effect of these factors on spatial genetic structure selecting two natural populations of sycamore maple, which is an insect-pollinated, autotetraploid and an indigenous hardwood species in Germany and in other central European countries. The two study populations had different shapes (''compact'' and ''elongated'') and tree densities. Significant SGS extended to *180 m in the elongated population and to *35 m in the compact population. Juvenile plants of the compact population showed significant SGS up to 40 m. Estimate of Sp statistic in high-density population was almost double of that in the population with low density. Gene dispersal distance in the low-density population was about 9 times higher than in the population with high density. The similar level of significant SGS in both adult and juvenile plants suggested minimal or no effect of life stages of individuals on SGS in the sycamore maple population. The data presented in this study can provide guidelines for seed collection and to establish populations for the conservation and management of genetic resources of the species.

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Modeling Population Genetic Data in Autotetraploid Species

Cited by 22 publications

References 24 publications

Constructing Genetic Linkage Maps Under a Tetrasomic Model

Constructing Genetic Linkage Maps Under a Tetrasomic Model

Segregation Models for Disomic, Tetrasomic and Intermediate Inheritance in Tetraploids: A General Procedure Applied to Rorippa (Yellow Cress) Microsatellite Data

Fine-scale spatial genetic structure of sycamore maple (Acer pseudoplatanus L.)

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