Theoretical basis for genetic linkage analysis in autotetraploid species

Luo, Zewei; Zhang, R. M.; Kearsey, M. J.

doi:10.1073/pnas.0304482101

Cited by 93 publications

(86 citation statements)

References 26 publications

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“…Construction of linkage maps in autotetraploids has been studied by Hackett and Luo (2003). Luo et al (2004) have presented a theoretical basis for linkage analysis in autotetraploids. Although inheritance patterns in polyploids are covered well in the literature, there is very little or no information about methods for estimating their allele frequencies.…”

Section: Introductionmentioning

confidence: 99%

Estimation of allele frequencies in polyploids under certain patterns of inheritance

et al. 2005

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Allele frequencies have long been studied by biologists interested in evolution and speciation. More recently, with the application of molecular markers in human DNA profiling we have also seen the need for reliable population allele frequency estimates for making probabilistic inferences. There is now interest in applying the same DNA profiling technology to identification of plant varieties. HortResearch maintains a large germplasm of horticultural plant species. It is becoming evident that accurate identification of these accessions through DNA fingerprinting is essential for effective utilisation and maintenance of this germplasm. Microsatellites are the markers of choice for this fingerprinting. However, such markers do not reveal the dosage of alleles in a polyploid. Polyploidy is common amongst horticultural plants. Estimating allele frequencies in a polyploid population is, therefore, complicated because of some marker genotypes being phenotypically indistinguishable. For example, in a tetraploid, with four alleles at a locus showing polysomic inheritance, although 35 genotypes are possible, these will fall into only 15 marker phenotypic classes. Furthermore 'null' individuals are rarely detected in polyploids. Furthermore, some polyploids can be cryptic exhibiting disomy, instead of the polysomic inheritance. We will discuss the implications of these factors and present an EM-type algorithm for estimating allele frequencies of a polyploid population under certain patterns of inheritance. The method will be demonstrated on simulated data. We also discuss the nature of some of the additional problems that may be encountered with estimating allele frequencies in polyploids for which other solutions still need to be developed. Heredity (2005) 95, 327-334.

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Section: Introductionmentioning

confidence: 99%

Estimation of allele frequencies in polyploids under certain patterns of inheritance

et al. 2005

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“…Significant improvement can be obtained in statistical reliability by incorporating only a single SSR marker through the multilocus analysis. The multilocus method confers the additional advantage of providing a direct calculation of likelihood for any given linkage map, thus achieving a step forward for the computational challenge of statistical inferring linkage order and linkage phase (17). Although active research efforts have been invested to develop theory and statistical methods for mapping QTL in tetraploid species (4,11,15,(18)(19)(20)(21), none of these have been built on a rigorous autotetrasomic model.…”

Section: Discussionmentioning

confidence: 99%

“…. ., 4 for the number of recombinant chromosomes in the fully informative genotype, whereas c k is a constant which can be calculated as described (17). Accordingly we have g Gik;j ðα k ; r k Þ ¼ ∑ ðξ;ηÞ∈Gik;j a ik;ξη .…”

Section: Prediction Of Two-locus Genotypic Distribution Under the Mulmentioning

confidence: 99%

“…; x im j z i1 ; rg; [8] which is derived in detail in SI Methods. We established a recursive relationship between the coefficients of double reduction at linked loci (17) and so the MLE of α k can be calculated from the MLE of α 1 and r ¼ ðr 1 ; . .…”

Section: Prediction Of Two-locus Genotypic Distribution Under the Mulmentioning

confidence: 99%

“…For example, if A 1 A 2 A 3 A 4 represent four copies of marker alleles at locus M k and the coefficient of double reduction at this locus is α k , there are 100 possible genotypes at this locus. We developed a computer-based approach to sort the genotypes into three different groups according to the number of double reduction gametes (n DR ) involved and to calculate their probabilities (17) given by…”

Section: Prediction Of Single-locus Genotypic Distribution Under the mentioning

confidence: 99%

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Multilocus tetrasomic linkage analysis using hidden Markov chain model

Leach

Wang

Kearsey

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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The availability of reliable genetic linkage maps is crucial for functional and evolutionary genomic analyses. Established theory and methods of genetic linkage analysis have made map construction a routine exercise in diploids. However, many evolutionarily, ecologically, and/or agronomically important species are autopolyploids, with autotetraploidy being a typical example. These species undergo much more complicated chromosomal segregation and recombination at meiosis than diploids. In addition, there is evidence of polyploidy-induced and highly dynamic changes in the structure of the genome. These polysomic characteristics indicate the inappropriateness of the theory and methods of linkage analysis in diploids for use in these species and a gap in the theory and methodology of tetraploid map construction. This paper presents a theoretical model and statistical framework for multilocus linkage analysis in autotetraploids for use with dominant and/or codominant DNA molecular markers. The theory and methods incorporate the essential features of allele segregation and recombination under tetrasomic inheritance and the major challenges in statistical modeling and marker data analysis. We validated the method and explored its statistical properties by intensive simulation study and demonstrated its utility by analysis of AFLP and SSR marker data from an outbred autotetraploid potato population.autotetraploid species | tetrasomic inheritance | outbred populations | map construction P olyploidization, the simultaneous duplication of all genes in a genome, has been ubiquitous in plant evolutionary history, with ≈70% of angiosperms being polyploids (1). Allopolyploids display disomic inheritance and their genetic analysis follows the same principles as diploids, whereas autopolyploids display more complicated polysomic inheritance. Among autopolyploids exist important autotetraploids including agricultural crops, notably cultivated potato, and aquaculture animals such as Atlantic salmon and trout, for which active genome projects are underway. These projects will generate abundant genetic polymorphisms and, thus, enable construction of genetic maps, which are essential for dissecting quantitative trait loci (QTL) and, in turn, for improving efficiency of breeding programs through marker assisted selection.Genetic linkage maps exist or are becoming rapidly available in almost all important diploid animal and plant species and humans, providing an essential starting point for an insightful genomic investigation. In sharp contrast, progress in autopolyploid linkage analysis, the theoretical kernel for map construction, lags far behind. In autopolyploids, multivalent meiotic pairing of homologous chromosomes, followed by crossing over between the locus and spindle attachment, may cause double reduction, in which sister chromatids enter into the same gamete (2). Recombination frequency between a pair of loci can be as high as 0.75 under a tetrasomic model (compared to 0.5 in diploids), and double reduction can occur at a fr...

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