Maximum-likelihood models for mapping genetic markers showing segregation distortion. 1. Backcross populations

Lorieux, Mathias; Goffinet, Bruno; Perrier, Xavier; Leon, Dacia; Lanaud, Claire

doi:10.1007/bf00220998

Cited by 189 publications

(100 citation statements)

References 21 publications

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“…Segregation distortion at the level introduced in this study had very little effect on marker order or length. For doubled-haploid populations, segregation distortion does not affect the equation for the maximum likelihood estimate of the recombination fraction when a single locus on a chromosome causes differential viability, although problems arise in the form of biased recombination fraction estimates when more than one locus is involved (Lorieux et al, 1995). Cheng et al (1998) have proposed a method for inferring the presence of and mapping a locus causing distortion, which they refer to as a partial lethal-factor locus, and have applied this to the barley Steptoe-Morex population.…”

Section: Factors Influencing Linkage Map Constructionmentioning

confidence: 99%

Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps

2003

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A simulation study was performed to investigate the effects of missing values, typing errors and distorted segregation ratios in molecular marker data on the construction of genetic linkage maps, and to compare the performance of three locus-ordering criteria (weighted least squares, maximum likelihood and minimum sum of adjacent recombination fractions criteria) in the presence of such effects. The study was based upon three linkage groups of 10 loci at 2, 6, and 10 cM spacings simulated from a doubled-haploid population of size 150. Criteria performance were assessed using the number of replicates with correctly estimated orders, the mean rank correlation between the estimated and the true order and the mean total map length. Bootstrap samples from replicates in the maximum likelihood analysis produced a measure of confidence in the estimated locus order. The effects of missing values and/or typing errors in the data are to reduce the proportion of correctly ordered maps, and this problem worsens as the distances between loci decreases. The maximum likelihood criterion is most successful at ordering loci correctly, but gives estimated map lengths, which are substantially inflated when typing errors are present. The presence of missing values in the data produces shorter map lengths for more widely spaced markers, especially under the weighted least-squares criterion. Overall, the presence of segregation distortion has little effect on this population.

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Section: Factors Influencing Linkage Map Constructionmentioning

confidence: 99%

Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps

2003

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“…3.0b, with threshold LOD values of 10.0 and a recombination fraction of 0.3. CentiMorgan (c) distances were calculated using the Kosambi function with corrections for segregation distortion using the program  (Lorieux et al, 1995). Linkage group numbers were assigned according to Cervera et al (2001).…”

Section: Mapping Of the Mxc3 And Mer Locimentioning

confidence: 99%

Genetic and physical mapping of Melampsora rust resistance genes in Populus and characterization of linkage disequilibrium and flanking genomic sequence

et al. 2004

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Summary• In an attempt to elucidate the molecular mechanisms of Melampsora rust resistance in Populus trichocarpa , we have mapped two resistance loci, MXC3 and MER , and intensively characterized the flanking genomic sequence for the MXC3 locus and the level of linkage disequilibrium (LD) in natural populations.• We used an interspecific backcross pedigree and a genetic map that was highly saturated with AFLP and SSR markers, and assembled shotgun-sequence data in the region containing markers linked to MXC3 .• The two loci were mapped to different linkage groups. Linkage disequilibrium for MXC3 was confined to two closely linked regions spanning 34 and 16 kb, respectively. The MXC3 region also contained six disease-resistance candidate genes.• The MER and MXC3 loci are clearly distinct, and may have different mechanisms of resistance, as different classes of putative resistance genes were present near each locus. The suppressed recombination previously observed in the MXC3 region was possibly caused by extensive hemizygous rearrangements confined to the original parent tree. The relatively low observed LD may facilitate association studies using candidate genes for rust resistance, but will probably inhibit marker-aided selection.

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“…The first is the method that does not consider the effect of distorted markers, named method I, implemented by MapMaker v3.0 or JoinMap v4.0. The second is the method that considers the effect of distorted markers, named method II (Lorieux et al, 1995a, b;Zhu et al, 2007). The third is the new method described in this study, which considers the effect of epistatic distorted markers.…”

Section: Statistical Propertiesmentioning

confidence: 99%

“…By using a similar approach, the statistical properties 2 and 3 can be obtained. Using method II, the recombinant fraction is estimated by ffiffiffiffiffiffi ffi Lorieux et al, 1995a). In the fitness model, the estimate is changed tô…”

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confidence: 99%

Linkage group correction using epistatic distorted markers in F2 and backcross populations

Zhang

2014

Heredity

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Epistasis has been frequently observed in all types of mapping populations. However, relatively little is known about the effect of epistatic distorted markers on linkage group construction. In this study, a new approach was proposed to correct the recombination fraction between epistatic distorted markers in backcross and F 2 populations under the framework of fitness and liability models. The information for three or four markers flanking with an epistatic segregation distortion locus was used to estimate the recombination fraction by the maximum likelihood method, implemented via an expectation-maximisation algorithm. A set of Monte Carlo simulation experiments along with a real data analysis in rice was performed to validate the new method. The results showed that the estimates from the new method are unbiased. In addition, five statistical properties for the new method in a backcross were summarised and confirmed by theoretical, simulated and real data analyses.

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Maximum-likelihood models for mapping genetic markers showing segregation distortion. 1. Backcross populations

Cited by 189 publications

References 21 publications

Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps

Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps

Genetic and physical mapping of Melampsora rust resistance genes in Populus and characterization of linkage disequilibrium and flanking genomic sequence

Linkage group correction using epistatic distorted markers in F2 and backcross populations

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