| Based on genetic map construction and quantitative trait locus(QTL)mapping,the breeding efficiency can be evidently improved by marker assisted selection.However,segregation distortion,a common biological phenomenon in the bi-parental segregation population,may usually affect the accuracy of genetic map construction and QTL mapping.Therefore,considering segregation distortion in genetic map construction and QTL mapping play a crucial role in the crop genetic improvement.At present,several approaches and programs to correct genetic distances and to map QTL using distorted markers are available,but little is known about epistatic segregation distortion loci(SDL),which is frequently observed in all kinds of mapping populations.To address this issue,this study was conducted in three aspects:1)a new approach was proposed to correct recombination fraction between adjacent markers with epistatic SDL in backcross and F2 populations under the framework of the fitness and liability models;2)based on the corrected genetic map,estimates of epistatic SDL parameters were used to correct conditional probabilities of QTL genotypes,and a multi-QTL mapping approach was proposed under epistatic SDL;and 3)a free and user friendly new program,named DistortedMap V1.0,was developed for the above two approaches.The results were as follows.1)When epistatic SDL exists,genetic distance was estimated by maximum likelihood method,implemented via expectation-maximization algorithm.To validate the new method,a set of simulated datasets and a rice backcross population data were analyzed by the method I(without considering distorted markers),?(considering distorted markers)and new(considering epistatic SDL).Results showed that:(1)if the presence of epistasis was ignored,biased estimate of recombination fraction was observed only for marker intervals of the SDL but not for marker intervals outside the SDL;(2)using the methods I and II,the deviation degree depended on the SDL size.Using method I,the estimate of recombination fraction in backcross was larger than the true value while the sum of SDL main effects u and v was larger than the sum of their interaction(x)and 1,and smaller than the true value while u+v<x+1.Using method II,the estimate of recombination fraction in backcross was larger than true value while uv>x,and smaller than true value while uv<x;and(3)using the new method,the estimate was unbiased under various situations,i.e.,various heritabilities,interval lengths and sample sizes.2)Based on the corrected genetic map,epistatic SDL were detected and these SDL parameters were used to correct the conditional probabilities of QTL genotypes.Thus,these corrections were incorporated into the new multi-QTL mapping approach.As compared with old method,the new one corrected genetic distance between distorted markers,and considered epistatic SDL.A set of simulated dataset's and a real data(304 mouse F2 individuals)were used to validate the new method.As a result,the power in the detection of QTL was higher for the new method than for the old one,and significant differences of estimates of QTL parameters between the two methods were observed,except for QTL position.Among two QTL for mouse weight,one significant difference for QTL additive effect between the above two methods was observed,because epistatic SDL between markers C66 and T93 exists(P=2.94e-4).3)For convenient application of the above proposed methods,a free and user friendly windows program,named DistortedMap V1.0,was developed using C#language under the framework of Microsoft Visual Studio 2010.The DistortedMap V1.0 included five aspects:simulating distorted segregation populations,analyzing data of molecular markers,correcting linkage map,comparing maps from various programs and QTL mapping using epistatic SDL. |
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