首页 | 本学科首页   官方微博 | 高级检索  
相似文献
 共查询到13条相似文献,搜索用时 156 毫秒
1.
A new statistical method for mapping QTLs underlying endosperm traits   总被引:6,自引:0,他引:6  
Genetic expression for an endosperm trait in seeds of cereal crops may be controlled simultaneously by the triploid endosperm genotypes and the diploid maternal genotypes. However, current statistical methods for mapping quantitative trait loci (QTLs) underlying endosperm traits have not been effective in dealing with the putative maternal genetic effects. Combining the quantitative genetic model for diploid maternal traits with triploid endosperm traits, here we propose a new statistical method for mapping QTLs controlling endosperm traits with maternal genetic effects. This method applies the data set of both DNA molecular marker genotypes of each plant in segregation population and the quantitative observations of single endosperms in each plant to map QTL. The maximum likelihood method implemented via the expectation-maximization algorithm was used to the estimate parameters of a putative QTL. Since this method involves the maternal effect that may contribute to endosperm traits, it might be more congruent with the genetics of endosperm traits and more helpful to increasing the precision of QTL mapping. The simulation results show the proposed method provides accurate estimates of the QTL effects and locations with high statistical power.  相似文献   

2.
Heterosis represents one of the most revolutionary advancements in crop improvement.In the genetic dissection of heterosis,NCIII design is one of the most powerful and widely used mating schemes.However,the methodologies for quantitative trait loci (QTL) detection in the design were mostly based on composite interval mapping.Therefore,in this study,our purpose was to develop a statistical method for mapping epistatic QTL associated with heterosis in the RIL-based NCIII design.First,we derivated the expectations of two classical linear transformations,Z 1 and Z 2,while a quantitative trait was controlled by two QTL with digenic epistasis and arbitrary linkage under the F ∞ and F 2 metric models.Then,we constructed an epistatic genetic model that includes all markers on the whole genome simultaneously,and estimated all the parameters in the model by the empirical Bayes approach.Finally,a series of Monte Carlo simulation experiments was carried out to confirm the proposed approach.The results show that:(1) all the augmented genetic parameters for main-effect QTL could be rightly identified with satisfactory statistical power and precision;(2) the statistical powers in the detection of augmented epistatic effects were substantively affected by the signs of pure epistatic effects;(3) it is more difficult to detect epistatic QTL than to detect main-effect QTL;(4) statistical power is higher in the RIL-based NCIII design than in the F 2-based NCIII design,especially in the detection of the augmented epistatic effect that consists of two pure epistatic effects in opposite directions.  相似文献   

3.
Most important agronomic and quality traits of crops are quantitative in nature.The genetic variations in such traits are usually controlled by sets of genes called quantitative trait loci (QTLs),and the interactions between QTLs and the environment.It is crucial to understand the genetic architecture of complex traits to design efficient strategies for plant breeding.In the present study,a new experimental design and the corresponding statistical method are presented for QTL mapping.The proposed mapping population is composed of double backcross populations derived from backcrossing both homozygous parents to DH (double haploid) or RI (recombinant inbreeding) lines separately.Such an immortal mapping population allows for across-environment replications,and can be used to estimate dominance effects,epistatic effects,and QTL-environment interactions,remedying the drawbacks of a single backcross population.In this method,the mixed linear model approach is used to estimate the positions of QTLs and their various effects including the QTL additive,dominance,and epistatic effects,and QTL-environment interaction effects (QE).Monte Carlo simulations were conducted to investigate the performance of the proposed method and to assess the accuracy and efficiency of its estimations.The results showed that the proposed method could estimate the positions and the genetic effects of QTLs with high efficiency.  相似文献   

4.
Most of the important agronomic traits in crops,such as yield and quality,are complex traits affected by multiple genes with gene × gene interaction as well as gene × environment interaction.Understanding the genetic architecture of complex traits is a long-term task for quantitative geneticists and plant breeders who wish to design efficient breeding programs.Conventionally,the genetic properties of traits can be revealed by partitioning the total variation into variation components caused by specific genetic effects.With recent advances in molecular genotyping and high-throughput technology,the unraveling of the genetic architecture of complex traits by analyzing quantitative trait locus (QTL) has become possible.The improvement of complex traits has also been achieved by pyramiding individual QTL.In this review,we describe some statistical methods for QTL mapping that can be used to analyze QTL × QTL interaction and QTL × environment interaction,and discuss their applications in crop breeding for complex traits.  相似文献   

5.
Residual feed intake (RFI) and carcass merit (CM) are both complex traits emerging as critical targets for beef genetic improvement.RFI and CM traits are difficult and expensive to measure and genetic improvement for these traits through traditional selection methods is not very effective.Therefore,genome-wide selection using DNA markers may be a potential alternative for genetic improvement of these traits.In this study,the efficiency of a genome-wide selection model for genetic improvement of RFI and CM was assessed.The Illumina Bovine50K bead chip was used to genotype 922 beef cattle from the Kinsella Beef Research Ranch of the University of Alberta.A Bayes model and multiple marker regression using a stepwise method were used to conduct the association test.The number of significant SNP markers for carcass weight (CWT),carcass back fat (BF),carcass rib eye area (REA),carcass grade fat (GDF),lean meat yield (LMY),and residual feed intake (RFI) were 75,54,67,57,44 and 50,respectively.Bi-variate analysis of marker scores and phenotypes for all traits were made using DMU Software.The genetic parameter for each trait was estimated.The genetic correlations of marker score and phenotype for CWT,BF,REA,GDF,LMY and RFI were 0.75,0.69,0.87,0.77,0.78,and 0.85,respectively.The average prediction accuracies of phenotypic EBV for the six traits were increased by 0.05,0.16,0.24,0.23,0.17 and 0.19,respectively.The results of this study indicated that the two-trait marker-assisted evaluation model used was a suitable alternative of genetic evaluation for these traits in beef cattle.  相似文献   

6.
Advances on methods for mapping QTL in plant   总被引:1,自引:1,他引:1  
Advances on methods for mapping quantitative trait loci (QTL) are firstly summarized. Then, some new methods, including mapping multiple QTL, fine mapping of QTL, and mapping QTL for dynamic traits, are mainly described. Finally, some future prospects are proposed, including how to dig novel genes in the germplasm resource, map expression QTL (eQTL) by the use of all markers, phenotypes and micro-array data, identify QTL using genetic mating designs and detect viability loci. The purpose is to direct plant geneticists to choose a suitable method in the inheritance analysis of quantitative trait and in search of novel genes in germplasm resource so that more potential genetic information can be uncovered.  相似文献   

7.
A method was proposed for the detection of outliers and influential observations in the framework of a mixed linear model, prior to the quantitative trait locus (QTL) mapping analysis. We investigated the impact of outliers on QTL mapping for complex traits in a mouse BXD population, and observed that the dropping of outliers could provide the evidence of additional QTL and epistatic loci affecting the 1 stBrain-OB and the 2ndBrain-OB in a cross of the abovementioned population. The results could also reveal a remarkable increase in estimating heritabilities of QTL in the absence of outliers. In addition, simulations were conducted to investigate the detection powers and false discovery rates (FDRs) of QTLs in the presence and absence of outliers. The results suggested that the presence of a small proportion of outliers could increase the FDR and hence decrease the detection power of QTLs. A drastic increase could be obtained in the estimates of standard errors for position, additive and additive× environment interaction effects of QTLs in the presence of outliers.  相似文献   

8.
Non-Mendelian segregation of markers, known as distorted segregation, is a common biological phenomenon. Although segregation distortion affects the estimation of map distances and the results of quantitative trait loci (QTL) mapping, the effects of distorted markers are often ignored in the construction of linkage maps and in QTL mapping. Recently, we have developed a multipoint method via a Hidden Markov chain method to reconstruct linkage maps in an F2 population that corrects for bias of map distances between distorted markers. In this article, the method is extended to cover backcross, doubled haploid and recombinant inbred line (RIL) populations. The results from simulated experiments show that: (1) the degree that two linked segregation distortion loci (SDL) affect the estimation of map distances increases as SDL heritability and interval length between adjacent markers increase, whereas sample size has little effect on the bias; (2) two linked SDL result in the underesti- mation of linkage distances for most cases, overestimation for an additive model with opposite additive effects, and unbiased estimation for an epistatic model with negative additive-by-additive effects; (3) the proposed method can obtain the unbiased estimation of linkage distance. This new method was applied to a rice RIL population with severely distorted segregation to reconstruct the linkage maps, and a bootstrap method was used to obtain 95% confidence intervals of map distances. The results from real data analysis further demonstrate the utility of our method, which provides a foundation for the inheritance analysis of quantitative and viability traits.  相似文献   

9.
Many QTL mapping methods have been developed in the past two decades.Statistically,the best method should have a high detection power but a low false discovery rate (FDR).Power and FDR cannot be derived theoretically for most QTL mapping methods,but they can be properly evaluated using computer simulations.In this paper,we used four genetic models (two for independent loci and two for linked loci) to illustrate power and FDR estimation for interval mapping (IM) and inclusive composite interval mapping (ICIM).For each model,we simulated 1000 populations each of 200 doubled haploids.A support interval (SI) was first defined to indicate to which predefined QTL the significant QTL belonged.Power was calculated by counting the number of simulation runs with significant peaks higher than the logarithm of odds (LOD) threshold in the SI.Quantitative trait loci not identified in any SIs were viewed as false positives.The FDR is the rate at which QTLs are identified as significant when they are actually non-significant.Simulation results allowed us to estimate power and FDR of IM and ICIM for two independent and two linkage genetic models.Our estimates allowed us to readily compare the efficiencies of different statistical methods for QTL mapping,including the ability to separate linkage,under a wide range of genetic models.We used IM and ICIM as examples of how to estimate power and FDR,but the principles shown in this paper can be used for power analysis and comparison of any other QTL mapping methods,especially those based on interval tests.  相似文献   

10.
11.
Maize is one of the most important cereal crops in the world. The hybrid yield advantage is responsible for about 10 percent of the total global maize production of 550 Mt[1]. It is exigent to study the yield traits so as to improve the hybrids per se in …  相似文献   

12.
Kroymann J  Mitchell-Olds T 《Nature》2005,435(7038):95-98
Complex traits such as human disease, growth rate, or crop yield are polygenic, or determined by the contributions from numerous genes in a quantitative manner. Although progress has been made in identifying major quantitative trait loci (QTL), experimental constraints have limited our knowledge of small-effect QTL, which may be responsible for a large proportion of trait variation. Here, we identified and dissected a one-centimorgan chromosome interval in Arabidopsis thaliana without regard to its effect on growth rate, and examined the signature of historical sequence polymorphism among Arabidopsis accessions. We found that the interval contained two growth rate QTL within 210 kilobases. Both QTL showed epistasis; that is, their phenotypic effects depended on the genetic background. This amount of complexity in such a small area suggests a highly polygenic architecture of quantitative variation, much more than previously documented. One QTL was limited to a single gene. The gene in question displayed a nucleotide signature indicative of balancing selection, and its phenotypic effects are reversed depending on genetic background. If this region typifies many complex trait loci, then non-neutral epistatic polymorphism may be an important contributor to genetic variation in complex traits.  相似文献   

13.
To detect genes underlying anxiety-related traits in mice,we performed univariate and multivariate QTL mapping analyses of phenotypes obtained from 71 mice of the BXD recombinant inbred (RI) strains (n=528 mice) and their parental strains (C57BL/6J and DBA/2J).Separate and joint mapping analyses were carried out using a linkage map composed of 506 simple sequence repeats (SSRs).The main QTL effects,interactions between pairs of QTLs (epistasis),and their environmental interactions were estimated.The results showed that anxiety-related traits were influenced by multiple QTLs (five main effect QTLs and three epistatic QTLs).Ten potential anxiety-related candidate genes within the QTL intervals on chromosomes 5,13 and 15 were identified.Some of these genes have been reported previously to be associated with the anxiety response.Based on our results,it is suggested that the multivariate QTL mapping approach improves the statistical power for detecting QTL and the precision of parameter estimation.Moreover,multivariate mapping can also detect pleiotropic QTL effects.  相似文献   

设为首页 | 免责声明 | 关于勤云 | 加入收藏

Copyright©北京勤云科技发展有限公司  京ICP备09084417号