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1.
QTLNetworkR is an R package that aims to provide a user-friendly and platform-independent tool to visualize quantitative trait loci (QTL) mapping results. The graphical functions of the QTLNetworkR are based upon lattice and grid packages, and the graphical user interface (GUI) of the QTLNetworkR is built upon RGtk2 and gWidgetsRGtk2 packages. Six functions are designed to help visualize marker interval, putative QTL, QTL-by- environment interactions, marker interval interactions, epistasis, and the predicted genetic architecture of complex traits. It is especially helpful in profiling results for multiple traits at multiple environments. The current version of QTLNetworkR is able to accept QTL mapping results from QTLNetwork, and it is ready for possible extensions to import results from some other QTL mapping software packages. In addition, we presented a QTL mapping result in rice (Oryza sativa) as an example to describe the features of QTLNetworkR.  相似文献   

2.
An approach for generating interactive 3D graphical visualization of the genetic architectures of complex traits in multiple environments is described. 3D graphical visualization is utilized for making improvements on traditional plots in quan- titative trait locus (QTL) mapping analysis. Interactive 3D graphical visualization for abstract expression of QTL, epistasis and their environmental interactions for experimental populations was developed in framework of user-friendly software QTLNetwork (http://ibi.zju.edu.cn/software/qtlnetwork). Novel definition of graphical meta system and computation of virtual coordinates are used to achieve explicit but meaningful visualization. Interactive 3D graphical visualization for QTL analysis provides geneticists and breeders a powerful and easy-to-use tool to analyze and publish their research results.  相似文献   

3.
Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) sug- gested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection.  相似文献   

4.
Immortalized F2 population of rice (Oryza sativa L.) was developed by randomly mating F1 among recombinant inbred (RI) lines derived from (Zhenshan 97B × Minghui 63), which allowed replications within and across environments. OTL (quantitative trait loci) mapping analysis on kilo-grain weight of immortalized F2 population was performed by using newly developed software for QTL mapping, QTLMapper 2.0. Eleven distinctly digenic epistatic loci included a total of 15 QTL were located on eight chromosome. QTL main effects of additive, domainance, and additive × additive, additive × domainance, and dominance × dominance interactions were estimated. Interaction effects between QTL main effects and environments (QE) were predicted. Less than 40% of single effects, most of which were additive effects, for identified QTL were significant at 5% level. The directional difference for QTL main effects suggested that these QTL were distributed in parents in the repulsion phase. This should make it feasible to improve kilo-grain weight of both parents by selecting apprents in the repulsion phase. This should make it feasible to improve kilo-grain weight of both parents by selecting appropriate new recombinants. Only few of theQE interaction effects were significant. Application prospect for QTL mapping achievements in genetic breeding was discussed. Project (No. 39893354) supported by the National Natural Science Foundation of China  相似文献   

5.
分别用单标记分析法、区间作图法、复合区间作图法和贝叶斯方法对油菜开花性状进行QTL作图,初步估计出QTL的位置,并分析比较各种作图方法．  相似文献   

6.
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 additivex environment interaction effects of QTLs in the presence of outliers.  相似文献   

7.
Immortalized F2 population of rice (Oryza sativa L.) was developed by randomly mating F1 among recombinant inbred (RI) lines derived from (Zhenshan 97B ( Minghui 63), which allowed replications within and across environments. QTL (quantitative trait loci) mapping analysis on kilo-grain weight of immortalized F2 population was performed by using newly developed software for QTL mapping, QTLMapper 2.0. Eleven distinctly digenic epistatic loci included a total of 15 QTL were located on eight chromosomes. QTL main effects of additive, dominance, and additive ( additive, additive ( dominance, and dominance ( dominance interactions were estimated. Interaction effects between QTL main effects and environments (QE) were predicted. Less than 40% of single effects, most of which were additive effects, for identified QTL were significant at 5% level. The directional difference for QTL main effects suggested that these QTL were distributed in parents in the repulsion phase. This should make it feasible to improve kilo-grain weight of both parents by selecting appropriate new recombinants. Only few of the QE interaction effects were significant. Application prospect for QTL mapping achievements in genetic breeding was discussed.  相似文献   

8.
Seed vigor is an important characteristic of seed quality, and rice cultivars with strong seed vigor are desirable in direct-sowing rice production for optimum stand establishment. In the present study, the quantitative trait loci (QTLs) of three traits for rice seed vigor during the germination stage, including germination rate, final germination percentage, and germination index, were investigated using one recombinant inbred line (RIL) population derived from a cross between japonica Daguandao and indica IR28, and using the multiple interval mapping (MIM) approach. The results show that indica rice presented stronger seed vigor during the germination stage than japonica rice. A total of ten QTLs, and at least five novel alleles, were detected to control rice seed vigor, and the amount of variation (R 2) explained by an individual QTL ranged from 7.5% to 68.5%, with three major QTLs with R 2>20%. Most of the QTLs detected here are likely to coincide with QTLs for seed weight, seed size, or seed dormancy, suggesting that the rice seed vigor might be correlated with seed weight, seed size, and seed dormancy. At least five QTLs are novel alleles with no previous reports of seed vigor genes in rice, and those major or minor QTLs could be used to significantly improve the seed vigor by marker-assisted selection (MAS) in rice.  相似文献   

9.
ＩＮＴＲＯＤＵＣＴＩＯＮＭａｎｙｇｅｎｅｔｉｃｍｏｄｅｌｓｂａｓｅｄｏｎｔｈｅａｐｐｒｏａｃｈｏｆＡＮＯＶＡ (ａｎａｌｙｓｉｓｏｆｖａｒｉａｎｃｅ)ｗｅｒｅｄｅｖｅｌ ｏｐｅｄｂｙＦｉｓｈｅｒ(1 92 5) .Ｓｏｍｅｏｆｔｈｅｓｅｍｏｄｅｌｓ,ｅ.ｇ .ＮＣｄｅｓｉｇｎＩａｎｄＩＩ(Ｃｏｍｓｔｏｃｋｅｔａｌ.,1 952 ;Ｈａｌｌａｕｅｒｅｔａｌ.,1 981 ) ,ｄｉａｌｌｅｌｍｏｄｅｌｓ(Ｙａｔｅｓ,1 94 7;Ｇｒｉｆｆｉｎｇ,1 956;ＧａｒｄｎｅｒａｎｄＥ ｂｅｒｈａｒｔ,1 966) ,ａｒｅｓｔｉｌｌｗｉｄｅｌｙｕｓｅｄｂｙｐｌａ…  相似文献   

10.
New approaches based on general mixed linear models were presented for analyzing complex quantitative traits in animal models, seed models and QTL (quantitative trait locus) mapping models. Variances and covariances can be appropriately estimated by MINQUE (minimum norm quadratic unbiased estimation) approaches. Random genetic effects can be predicted without bias by LUP (linear unbiased prediction) or AUP (adjusted unbiased prediction) methods. Mixed-model based composite interval mapping (MCIM) methods are suitable for efficiently searching QTLs along the whole genome. Bayesian methods and Markov Chain Monte Carlo (MCMC) methods can be applied in analyzing parameters of random effects as well as their variances. Projects supported by NSFC (39670390, 39893350) and the NIH Grant GM32518  相似文献   

11.
Quantitative trait loci (QTL) and their additive, dominance and epistatic effects play a critical role in complex trait variation. It is often infeasible to detect multiple interacting QTL due to main effects often being confounded by interaction effects. Positioning interacting QTL within a small region is even more difficult. We present a variance component approach nested in an empirical Bayesian method, which simultaneously takes into account additive, dominance and epistatic effects due to multiple interacting QTL. The covariance structure used in the variance component approach is based on combined linkage disequilibrium and linkage (LDL) information. In a simulation study where there are complex epistatic interactions between QTL, it is possible to simultaneously fine map interacting QTL using the proposed approach. The present method combined with LDL information can efficiently detect QTL and their dominance and epistatic effects, making it possible to simultaneously fine map main and epistatic QTL.  相似文献   

12.
In standard interval mapping (IM) of quantitative trait loci (QTL), the QTL effect is described by a normal mixture model. When this assumption of normality is violated, the most commonly adopted strategy is to use the previous model after data transformation. However, an appropriate transformation may not exist or may be difficult to find. Also this approach can raise interpretation issues. An interesting alternative is to consider a skew-normal mixture model in standard IM, and the resulting method is here denoted as skew-normal IM. This flexible model that includes the usual symmetric normal distribution as a special case is important, allowing continuous variation from normality to non-normality. In this paper we briefly introduce the main peculiarities of the skew-normal distribution. The maximum likelihood estimates of parameters of the skew-normal distribution are obtained by the expectation-maximization (EM) algorithm. The proposed model is illustrated with real data from an intercross experiment that shows a significant departure from the normality assumption. The performance of the skew-normal IM is assessed via stochastic simulation. The results indicate that the skew-normal IM has higher power for QTL detection and better precision of QTL location as compared to standard IM and nonparametric IM.  相似文献   

13.
INTRODUCTION Aluminum (Al) toxicity is one of the mostimportant yield-limiting factors for crop grown onacid upland and lowland acid sulphate soils (IRRI,1978). Al toxicity results in a reduced and damagedroot system, which in turn causes the affectedplants to be susceptible to drought stress and min-eral nutrient deficiencies (Foy, 1988). The physio-logical and biochemical mechanisms of the toxiceffect of Al on root elongation had been extensivelyinvestigated (Matsumoto, 2000). T…  相似文献   

14.
Aluminum (Al) toxicity is the major factor limiting crop productivity in acid soils. In this study, a recombinant inbreed line (RIL) population derived from a cross between an A1 sensitive lowland indica rice variety IR1552 and an Al tolerant upland japonica rice variety Azucena, was used for mapping quantitative trait loci (QTLs) for A1 tolerance. Three QTLs for relative root length (RRL) were detected on chromosome 1, 9, 12, respectively, and I QTL for root length under Al stress is identical on chromosome I after one week and two weeks stress. Comparison of QTLs on chromosome 1 from different studies indicated an identical interval between C86 and RZ801 with gene(s) for Al tolerance. This interval provides an important start point for isolating genes responsible for A1 tolerance and understanding the genetic nature of Al tolerance in rice. Four Al induced ESTs located in this interval were screened by reverse Northern analysis and confirmed by Northern analysis. They would be candidate genes for the QTL.  相似文献   

15.
Rice straw is always regarded as a by-product of rice production, but it could be a significant energy source for ruminant animals. Knowledge of the genetic variation and genetic architecture of cell wall traits will facilitate rice breeders by improving relevant traits through selective breeding and genetic engineering. The common wild rice, Oryza rufipogon Griff., which is considered to be the progenitor of Oryza sativa, has been widely utilized for the identification of genes of agronomic importance for rice genetic improvement. In the present study, the mapping of quantitative trait loci (QTLs) for acid detergent fiber (ADF), neutral detergent fiber (NDF), acid detergent lignin (ADL), and ADL/NDF ratio was carried out in two environments using a backcrossed inbred line (BIL) population derived from a cross between the recurrent parent Xieqingzao B (XB) and an accession of Dongxiang wild rice (DWR). The results indicated that all four traits tested were continuously distributed among the BILs, but many BILs showed transgressive segregation. A total of 16 QTLs were identified for the four traits, but no QTLs were in common in two environments, suggesting that environment has dramatic effects on fiber and lignin syntheses. Compared to the QTL positions for grain yield-related traits, there were no unfavorable correlations between grain yield components and cell wall traits in this population. The QTLs identified in this study are useful for the development of dual-purpose rice varieties that are high in grain yield and are also high in straw quality.  相似文献   

16.
INTRODUCTION Drought stress is a major constraint to rice(Oryza sativa) production and yield stability in rainedecosystems (Dey and Upadhyaya, 1996). Rice mustbe made more drought tolerant, but this is a somewhatcontradictory objective considering that rice is mostcommonly grown under flooded conditions. Achiev-ing drought tolerance in rice will require a deeperunderstanding of the possible physiological mecha-nisms available for water stress tolerance and theidentification of favo…  相似文献   

17.
Objective:To evaluate the effect and profitability of using the quantitative trait loci (QTL)-linked direct marker (DR marker) in gene-assisted selection (GAS). Methods: Three populations (100, 200, or 300 sows plus 10 boars within each group) with segregating QTL were simulated stochastically. Five economic traits were investigated, including number of born alive (NBA), average daily gain to 100 kg body weight (ADG), feed conversion ratio (FCR), back fat at 100 kg body weight (BF) and intramuscular fat (IMF). Selection was based on the estimated breeding value (EBV) of each trait. The starting frequencies of the QTL's favorable allele were 0.1, 0.3 and 0.5, respectively. The economic return was calculated by gene flow method. Results: The selection efficiency was higher than 100% when DR markers were used in GAS for 5 traits. The selection efficiency for NBA was the highest, and the lowest was for ADG whose QTL had the lowest variance. The mixed model applied DR markers and obtained higher extra genetic gain and extra economic returns. We also found that the lower the frequency of the favorable allele of the QTL, the higher the extra return obtained. Conclusion: GAS is an effective selection scheme to increase the genetic gain and the eco- nomic returns in pig breeding.  相似文献   

18.
INTRODUCTIONKilo-grainweight,characteristicallyacom-plextrait,isanimportantcomponentofyieldinrice.QTLmappingforkilo-grainweightofricewascon-ductedusingpopulationsofF2(Linetal.,1996),doubledhaploidlines(Luetal.,1997),recombi-nantinbredlines(Xiaoetal.,1996),backcrosstestcross(Xiaoetal.,1995;Lietal.,1997)andratoonedF2(Lietal.,2000).Consideringthesen-sitivityofkilo-grainweighttoenvironments,Luetal.(1997)andZhuangetal.(1997)comparedthedifferentialdetectionofQTLacrossenvironmentstodetermin…  相似文献   

19.
To understand genetic patterns of the morphological and physiological traits in flag leaf of barley, a double haploid (DH) population derived from the parents Yerong and Franklin was used to determine quantitative trait loci (QTL) controlling length, width, length/width, and chlorophyll content of flag leaves. A total of 9 QTLs showing significantly additive effect were detected in 8 intervals on 5 chromosomes. The variation of individual QTL ranged from 1.9% to 20.2%. For chlorophyll content expressed as SPAD value, 4 QTLs were identified on chromosomes 2H, 3H and 6H; for leaf length and width, 2 QTLs located on chromosomes 5H and 7H, and 2 QTLs located on chromosome 5H were detected; and for length/width, 1 QTL was detected on chromosome 7H. The identification of these QTLs associated with the properties of flag leaf is useful for barley improvement in breeding programs. Project supported by the National Natural Science Foundation of China (No. 30630047) and the Project on Absorption of Intellects by Institutions of Higher Education for Academic Disciplinary Innovations (the 111 Project) (No. B06014), China  相似文献   

20.
To understand genetic patterns of the morphological and physiological traits in flag leaf of barley, a double haploid (DH) population derived from the parents Yerong and Franklin was used to determine quantitative trait loci (QTL) controlling length, width, length/width, and chlorophyll content of flag leaves. A total of 9 QTLs showing significantly additive effect were detected in 8 intervals on 5 chromosomes. The variation of individual QTL ranged from 1.9% to 20.2%. For chlorophyll content expressed as SPAD value, 4 QTLs were identified on chromosomes 2H, 3H and 6H; fur leaf length and width, 2 QTLs located on chromosomes 5H and 7H, and 2 QTLs located on chromosome 5H were detected; and for length/width, 1 QTL was detected on chromosome 7H. The identification of these QTLs associated with the properties of flag leaf is useful for barley improvement in breeding programs.  相似文献   

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