Map Manager QTX, cross-platform software for genetic mapping.
TL;DR: Map Manager QTX is an enhanced version of Map Manager QT, rewritten with the aid of cross-platform libraries (XVT, Boulder Software Foundry, Inc.), which allow it to be compiled for multiple computer platforms.
Abstract: Map Manager QTX (QTX) is software for analysis of genetic mapping experiments in experimental plants and animals. It includes functions for mapping both Mendelian and quantitative trait loci. QTX is an enhanced version of Map Manager QT, rewritten with the aid of cross-platform libraries (XVT, Boulder Software Foundry, Inc.), which allow it to be compiled for multiple computer platforms. It currently is distributed for Microsoft Windows and Mac OS and is available at http://mapmgr.roswellpark.org/mmQTX.html.
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TL;DR: R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental populations derived from inbred lines and includes functions for estimating genetic maps, identifying genotyping errors, and performing single-QTL and two-dimensional, two- QTL genome scans by multiple methods.
Abstract: Summary R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental populations derived from inbred lines. It is implemented as an add-on package for the freely-available statistical software, R, and includes functions for estimating genetic maps, identifying genotyping errors, and performing single-QTL and two-dimensional, two-QTL genome scans by multiple methods, with the possible inclusion of covariates. Availability The package is freely available at http://www.biostat.jhsph.edu/~kbroman/qtl.
3,111 citations
Cites methods from "Map Manager QTX, cross-platform sof..."
...There exist numerous computer programs for QTL mapping in experimental crosses, including Mapmaker/QTL (Landeret al., 1987) and Map Manager QTX (Manlyet al., 2001)....
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TL;DR: This review provides an introduction to DNA markers and the concept of polymorphism, linkage analysis and map construction, the principles of QTL analysis and how markers may be applied in breeding programs using MAS.
Abstract: Recognizing the enormous potential of DNA markers in plant breeding, many agricultural research centers and plant breeding institutes have adopted the capacity for marker development and marker-assisted selection (MAS). However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci (QTLs) and the jargon used by molecular biologists, the utility of DNA markers in plant breeding may not be clearly understood by non-molecular biologists. This review provides an introduction to DNA markers and the concept of polymorphism, linkage analysis and map construction, the principles of QTL analysis and how markers may be applied in breeding programs using MAS. This review has been specifically written for readers who have only a basic knowledge of molecular biology and/or plant genetics. Its format is therefore ideal for conventional plant breeders, physiologists, pathologists, other plant scientists and students.
1,588 citations
Cites background or methods from "Map Manager QTX, cross-platform sof..."
...Many researchers have used QTL Cartographer (Basten et al., 1994, 2001), MapManager QTX (Manly et al., 2001) and PLABQTL (Utz & Melchinger, 1996) to perform CIM....
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...‘Bootstrapping’ – a statistical method for resampling–is another method to determine the confidence interval of QTLs (Liu, 1998; Visscher et al., 1996), and can be easily applied within some mapping software programs such as MapManager QTX (Manly et al., 2001)....
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...The mapping program MapManager QTX reports QTL mapping results with this classification (Manly et al., 2001)....
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...QGene and MapManager QTX are commonly used computer programs to perform single-marker analysis (Manly et al., 2001; Nelson, 1997)....
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...This linkage map was constructed using Map Manager QTX (Manly et al., 2001) using the Haldane mapping function....
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Book•
20 Jul 2009
TL;DR: In this article, a single-QTL analysis was performed on two-dimensional, two-Q-TL scans and the model was extended to include multiple Q-TL models.
Abstract: Importing and simulating data.- Data checking.- Single-QTL analysis.- Non-normal phenotypes.- Experimental design and power.- Working with covariates.- Two-dimensional, two-QTL scans.- Fit and exploration of multiple-QTL models.- Case study I.- Case study II.
763 citations
TL;DR: Diversity Arrays Technology can be effectively applied to genetic mapping and diversity analyses of barley and is highlighted as a generic technique for genome profiling in the context of molecular breeding and genomics.
Abstract: Diversity Arrays Technology (DArT) can detect and type DNA variation at several hundred genomic loci in parallel without relying on sequence information. Here we show that it can be effectively applied to genetic mapping and diversity analyses of barley, a species with a 5,000-Mbp genome. We tested several complexity reduction methods and selected two that generated the most polymorphic genomic representations. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 98.0% and a scoring reproducibility of at least 99.8%. The fingerprints grouped barley lines according to known genetic relationships. To validate the Mendelian behavior of DArT markers, we constructed a genetic map for a cross between cultivars Steptoe and Morex. Nearly all polymorphic array features could be incorporated into one of seven linkage groups (98.8%). The resulting map comprised ≈385 unique DArT markers and spanned 1,137 centimorgans. A comparison with the restriction fragment length polymorphism-based framework map indicated that the quality of the DArT map was equivalent, if not superior, to that of the framework map. These results highlight the potential of DArT as a generic technique for genome profiling in the context of molecular breeding and genomics.
593 citations
TL;DR: Fbxl3(Ovtm) defines a molecular link between CRY turnover and CLOCK/BMAL1-dependent circadian transcription to modulate circadian period.
517 citations
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...CryptochromeandPeriodGeneExpression...
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References
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TL;DR: The genetic map is a tool to quantify the distance between genes on a chromosome, based on the observed frequency of crossovers during cell division, which is used to estimate the total distance between chromosomes.
Abstract: The genetic map is a tool to quantify the distance between genes on a chromosome, based on the observed frequency of crossovers during cell division.
5,845 citations
TL;DR: Methods for mapping QTL based on multiple regression which can be applied using any general statistical package are developed and it is shown that these regression methods produce very similar results to those obtained using maximum likelihood.
Abstract: The use of flanking marker methods has proved to be a powerful tool for the mapping of quantitative trait loci (QTL) in the segregating generations derived from crosses between inbred lines. Methods to analyse these data, based on maximum-likelihood, have been developed and provide good estimates of QTL effects in some situations. Maximum-likelihood methods are, however, relatively complex and can be computationally slow. In this paper we develop methods for mapping QTL based on multiple regression which can be applied using any general statistical package. We use the example of mapping in an F(2) population and show that these regression methods produce very similar results to those obtained using maximum likelihood. The relative simplicity of the regression methods means that models with more than a single QTL can be explored and we give examples of two lined loci and of two interacting loci. Other models, for example with more than two QTL, with environmental fixed effects, with between family variance or for threshold traits, could be fitted in a similar way. The ease, speed of application and generality of regression methods for flanking marker analysis, and the good estimates they obtain, suggest that they should provide the method of choice for the analysis of QTL mapping data from inbred line crosses.
2,079 citations
"Map Manager QTX, cross-platform sof..." refers background in this paper
...The following expressions for expected QTL effect are straightforward extensions of similar expressions previously published for backcrosses and intercrosses (Knapp et al. 1990; Carbonell et al. 1992; Haley and Knott 1992; Martinez and Curnow 1992; Moreno-Gonzalez 1992; Jiang and Zeng 1997)....
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TL;DR: If successfully employed, advanced backcross QTL analysis can open the door to exploiting unadapted and exotic germplasm for the quantitative trait improvement of a number of crop plants.
Abstract: Advanced backcross QTL analysis is proposed as a method of combining QTL analysis with variety development. It is tailored for the discovery and transfer of valuable QTL alleles from unadapted donor lines (e.g., land races, wild species) into established elite inbred lines. Following this strategy, QTL analysis is delayed until the BC2 or BC3 generation and, during the development of these populations, negative selection is exercised to reduce the frequency of deleterious donor alleles. Simulations suggest that advanced backcross QTL analysis will be effective in detecting additive, dominant, partially dominant, or overdominant QTLs. Epistatic QTLs or QTLs with gene actions ranging from recessive to additive will be detected with less power than in selfing generations. QTL-NILs can be derived from advanced backcross populations in one or two additional generations and utilized to verify QTL activity. These same QTL-NILs also represent commercial inbreds improved (over the original recurrent inbred line) for one or more quantitative traits. The time lapse from QTL discovery to construction and testing of improved QTL-NILs is minimal (1-2 years). If successfully employed, advanced backcross QTL analysis can open the door to exploiting unadapted and exotic germplasm for the quantitative trait improvement of a number of crop plants.
995 citations
TL;DR: Simulation results showed that to obtain the anticipated reduction in the confidence interval, breeding population size of the AIL in all generations should comprise an effective number of > or = 100 individuals, which is a useful resource for fine genetic mapping.
Abstract: An advanced intercrossed line (AIL) is an experimental population that can provide more accurate estimates of quantitative trait loci (QTL) map location than conventional mapping populations. An AIL is produced by randomly and sequentially intercrossing a population that initially originated from a cross between two inbred lines or some variant thereof. This provides increasing probability of recombination between any two loci. Consequently, the genetic length of the entire genome is stretched, providing increased mapping resolution. In this way, for example, with the same population size and QTL effect, a 95% confidence interval of QTL map location of 20 cM in the F2 is reduced fivefold after eight additional random mating generations (F10). Simulation results showed that to obtain the anticipated reduction in the confidence interval, breeding population size of the AIL in all generations should comprise an effective number of > or = 100 individuals. It is proposed that AILs derived from crosses between known inbred lines may be a useful resource for fine genetic mapping.
596 citations
"Map Manager QTX, cross-platform sof..." refers background or methods in this paper
...Advanced intercrosses are those in which F2 intercross progeny are further intercrossed randomly in successive generations (Darvasi and Soller 1995)....
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...Although this is an approximation (Darvasi and Soller 1995; Jiang and Zeng 1997), it greatly simplifies calculations....
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TL;DR: This study illustrates the usefulness of RI lines for mapping a complex trait such as blast resistance and suggests that durable resistance in the traditional variety, Moroberekan, involves a complex of genes associated with both partial and complete resistance.
Abstract: Moroberekan, a japonica rice cultivar with durable resistance to blast disease in Asia, was crossed to the highly susceptible indica cultivar, CO39, and 281 F7 recombinant inbred (RI) lines were produced by single seed descent. The population was evaluated for blast resistance in the greenhouse and the field, and was analyzed with 127 restriction fragment length polymorphism (RFLP) markers. Two dominant loci associated with qualitative resistance to five isolates of the fungus were tentatively named Pi-5(t) and Pi-7(t). They were mapped on chromosomes 4 and 11, respectively. To identify quantitative trait loci (QTLs) affecting partial resistance, RI lines were inoculated with isolate PO6-6 of Pyricularia oryzae in polycyclic tests. Ten chromosomal segments were found to be associated with effects on lesion number (P 6.0). Three of the markers associated with QTLs for partial resistance had been reported to be linked to complete blast resistance in previous studies. QTLs identified in greenhouse tests were good predictors of blast resistance at two field sites. This study illustrates the usefulness of RI lines for mapping a complex trait such as blast resistance and suggests that durable resistance in the traditional variety, Moroberekan, involves a complex of genes associated with both partial and complete resistance.
583 citations
"Map Manager QTX, cross-platform sof..." refers background in this paper
...Segregation distortion caused by selection at multiple loci (Wang et al. 1994), however, invalidates the classical methods....
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