Combined Linkage Disequilibrium and Linkage Analysis (cLDLA): implementation of a powerful approach to identify the genetic basis of complex traits in a bioinformatics workflow.
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Identifying the relationship between the polymorphism segregating in a population and phenotypic differences of a trait observed between the individuals of a population is of major biological interest and represents the basis of forward genetics. Much of the traits of interest are influenced by several polymorphic genes and environmental conditions. Often the loci associated with such measurable traits are referred to as Quantitative trait loci. These loci are identified using several statistical approaches. One of them is combined linkage disequilibrium and linkage analysis (cLDLA). This approach, first proposed by Meuwissen and colleagues in 2002, is shown to be robust against population stratification/family structure and requires a relatively lower sample size compared to a genome-wide association study design. Previously, we have successfully used this approach in mapping several important traits in livestock such as identifying the genetic basis of polled condition in cattle and tail length in sheep. A cLDLA requires several complex computation processing and intermediary file conversion steps; for some of these steps no open-source tools are available. Therefore, running this analysis, manually, can prove challenging, tedious, or error-prone. We present, cldla, a bioinformatics workflow implemented in nextflow which takes the vcf file and phenotype file as inputs and implements all the downstream processing required for cLDLA. Additionally, it also has a separate workflow to estimate SNP-based heritability and features for interactive visualization of the results. The workflow is freely available at: https://github.com/Popgen48/cldla.Keywords:
Linkage (software)
Linkage Disequilibrium
Disequilibrium
Basis (linear algebra)
The traditional transportation planning takes the microeconomics Walras equilibrium principle as its theoretical base. Transportation planning is revealed at the point of market equilibrium, and doesn't consider the market disequilibrium cases. Actually, an equilibrium state is a special disequilibrium. Under some market conditions, an equilibrium case can be realized. However, these conditions are very rigorous, we scarcely obtain them. Even if an equilibrium state is carried out, it is still temporary, and can't represent the real market. Transportation market is usually in disequilibrium state. Based on the macroeconomics disequilibrium theory and pertinent research achievements, the idea of disequilibrium transportation planning is proposed in this paper. In order to establish a basic theoretical framework, the existence of market disequilibrium is shown by analyzing the price and quantity regulation mechanism. The unified model of market equilibrium and disequilibrium is introduced by virtue of variational inequality. In this paper, the concept of disequilibrium degree is also posed, and the method for disequilibrium traffic demand forecasting is proposed by incorporating the disequilibrium degree. Finally, the price quantity regulation principle of macroeconomics disequilibrium theory is introduced into the user's route choice behavior, a more general behavior principle is proposed as a result.
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Summary Time-dependent behaviour of linkage disequilibrium when there was initial linkage disequilibrium is studied in a finite island model assuming neutrality. Explicit expressions for linkage disequilibrium parameters are obtained. From these expressions, the initial and the ultimate decay rates of linkage disequilibrium parameters are found to be increased and decreased, respectively, by finiteness of the population when recombination rate, migration rate and inverse of subpopulation size are of comparable order. Thus, linkage disequilibrium created in the past may persist longerin smaller subdivided populations. Also, differentiation of the gametic parameter of linkage disequilibrium among subpopulations is found to diminish quickly compared tothe linkage disequilibrium in the whole population. Implications of these results for the interpretation of linkage disequilibria in natural populations are discussed.
Disequilibrium
Linkage Disequilibrium
Linkage (software)
Population Genetics
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Disequilibrium
Linkage Disequilibrium
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Abstract This article presents an econometric model of winegrape prices which recognizes the existence of demand and supply imbalances in the Australian market. A “markets in disequilibrium” framework is employed to motivate modeling price changes as responding to variations in excess demand/supply. The disequilibrium price equation provides estimates of regional and varietal price discounts/premiums and a measure of the speed of disequilibrium price adjustment. The equilibrium assumption is rejected for the market and substantial differences between equilibrium and disequilibrium estimates point to the inaccuracies of assuming market clearing. Disequilibrium estimates point to significant differences between warm and cool regions and changing speed of disequilibrium adjustment over time.
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Abstract In this paper current theory and estimation procedures are applied in an analysis of disequilibrium price behavior in the U.S. fed beef sector. Although tests of equilibrium versus disequilibrium hypotheses are not well developed, results indicate the possible presence of disequilibrium prices in the market for fed beef; at least the hypothesis of significant disequilibrium could not be rejected.
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Regional coordinate development is strongly dependent on disequilibrium,i.e.the disequilibrium of regional development is an objective thing.The essence of regional coordination is to promote the orderly development of regional economy and achieve the fairness of market opportunities on the basis of the close corelation between industries through the free circulation of regional economic factors.Disequilibrium development is influenced by three forces: the inherent law of economic development,the working of markets and government intervention;whether the effect of disequilibrium development is the result of the combination of these three forces or any one of the three factors,the measures that ignore the implication of regional coordination and implement the strategy of disequilibrium development directly may lead to worse results.
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Economic interventionism
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Unlike gametic linkage disequilibrium defined for a random-mating population, zygotic disequilibrium describes the nonrandom association between different loci in a nonequilibrium population that deviates from Hardy-Weinberg equilibrium. Zygotic disequilibrium specifies five different types of disequilibria simultaneously that are (1) Hardy-Weinberg disequilibria at each locus, (2) gametic disequilibrium (including two alleles in the same gamete, each from a different locus), (3) nongametic disequilibrium (including two alleles in different gametes, each from a different locus), (4) trigenic disequilibrium (including a zygote at one locus and an allele at the other), and (5) quadrigenic disequilibrium (including two zygotes each from a different locus). However, because of the uncertainty on the phase of the double heterozygote, gametic and nongametic disequilibria need to be combined into a composite digenic disequilibrium and further define a composite quadrigenic disequilibrium together with the quadrigenic disequilibrium. To investigate the extent and distribution of zygotic disequilibrium across the canine genome, a total of 148 dogs were genotyped at 247 microsatellite markers located on 39 pairs of chromosomes for an outbred multigenerational pedigree, initiated with a limited number of unrelated founders. A major portion of zygotic disequilibrium was contributed by the composite digenic and quadrigenic disequilibrium whose values and numbers of significant marker pairs are both greater than those of trigenic disequilibrium. All types of disequilibrium are extensive in the canine genome, although their values tend to decrease with extended map distances, but with a greater slope for trigenic disequilibrium than for the other types of disequilibrium. Considerable variation in the pattern of disequilibrium reduction was observed among different chromosomes. The results from this study provide scientific guidance about the determination of the number of markers used for whole-genome association studies.
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Linkage Disequilibrium
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Disequilibrium is more frequently and widely found than equilibrium in the economic development,therefore,enough attention should be paid to disequilibrium and regulation is necessary.In this paper,the regulation control of the disequilibrium economics for micro-macro multi-market are studied at the optimal control theory.Furthermore,the comprehensive applications of regulation measures are put forward.
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Macro
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