Linkage disequilibrium(LD) can be applied for mapping the actual genes responsible for variation of economically important traits through association mapping.The feasibility and efficacy of association studies are str...Linkage disequilibrium(LD) can be applied for mapping the actual genes responsible for variation of economically important traits through association mapping.The feasibility and efficacy of association studies are strongly dependent on the extent of LD which determines the number and density of markers in the studied population,as well as the experimental design for an association analysis.In this study,we first characterized the extent of LD in a wild population and a cultured mass-selected line of Pacific oyster(Crassostrea gigas).A total of 88 wild and 96 cultured individuals were selected to assess the level of genome-wide LD with 53 microsatellites,respectively.For syntenic marker pairs,no significant association was observed in the wild population;however,three significant associations occurred in the cultured population,and the significant LD extended up to 12.7 c M,indicating that strong artificial selection is a key force for substantial increase of genome-wide LD in cultured population.The difference of LD between wild and cultured populations showed that association studies in Pacific oyster can be achieved with reasonable marker densities at a relatively low cost by choosing an association mapping population.Furthermore,the frequent occurrence of LD between non-syntenic loci and rare alleles encourages the joint application of linkage analysis and LD mapping when mapping genes in oyster.The information on the linkage disequilibrium in the cultured population is useful for future association mapping in oyster.展开更多
The Rayleigh distillation isotope fractionation(RDIF) model is one of the most popular methods used in isotope geochemistry. Numerous isotope signals observed in geologic processes have been interpreted with this mode...The Rayleigh distillation isotope fractionation(RDIF) model is one of the most popular methods used in isotope geochemistry. Numerous isotope signals observed in geologic processes have been interpreted with this model. The RDIF model provides a simple mathematic solution for the reservoir-limited equilibrium isotope fractionation effect. Due to the reservoir effect, tremendously large isotope fractionations will always be produced if the reservoir is close to being depleted. However, in real situations, many prerequisites assumed in the RDIF model are often difficult to meet. For instance, it requires the relocated materials, which are removed step by step from one reservoir to another with different isotope compositions(i.e., with isotope fractionation), to be isotopically equilibrated with materials in the first reservoir simultaneously. This ‘‘quick equilibrium requirement’’ is indeed hard to meet if the first reservoir is sufficiently large or the removal step is fast. The whole first reservoir will often fail to re-attain equilibrium in time before the next removal starts.This problem led the RDIF model to fail to interpret isotope signals of many real situations. Here a diffusion-coupled and Rayleigh-like(i.e., reservoir-effect included) separation process is chosen to investigate this problem. We find that the final isotope fractionations are controlled by both the diffusion process and the reservoir effects via the disequilibrium separation process. Due to its complexity, we choose to use a numerical simulation method to solve this problem by developing specific computing codes for the working model.According to our simulation results, the classical RDIF model only governs isotope fractionations correctly at the final stages of separation when the reservoir scale(or thickness of the system) is reduced to the order of magnitude of the quotient of the diffusivity and the separation rate. The RDIF model fails in other situations and the isotope fractionations will be diffusion-limited when the reservoir is relatively large, or the separation rate is fast. We find that the effect of internal isotope distribution inhomogeneity caused by diffusion on the Rayleigh-like separation process is significant and cannot be ignored. This method can be applied to study numerous geologic and planetary processes involving diffusion-limited disequilibrium separation processes including partial melting,evaporation, mineral precipitation, core segregation, etc.Importantly, we find that far more information can be extracted through analyzing isotopic signals of such ‘‘disequilibrium’’processes than those of fully equilibrated ones, e.g., reservoir size and the separation rate. Such information may provide a key to correctly interpreting many isotope signals observed from geochemical and cosmochemical processes.展开更多
基金supported by the Shandong Seed Project and the National Natural Science Foundation of China (31372524)
文摘Linkage disequilibrium(LD) can be applied for mapping the actual genes responsible for variation of economically important traits through association mapping.The feasibility and efficacy of association studies are strongly dependent on the extent of LD which determines the number and density of markers in the studied population,as well as the experimental design for an association analysis.In this study,we first characterized the extent of LD in a wild population and a cultured mass-selected line of Pacific oyster(Crassostrea gigas).A total of 88 wild and 96 cultured individuals were selected to assess the level of genome-wide LD with 53 microsatellites,respectively.For syntenic marker pairs,no significant association was observed in the wild population;however,three significant associations occurred in the cultured population,and the significant LD extended up to 12.7 c M,indicating that strong artificial selection is a key force for substantial increase of genome-wide LD in cultured population.The difference of LD between wild and cultured populations showed that association studies in Pacific oyster can be achieved with reasonable marker densities at a relatively low cost by choosing an association mapping population.Furthermore,the frequent occurrence of LD between non-syntenic loci and rare alleles encourages the joint application of linkage analysis and LD mapping when mapping genes in oyster.The information on the linkage disequilibrium in the cultured population is useful for future association mapping in oyster.
基金supported by the Strategic Priority Research Program (B) of CAS (No. XDB41000000)Pre-research Project on Civil Aerospace Technologies No. D020202 funded by the Chinese National Space Administration (CNSA) and Chinese NSF projects (No. 42130114)。
文摘The Rayleigh distillation isotope fractionation(RDIF) model is one of the most popular methods used in isotope geochemistry. Numerous isotope signals observed in geologic processes have been interpreted with this model. The RDIF model provides a simple mathematic solution for the reservoir-limited equilibrium isotope fractionation effect. Due to the reservoir effect, tremendously large isotope fractionations will always be produced if the reservoir is close to being depleted. However, in real situations, many prerequisites assumed in the RDIF model are often difficult to meet. For instance, it requires the relocated materials, which are removed step by step from one reservoir to another with different isotope compositions(i.e., with isotope fractionation), to be isotopically equilibrated with materials in the first reservoir simultaneously. This ‘‘quick equilibrium requirement’’ is indeed hard to meet if the first reservoir is sufficiently large or the removal step is fast. The whole first reservoir will often fail to re-attain equilibrium in time before the next removal starts.This problem led the RDIF model to fail to interpret isotope signals of many real situations. Here a diffusion-coupled and Rayleigh-like(i.e., reservoir-effect included) separation process is chosen to investigate this problem. We find that the final isotope fractionations are controlled by both the diffusion process and the reservoir effects via the disequilibrium separation process. Due to its complexity, we choose to use a numerical simulation method to solve this problem by developing specific computing codes for the working model.According to our simulation results, the classical RDIF model only governs isotope fractionations correctly at the final stages of separation when the reservoir scale(or thickness of the system) is reduced to the order of magnitude of the quotient of the diffusivity and the separation rate. The RDIF model fails in other situations and the isotope fractionations will be diffusion-limited when the reservoir is relatively large, or the separation rate is fast. We find that the effect of internal isotope distribution inhomogeneity caused by diffusion on the Rayleigh-like separation process is significant and cannot be ignored. This method can be applied to study numerous geologic and planetary processes involving diffusion-limited disequilibrium separation processes including partial melting,evaporation, mineral precipitation, core segregation, etc.Importantly, we find that far more information can be extracted through analyzing isotopic signals of such ‘‘disequilibrium’’processes than those of fully equilibrated ones, e.g., reservoir size and the separation rate. Such information may provide a key to correctly interpreting many isotope signals observed from geochemical and cosmochemical processes.
