Features of Fractal Conformity and Bioconsolidation in the Early Myogenesis Gene Expression and Their Relationship to the Genetic Diversity of Chicken Breeds.

Elements of fractal analysis are widely used in scientific research, including several biological disciplines. In this study, we hypothesized that chicken breed biodiversity manifests not only at the phenotypic level, but also at the genetic-system level in terms of different profiles of fractal conformity and bioconsolidation in the early myogenesis gene expression. To demonstrate this effect, we developed two mathematical models that describe the fractal nature of the expression of seven key genes in the embryonic breast and thigh muscles in eight breeds of meat, dual purpose, egg and game types. In the first model, we produced breed-specific coefficients of gene expression conformity in each muscle type using the slopes of regression dependencies, as well as an integral myogenesis gene expression index (MGEI). Additionally, breed fractal dimensions and integral myogenesis gene expression fractal dimension index (MGEFDI) were determined. The second gene expression model was based on plotting fractal portraits and calculating indices of fractal bioconsolidation. The bioconsolidation index of myogenesis gene expression correlated with the chick growth rate and nitric oxide (NO) oxidation rate. The proposed fractal models were instrumental in interpreting the genetic diversity of chickens at the level of gene expression for early myogenesis, NO metabolism and the postnatal growth of chicks.

Unraveling signatures of chicken genetic diversity and divergent selection in breed-specific patterns of early myogenesis, nitric oxide metabolism and post-hatch growth.

Introduction: Due to long-term domestication, breeding and divergent selection, a vast genetic diversity in poultry currently exists, with various breeds being characterized by unique phenotypic and genetic features. Assuming that differences between chicken breeds divergently selected for economically and culturally important traits manifest as early as possible in development and growth stages, we aimed to explore breed-specific patterns and interrelations of embryo myogenesis, nitric oxide (NO) metabolism and post-hatch growth rate (GR). Methods: These characteristics were explored in eight breeds of different utility types (meat-type, dual purpose, egg-type, game, and fancy) by incubating 70 fertile eggs per breed. To screen the differential expression of seven key myogenesis associated genes (MSTN, GHR, MEF2C, MYOD1, MYOG, MYH1, and MYF5), quantitative real-time PCR was used. Results: We found that myogenesis associated genes expressed in the breast and thigh muscles in a coordinated manner showing breed specificity as a genetic diversity signature among the breeds studied. Notably, coordinated ("accord") expression patterns of MSTN, GHR, and MEFC2 were observed both in the breast and thigh muscles. Also, associated expression vectors were identified for MYOG and MYOD1 in the breast muscles and for MYOG and MYF5 genes in the thigh muscles. Indices of NO oxidation and post-hatch growth were generally concordant with utility types of breeds, with meat-types breeds demonstrating higher NO oxidation levels and greater GR values as compared to egg-type, dual purpose, game and fancy breeds. Discussion: The results of this study suggest that differences in early myogenesis, NO metabolism and post-hatch growth are breed-specific; they appropriately reflect genetic diversity and accurately capture the evolutionary history of divergently selected chicken breeds.

Simulation of evolution implemented in the mutualistic symbioses towards enhancing their ecological efficiency, functional integrity and genotypic specificity.

We created the mathematical model for the evolution of the Efficiency of Mutualistic Symbioses (EMS) which was estimated as the microsymbiont impacts on the host's reproductive potential. Using the example of rhizobia-legume interaction, the relationships were studied between EMS and Functional Integrity of Symbiosis (FIS) which is represented as a measure for concordance of changes in the partners' genotypic frequencies under the environmental fluctuations represented by the minor deviations of the systemic model parameters. The FIS indices correlate positively with EMS values suggesting an enhancement of FIS via the natural selection operating in the partners' populations in favor of high EMS. Due to this selection, nodular habitats may be closed for colonization by the non-beneficial bacterial strains and the Genotypic Specificity of Mutualism (GSM) in partners' interactions is enhanced: the selective advantage of host-specific vs non-host-specific mutualists is increasing. The novelty of our model is to suggest a selective background for macroevolutionary events reorganizing the structure and functions of symbiotic systems and to present its evolution as a result of shifting the equilibrium between different types of mutualists under the impacts of the symbiosis-stipulated modes of natural selection.

Equilibrium between the "genuine mutualists" and "symbiotic cheaters" in the bacterial population co-evolving with plants in a facultative symbiosis.

The mathematical model for evolution of the plant-microbe facultative mutualistic interactions based on the partners' symbiotic feedbacks is constructed. Using the example of rhizobia-legume symbiosis, we addressed these feedbacks in terms of the metabolic (C<-->N) exchange resulting in the parallel improvements of the partners' fitness (positive feedbacks). These improvements are correlated to the symbiotic efficiency dependent on the ratio of N(2)-fixing bacterial strains ("genuine mutualists") to the non- N(2)-fixing strains ("symbiotic cheaters") in the root nodules. The computer experiments demonstrated that an interplay between the frequency-dependent selection (FDS) and the Darwinian (frequency-independent) selection pressures implemented in the partners' populations ensures an anchoring or even domination for the newly generated host-specific mutualists (which form N(2)-fixing nodules only with one of two available plant genotypes) more successfully than for the non-host-specific mutualists (which form N(2)-fixing nodules with both plant genotypes). The created model allows us to consider the mutualistic symbiosis as a finely balanced polymorphic system wherein the equilibrium in bacterial population may be shifted in favor of "genuine mutualists" due to the partner-stipulated selection for an improved symbiotic efficiency implemented in the plant population.

Interplay of Darwinian and frequency-dependent selection in the host-associated microbial populations.

In order to analyze the microevolutionary processes in host-associated microorganisms, we simulated the dynamics of rhizobia populations composed of a parental strain and its mutants possessing the altered fitness within "plant-soil" system. The population dynamics was presented as a series of cycles (each one involves "soil-->rhizosphere-->nodules-->soil" succession) described using recurrent equations. For representing the selection and mutation pressures, we used a universal approach based on calculating the shifts in the genetic ratios of competing bacterial genotypes within the particular habitats and across several habitats. Analysis of the model demonstrated that a balanced polymorphism may be established in rhizobia population: mutants with an improved fitness do not supplant completely the parental strain while mutants with a decreased fitness may be maintained stably. This polymorphism is caused by a rescue of low-fitted genotypes via negative frequency-dependent selection (FDS) that is implemented during inoculation of nodules and balances the Darwinian selection that occurs during multiplication or extinction of bacteria at different habitats. The most diverse populations are formed if the rhizobia are equally successful in soil and nodules, while a marked preference for any of these habitats results in the decrease of diversity. Our simulation suggests that FDS can maintain the mutualistic rhizobia-legume interactions under the stress conditions deleterious for surviving the bacterial strains capable for intensive N2 fixation. Genetic consequences of releasing the modified rhizobia strains may be addressed using the presented model.