Analysis of genetic models of the diallele crossing system. Additivity in Hayman's algorithms

Analysis of Hayman's algorithms was carried out on models by dependent gene distribution with various contributions of genes from parents. It is shown that resultant additivity of traits can be explained by various interaction of alleles both within locus and between loci.     

Analysis of genetic control of maize response in anther culture within a diallelic set

The androgenic ability in anther culture in vitro was examined within a diallel set of five maize lines. The complex analysis of genetic variation components, Hayman's diagram, and genetic parameters showed that the anther response is under the control of an additive-dominant genetic system. The examined lines possessed the different correlation of dominant and recessive alleles controlling androgenesis. And 44 was the line with the biggest number of recessive genes, which determined the increase in the trait. The level of dominance varied in different loci, though in the whole the degree of dominance approached to the complete one.     

Effects of misspecifying genetic parameters in lod score analysis

The lod score method is widely used to test linkage and to estimate the recombination fraction between a disease locus and a marker locus. The parameters (gene frequency, penetrance, and degree of dominance) are assumed to be known at each locus. This condition may not be fulfilled at the disease locus. In this paper, we evaluate the errors due to the use of wrong parameters. The power of the linkage test is sensitive to the degree of dominance, and slightly to the penetrance, but not to the gene frequency. In contrast, the estimation of the recombination fraction may be strongly affected by an error on any genetic parameter.     

Systems genetic analysis of peripheral iron parameters in the mouse

Iron homeostasis is one of the most critical functions in living systems. Too little iron can lead to anemia and tissue-specific disorders, such as splenomegaly. Excessive systemic iron is characteristic of hemochromatosis and is implicated in the brain in Parkinson's disease. With the exception of some single gene diseases like hemochromatosis, we know little about genetic-based, individual differences in iron-related parameters and their impact on biology. To model genetic control of iron homeostasis, we measured liver, spleen, and plasma iron concentrations, hematocrit and hemoglobin, transferrin saturation, and total iron-binding capacity in several BXD/Ty recombinant inbred mouse strains derived from C57BL/6 and DBA/2 progenitors. At 120 days of age, the animals were killed for iron analysis. All measures showed genetic-based variability consistent with polygenic influence. Analysis of principal components of the seven measures revealed three factors that we named availability, transport, and storage. Quantitative trait loci (QTL) analysis revealed one suggestive QTL on chromosome 5 for availability, two suggestive QTL (one on chromosome 1 and the other on chromosome 7) for transport, and one weak QTL on chromosome 2 for storage. The results show that iron homeostasis is a complex trait and is influenced by multiple genes.     

Sex ratios in dairy cattle under various conditions

Current calving information was obtained on 35,102 single births in 2254 dairy herds. The overall proportion of males to females was 50.8%. The 5 dairy breeds did not differ. Only 6 of 111 sires studied produced calves with a sex ratio different from breed average at P≤0.5. This is the number expected by chance alone. A slight bias seems to occur when reporting the sires of the cows according to the sex of the cow's calf. The sex ratio deviated from expected in a small sample of repeat breeder cows, but when a new and larger sample of 2,084 such cows which calved was obtained, there was no change associated with service number. The time of insemination was recorded for 12,764 heifers and cows first seen in estrus in the morning and 4,799 animals first seen in estrus in the evening. There was no effect of time of insemination on sex ratio. Likewise there was no effect of age of cows or season of breeding on sex ratio at birth. Because the sex ratio for cows requiring one insemination per pregnancy was not different from repeat breeders it is suggested that the sex ratio at fertilization and birth may be similar.     

Hayman's Graphical Analysis in Segregating Generations of a Diallel Cross

The expected values of average degree of dominance in F₂ and later segregating generations of a diallel cross have been mathematically derived, and compared to its value in F₁ generation. The interpretation of intercepts on W_r axis, a measure of average degree of dominance, differed in segregating generations from that of F₁ at origin, and between origin and tangent in W_r, V_r-graph.     

Comparative analysis of variability of various genetic systems in farm animals]

The particularities of the genetic structure formings of the different genetic systems (biochemical and immunogenetic markers) in the breeds, interbreed crosses of sheep and groups of cattle in connections with the locus, breed and the way of the productivity trait selections were described. The uniqueness of the characteristics and forming mechanisms of the genetic structure related with these factors and the inadequacy of the suppositions about them on the genealogical data were discussed.     

Multivariate genetic analysis of the neurodynamic and psychodynamic parameters in human populations

The first attempt at using multivariate genetic analysis to study the neurodynamic and psychodynamic levels of individual organization in Daghestan isolates is described. The absence of close similarity between dendrograms of templates of phenotypical and genotypical correlations is explained by lower heritability of the parameters under study. Interpopulation differences revealed by the multivariate genetic analysis are the result of differences in the genetic and social structures of the populations.     

Maximum likelihood estimation of genetic parameters of HLA-linked diseases using data from families of various sizes

This paper is concerned with estimating parameters associated with HLA-linked diseases. We consider a single disease locus closely linked to HLA, allowing a disease and a normal allele. The parameters to be estimated are the penetrances of the genotypes at the disease locus, the population frequency of the disease allele, and the distance of the disease locus from HLA. The presently used method of estimation uses HLA-sharing information from affected sib-pairs. The method proposed here generalizes the previous approach, using data from all sibs (affected or unaffected) in a family of any size. It allows immediate generalizations to the use of information on parental affectedness status and population prevalence.     

Quantitative genetic analysis of chlorophyll a fluorescence parameters in maize in the field environments

Chlorophyll fluorescence transient from initial to maximum fluorescence(P step) throughout two intermediate steps(J and I)(JIP‐test) is considered a reliable early quantitative indicator of stress in plants. The JIP‐test is particularly useful for crop plants when applied in variable field environments. The aim of the present study was to conduct a quantitative trait loci(QTL) analysis for nine JIP‐test parameters in maize during flowering in four field environments differing in weather conditions. QTL analysis and identification of putative candidate genes might help to explain the genetic relationship between photosynthesis and different field scenarios in maize plants. The JIP‐test parameters were analyzed in the intermated B73 Mo17(IBM) maize population of 205 recombinant inbred lines. A set of 2,178 molecular markers across the whole maize genome was used for QTL analysis revealing 10 significant QTLs for seven JIP‐test parameters, of which five were co‐localized when combinedover the four environments indicating polygenic inheritance and pleiotropy. Our results demonstrate that QTL analysis of chlorophyll fluorescence parameters was capable of detecting one pleiotropic locus on chromosome 7, coinciding with the gene gst23 that may be associated with efficient photosynthesis under different field scenarios.     

Sex ratios in mule duck embryos at various stages of incubation

Mule duck hatcheries have long reported varying degrees of unbalance in the sex ratio, with a preponderance of male mules at hatching. The aim of the present study was to assess the distributions of sex ratios at various stages of development in embryos originating from intra- and intergeneric crosses between parental lineages (Muscovy male x Muscovy female, Pekin male x Pekin female, Muscovy male x Pekin female or Mule, and Pekin male x Muscovy female or Hinny). In Experiment I, embryo sexing was performed on Days 1 and 5 of incubation (by multiplex PCR) and at hatching (by vent observation). The sex ratio was not significantly modified during the early stages of embryo development whatever the genetic origin (P>0.05, Days 1 and Day 5) but our results in mule and hinny ducklings confirmed the preponderance of males among normally hatched ducklings originating from the intergeneric lineage (58.9 and 55.4% males in mules and hinnies, respectively; P<0.05 in both cases). Sex ratio (vent sexing) in second grade (cull) ducklings revealed that 68% of these ducklings were females (P<0.05). In Experiment II, the distribution of sex ratio was also performed in mule duck eggs from 6 batches (400,000 eggs/batch) first examined for fertility (candling) on Day 18 of incubation. These results indicate that the percentage of males present in the population of normally hatched ducklings increases when fertility decreases. In addition, this experiment also revealed that 83.7-90.5% of viable male mule embryos develop up to hatching, compared to only 43.0-51.0% of female mule embryos. Given that a deviation in sex ratio during the first stages of incubation is unlikely (Experiment I), it is concluded that the skewed sex ratio of mule ducks at hatching is primarily due to increased late mortality in female mule embryos occurring between egg transfer and hatching. This mortality originated, at least in part, from the intergeneric origin of female mules, and was marked to a greater or lesser extent depending on the initial success of fertilization in a given batch, a possible indication that the initial quality of gametes may selectively exert its influence at the later stages of embryo development.     

High throughput analysis of 10 microsatellite and 11 diallelic polymorphisms on the human Y-chromosome

We describe an integrated approach to the determination of complex Y chromosome haplotypes that is both fast and relatively inexpensive. The method employs GeneScan technology to enable a researcher to assay repeat number variation at ten microsatellite loci and determine the status of 11 diallelic polymorphisms. The method requires only four PCRs and four GeneScan runs per sample and is relatively insensitive to sample DNA concentration.     

Estimation of quantitative genetic parameters

This paper gives a short review of the development of genetic parameter estimation over the last 40 years. This shows the development of more statistically and computationally efficient methods that allow the fitting of more biologically appropriate models. Methods have evolved from direct methods based on covariances between relatives to methods based on individual animal models. Maximum-likelihood methods have a natural interpretation in terms of best linear unbiased predictors. Improvements in iterative schemes to give estimates are discussed. As an example, a recent estimation of genetic parameters for a British population of dairy cattle is discussed. The development makes a connection to relevant work by Bill Hill.     

Estimation of quantitative genetic parameters

This paper gives a short review of the development of genetic parameter estimation over the last 40 years. The need to analyse genetic processes in both animal selection experiments and animal breeding improvement programmes motivated the majority of this work. The usage of animal model in conjunction with residual maximum likelihood (REML) techniques for mixed models has revolutionized the methods. These methods to estimate quantitative genetic parameters have recently been advocated for use in evolutionary studies of natural populations. Therefore, it is perhaps timely to discuss the development of REML methods and their application to the analysis of artificial selection experiments and breeding programmes in animals. This should give extra insight into the methods and hopefully lead to synergy between both the areas.     

Mechanistic analysis of complex enzyme deactivations: influence of various parameters on series-type inactivations

A series-type enzyme deactivation model is used to model and to quantitate some more complex enzyme deacti-vations. The influence of temperature, pH, immobilization, chemical modifier (inhibitor or protector), substrate, and metal ion on the inactivation kinetics and on the parameter values is examined. In some cases the influence of two parameters on enzyme inactivations is presented. This provides further physical insights into enzyme inactivation and stabilization processes.     

A genetic analysis of various functions of the TyrR protein of Escherichia coli.

The TyrR protein is involved in both repression and activation of the genes of the TyrR regulon. Correction of an error in a previously published sequence has revealed a Cro-like helix-turn-helix DNA-binding domain near the carboxyl terminus. Site-directed mutagenesis in this region has generated a number of mutants that can no longer repress or activate. Deletions of amino acid residues 5 to 42 produced a protein that could repress but not activate. The central domain of TyrR contains an ATP-binding site and is homologous with the NtrC family of activator proteins. A mutation to site A of the ATP-binding site and other mutations in this region affect tyrosine-mediated repression but do not prevent activation or phenylalanine-mediated repression of aroG.     

Inequality constrained estimation of genetic parameters

Summary A method is presented for computing estimates of genetic parameters under linear inequality constraints such that solutions are within theoretical limits. The method produces biased estimators, yet a small scale numerical study, also presented, shows that the inequality constrained estimators have a small mean squared error of prediction than the best of unbiased estimators. The increase in efficiency of estimation is particularly useful for traits where heritability is near the boundary values of zero or one.     

Equilibrium between genetic drift and migration at various mutation rates: simulation analysis

Rates of approach to equilibrium values of F(ST)/R(ST) at various mutation rates and using different mutation models (K-allele model KAM and stepwise model SMM) were analyzed numerically for the finite island model and the one-dimensional stepping stone models of migration, using simulation. In the island model of migration and the KAM mutation model, the rate of approach to the equilibrium F(ST) value was appreciably higher and the equilibrium value was almost twofold lower at micro (mutation rate) = m (migration rate) than at micro < m. In the one-dimensional stepping stone model of migration and the KAM model of mutation, the mutation rate significantly affected both the rate of approaching F(ST) equilibrium and the equilibrium value. In both island and one-dimensional stepping stone models and SMM, R(ST) was not influenced by various mutation rates. The rate of approach to the equilibrium values of both F(ST) and R(ST) was lower for the stepping stone model than to the island model. RST was rather resistant to deviations from the SMM mutation model.