Cluster analysis as a method for evaluation of genetic similarity in specific host — parasite interaction (Lactuca sativa — Bremia lactucae)

Summary In gene-for-gene systems, specificity of hostparasite interactions is most often estimated qualitatively using the symbols +, –, (i.e. susceptibility and/or resistance). In large sets (interaction patterns) it becomes impossible to analyze numerous data by mere comparison. This is overcome by application of cluster analysis. In our experiments the methods in question were used to estimate the data obtained in a study on interactions between more than 220 Lactuca sativa cultivars and 12 Bremia lactucae physiological races (isolates) of Czechoslovak origin. The matrix of similarity coefficients was analyzed by hierarchical clustering. Similarity and/or dissimilarity of host R-genotypes was graphically expressed using the method of two principal components. The results obtained are related to genetic constitution of race specific resistance of the host and the possibility of predicting effective resistance sources.     

The genetic relationships between the kringle domains of human plasminogen,prothrombin, tissue plasminogen activator,urokinase, and coagulation factor XII

Summary A computer-based statistical evaluation of the optimal alignments of the kringle domains of human plasminogen, human prothrombin, human tissue plasminogen activator, human urokinase, and human coagulation Factor XIIa, as well as the putative kringle of human haptoglobin, has been performed. A variety of different alignments has been examined and scores calculated in terms of the number of standard deviations (SD) of a given match from randomness. With the exception of human haptoglobin, it was found that very high alignment scores (8.9–23.0 SD from randomness) were obtained between each of the kringles, with the kringle 1 and kringle 5 regions of human plasminogen displaying the highest similarity, and the S kringle of human prothrombin and the human Factor XII kringle showing the least similarity. The relationships obtained were employed to construct an evolutionary tree for the kringles. The predicted alignments have also allowed nucleotide mutations in these regions to be evaluated more accurately. For those regions for which nucleotide sequences are known, we have employed the maximal alignments from the protein sequences to assess nucleotide sequence similarities. It was found that a range of approximately 40–55% of the nucleotide bases were placed at identical positions in the kringles, with the highest number found in the alignment of the two kringles of human tissue plasminogen activator and the lowest number in the alignment of the S kringle of prothrombin with the second kringle of tissue plasminogen activator. From both protein and nucleotide alignments, we conclude that haptoglobin is not statistically homologous to any other kringle.Secondary structural comparisons of the kringle regions have been predicted by a combination of the Burgess and Chou-Fasman methods. In general, the kringles display a very high number of -turns, and very low -helical contents. From analysis of the predicted structures in relationship to the functional properties of these domains, it appears as though many of their functional differences can be related to possible conformational alterations resulting from amino acid substitutions in the kringles.     

Estimating the number of genetic elements that defer senescence inDrosophila

Summary Although many different physiological and biochemical changes characterize the process of senescence, little is understood of the genetic elements that determine its age of onset. We provide here the first estimates of the number of genetic factors that extend longevity inDrosophila melanogaster. Life span was measured in F₁, F₂ and backcrosses of true-breeding long and short-lived stocks ofD. melanogaster, established by selection. Estimates of the number of effective factors delaying senescence range from about 0.3 to 1.5, indicating control by a single factor. The distribution of longevity shows this to arise as selection acts on the short-lived parental stock. Life span is extended at the cost of early fecundity.     

Effect of mass selection on the within-family genetic variance in finite populations

Summary The adequacy of an expression for the withinfamily genetic variance under pure random drift in an additive infinitesimal model was tested via simulation in populations undergoing mass selection. Two hundred or one thousand unlinked loci with two alleles at initial frequencies of 1/2 were considered. The size of the population was 100 (50 males and 50 females). Full-sib matings were carried out for 15 generations with only one male and one female chosen as parents each generation, either randomly or on an individual phenotypic value. In the unselected population, results obtained from 200 replicates were in agreement with predictions. With mass selection, within-family genetic variance was overpredicted by theory from the 12th and 4th generations for the 1,000 and 200 loci cases, respectively. Taking into account the observed change in gene frequencies in the algorithm led to a much better agreement with observed values. Results for the distribution of gene frequencies and the withinlocus genetic covariance are presented. It is concluded that the expression for the within-family genetic variance derived for pure random drift holds well for mass selection within the limits of an additive infinitesimal model.     

Experimental study of the influence of errors of genetic correlation estimates on unrestricted,optimum, and desired gains selection indices

Summary Effects of errors in estimates of the genetic correlation on the accuracy of unrestricted, optimum, and desired gains selection indices were examined experimentally in Tribolium castaneum. Three lines were selected for three generations for pupal weight at 21 days and adult weight at 31 days, using unrestricted (I9), optimum (O9), and desired gains (G9) index selection methods. The genetic correlation between pupal and adult weights in the base population was 0.95. The optimum index was designed to set the response of pupal weight by a fixed amount, while in the desired gains index the responses of pupal and adult weights were specified as being equal to 31. Three other indices were constructed using a deliberately incorrect genetic correlation (0.25), i.e., unrestricted (I2), optimum (O2), and desired gains (G2). Responses observed in unrestricted index lines (I9 versus I2) and optimum index lines (O9 versus O2) did not differ significantly, even though lines I9 and I2 differed in a practical sense. Responses in desired gains index lines (G9 versus G2) differed significantly. Responses obtained for aggregate genotype (pupal weight + adult weight) and for the component traits were greater in line I9 than those obtained in line I2. Responses obtained in the O9 and O2 lines for pupal and adult weights were similar, while those obtained in the G9 and G2 lines were similar for pupal weight but not (P<0.05) for adult weight. Therefore, underestimation of the genetic correlation seems to affect the efficiency of a desired gains index more than that of unrestricted or optimum indices.     

RFLP-based genetic maps of wheat homoeologous group 7 chromosomes

Summary Restriction fragment length polymorphism (RFLP) mapping was attempted using 18 cDNA clones, 14 anonymous and 4 of known function, which had been shown to have homologous DNA sequences on the group 7 chromosomes of wheat. The loci identified by these probes have been mapped on one or more chromosomes in this homoeologous group using linkage data derived from various F₂, random inbred, doubled haploid and single chromosome recombinant populations. The maps also include three isozyme loci, five disease resistance loci, two anthocyanin pigment loci and a vernalisation response locus. The mapping data have been used to determine the extent of map co-linearity over the A, B and D genomes, the degree of RFLP variability in the three genomes and the relative efficiency of various restriction enzymes in detecting RFLPs in wheat. The strategy for future mapping in wheat, particularly the use of alien genomes or segments, such as that from Aegilops ventricosa used here, is discussed.     

Method to estimate genotype probabilities at individual loci in farm livestock

Summary A Bayesian method to estimate genotype probabilities at a single locus using information on the individual and all its relatives and their mates has been developed. The method uses data over several generations, can deal with large numbers of individuals in large livestock families and allows for missing information. It can be extended to multiple alleles and can be used for autosomal or sex-linked loci. The allele frequencies and the form of expression (dominance, penetrance) must be specified. An algorithm using the method and involving an iterative procedure has been developed to calculate the genotype probabilities for practical use in livestock breeding. The method and algorithm were used to determine the accuracy of estimating genotype probabilities of sires for a female sex-limited trait, such as genetic variants of milk proteins. Data were similated and genotype probabilities estimated for 100 sires (20 replicates) with 3, 6 and 12 female offspring per sire, for different population frequencies, for additive and dominance gene action and for variable genotypic expression. Such simulation is useful in the design of testing systems for the use of information on specific genetic loci in selection.Prepared during a leave at Centre for Genetic Improvement of Livestock, Guelph, Canada     

Inheritance of resistance to bacterial blight in common bean

Summary Inheritance of resistance to common bacterial blight in the trifoliate leaf, plant canopy, and pods was controlled by a single major gene. Additive followed by dominance effects were more important than epistatic interactions. Narrow-sense heritability values ranged from 0.18 to 0.87 for trifoliate leaf, from 0.26 to 0.76 for canopy, and from 0.11 to 0.36 for pods. Observed gains from selection for resistance were higher than expected gains. Implications of these results in breeding for resistance are discussed.     

Relationships between some genetic parameters and test environments in open-pollinated families of Pinus elliottii in South Africa

Summary Growth traits, stem form and branch characteristics in three series of well-replicated trials, comprising open-pollinated families of Pinus elliottii Engelmann, were analysed to investigate whether the absolute value of the component of variance for family effect and its relative value (which is equivalent to one-quarter of heritability on individual values) were related, with trial averages of the traits studied taken as productivity indices of the sites tested. The first series, called the foreign selection series, consisted of four trials comprising open-pollinated families from single clones from a Florida seed orchard and from selected trees in Queensland, Australia. Two trials were established in the eastern Transvaal, at Tweefontein and Frankfort State Forests (SF), and two in Zululand, at Dukuduku and KwaMbonambi SF. The second series, called the Zululand selection series, consisted of open-pollinated families from single trees selected in Zululand that were compared in three trials: in the eastern Transvaal at Wilgeboom SF, in Zululand at Dukuduku SF and in the southern Cape at Lottering SF. The third series, called the South African selection series, consisted of open-pollinated families from single trees selected in the different forest areas of South Africa and compared in four trials: two trials in the eastern Transvaal at Tweefontein and Mariti SF and two in the Natal province at Dukuduku and Weza SF. Some positive and linear relationships between absolute sizes of the variance component for family and trial average for all traits studied, except stem form, were discernible for the foreign selections and for the Zululand selections. The South African selections presented a more erratic pattern of variation. However, when the origin of the genetic material was disregarded, the positive trends were undeniable. Curvilinear relationships between relative values and site averages were discernible, when the origin of the genetic material was disregarded. Further research is needed in order to confirm the suggested effect of site on genetic expressivity of open-pollinated families of slash pine grown in South Africa.     

Statistical techniques for detection of major genes in animal breeding data

Summary Statistical techniques for detection of major loci and for making inferences about major locus parameters such as genotypic frequencies, effects and gene action from field-collected data are presented. In field data, major genotypic effects are likely to be masked by a large number of environmental differences in addition to additive and nonadditive polygenic effects. A graphical technique and a procedure for discriminating among genetic hypotheses based on a mixed model accounting for all these factors are proposed. The methods are illustrated by using simulated data.Journal Paper No. J-12733 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa. Project No. 1901