Including copy number variation in association studies to predict genotypic values

The objective of this study was to investigate, both empirically and deterministically, the ability to explain genetic variation resulting from a copy number polymorphism (CNP) by including the CNP, either by its genotype or by a continuous derivation thereof, alone or together with a nearby single nucleotide polymorphism (SNP) in the model. This continuous measure of a CNP genotype could be a raw hybridization measurement, or a predicted CNP genotype. Results from simulations showed that the linkage disequilibrium (LD) between an SNP and CNP was lower than LD between two SNPs, due to the higher mutation rate at the CNP loci. The model R2 values from analysing the simulated data were very similar to the R2 values predicted with the deterministic formulae. Under the assumption that x copies at a CNP locus lead to the effect of x times the effect of 1 copy, including a continuous measure of a CNP locus in the model together with the genotype of a nearby SNP increased power to explain variation at the CNP locus, even when the continuous measure explained only 15% of the variation at the CNP locus

Quantitative genetics of maize (Zea mays L.) during seedling establishment under cool conditions : a thesis presented in partial fulfillment of the requirements for the degree of Master of Agricultural Science in Plant Science at Massey University

Two experiments were conducted to study cool tolerance in maize (Zea mays L.). The first experiment was carried out under controlled environment to evaluate several genotypes from five synthetic populations which are currently being used to develop hybrid maize for better adaptation to New Zealand climate and to study the qualitative inheritance of maize seedling growth under cool conditions. In this study, diurnal temperature of 16 °C day/6 °C night was used and characters related to seedling growth were examined. The second experiment conducted to study the effect of temperature on maize during its early growth and to examine whether the initial seed constitution and germination characteristics could be used as selection criteria for improvement of the subsequent seedling growth. Eleven physical, chemical, and morphological characters were measured. The growth was studied in germinators under two temperature regimes of 25/20 and 16/6 °C. The genotypic variation was highly significant for all nine characters examined in the first experiment. For the three repeatedly measured characters (i.e. chlorophyll content, shoot and root dry masses), the genotype x time interaction effect was significant. In the second experiment, the variation due to genotypic difference was highly significant only for the initial seed constitution characters and the amount of ion leakage during the early hours of germination process. It was non significant for the time to germinate, seedling growth rates, and seedling growth functions. The variation due to the difference of temperature regimes was significant for the time to germinate and seedling growth but not the growth functions. The genotypes of synthetic line NZS3 showed the best performance for general combining ability (GCA) for almost all characters studied in the first experiment. From all genotypes evaluated, however, only few of them consistently showed good GCA over the characters. Four of the characters studied in the first experiment had moderate to high narrow sense heritabilities, namely total leaves at 50 days after planting (82 %), chlorophyll content (46 %), anthocyanin (69%), and leaf area (62 %). In the second experiment, the estimated broad sense heritabilities observed ranged from very low to very high over all characters. The high broad sense heritabilities were recorded on most of the initial seed constitution characters, the conductivity of ion leakage, and the growth rates of root (length) and shoot (dry mass). Both the phenotypic and genotypic correlation coefficients between pairs are in good agreement and followed the same direction. Amongst the characters examined in the first experiment only time to achieve second mature leaf, total leaf number at 50 day after planting, chlorophyll content, leaf area had considerable correlations to the dry masses. In the second experiment a good correlation with growth rate was observed for the seed weight, nitrogen and maltose contents

An evolutionary model for simple ecosystems

In this review some simple models of asexual populations evolving on smooth landscapes are studied. The basic model is based on a cellular automaton, which is analyzed here in the spatial mean-field limit. Firstly, the evolution on a fixed fitness landscape is considered. The correspondence between the time evolution of the population and equilibrium properties of a statistical mechanics system is investigated, finding the limits for which this mapping holds. The mutational meltdown, Eigen's error threshold and Muller's ratchet phenomena are studied in the framework of a simplified model. Finally, the shape of a quasi-species and the condition of coexistence of multiple species in a static fitness landscape are analyzed. In the second part, these results are applied to the study of the coexistence of quasi-species in the presence of competition, obtaining the conditions for a robust speciation effect in asexual populations.Comment: 36 pages, including 16 figures, to appear in Annual Review of Computational Physics, D. Stauffer (ed.), World Scientific, Singapor

Genetic variability and correlation analysis of rice (Oryza sativa L.) inbred lines based on agro-morphological traits

In order to evaluate genetic variability of agro-morphological traits and also determine the correlation between grain yield with its components in rice lines, 17 recombinants inbred lines, their parents and a check variety were grown in research station of Africa rice center in Benin republic during two consecutive years 2013 and 2014. The experiments were laid out in a randomized complete block design with four replications. Phenotypic coefficients of variance were higher than genotypic coefficients of variance in all the characters across the two years. High heritability in broad sense (H2) estimates were obtained for biomass (68.77%), date of 50% flowering (98.11%), plant height (81.94%), leaf area (82.90%), number of panicles (64.40%), leaf dry weight (72.91%), root weight (67.43%) and yield/plant (62.23%) suggesting that the traits were primarily under genetic control. A joint consideration of broad sense heritability (H2) and genetic advance as per cent mean expected (GAM) revealed that leaves dries weight and roots weight combined high heritability and high GAM. Furthermore, high (H2) and high GAM recorded in these characters could be explained by additive gene action. However, high estimates (H2) combined with moderate GAM recorded for biomass, day to 50% flowering, leaf area, number of panicle and yield/plant could be due to non-additive gene effect. Grain yield/plant recorded positive and significant correlation with stem weight (r=0.5262) and biomass (r=0.9291). This result indicates that selection based on these two characters will be highly effective for yield improvement in rice. (Résumé d'auteur

The selective advantage of reaction norms for environmental tolerance

A tolerance curve defines the dependence of a genotype's fitness on the state of an environmental gradient. It can be characterized by a mode (the genotype's optimal environment) and a width (the breadth of adaptation). It seems possible that one or both of these characters can be modified in an adaptive manner, at least partially, during development. Thus, we extend the theory of environmental tolerance to include reaction norms for the mode and the width of the tolerance curve. We demonstrate that the selective value of such reaction norms increases with increasing spatial heterogeneity and between-generation temporal variation in the environment and with decreasing within-generation temporal variation. Assuming that the maintenance of a high breadth of adaptation is costly, reaction, norms are shown to induce correlated selection for a reduction in this character. Nevertheless, regardless of the magnitude of the reaction norm, there is a nearly one to one relationship between the optimal breadth of adaptation and the within-generation temporal variation perceived by the organism. This suggests that empirical estimates of the breadth of adaptation may provide a useful index of this type of environmental variation from the organism's point of view

Genetic Diversity of Selected Upland Rice Genotypes (Oryza sativa L.) for Grain Yield and Related Traits

Seventy-seven upland rice genotypes including popular cultivars in Nigeria and introduced varieties selected from across rice-growing regions of the world were evaluated under optimal upland ecology. These genotypes were characterised for 10 traits and the quantitative data subjected to Pearson correlation matrix, Principal Component Analysis and cluster analysis to determine the level of diversity and degree of association existing between grain yield and its related component traits. Yield and most related component traits exhibited higher PCV compared to growth parameters. Yield had the highest PCV (41.72%) while all other parameters had low to moderate GCV. Genetic Advance (GA) ranged from 9.88% for plant height at maturity to 41.08% for yield. High heritability estimates were recorded for 1000 grain weight (88.71%), days to 50% flowering (86.67%) and days to 85% maturity (71.98%). Furthermore, grain yield showed significant positive correlation with days to 50% flowering and number of panicles m-2. Three cluster groups were obtained based on the UPGMA and the first three principal components explained about 64.55% of the total variation among the 10 characters. The PCA results suggests that characters such as grain yield, days to flowering, leaf area and plant height at maturity were the principal discriminatory traits for this rice germplasm indicating that selection in favour of these traits might be effective in this population and environment

Effects of inter-varietal diversity, biotic stresses and environmental productivity on grain yield of spring barley variety mixtures

Varietal seed mixtures tend to increase and stabilize crop yields, yet their application is sparse. Large-scale cultivation of variety mixtures may require a better understanding of how inter-varietal interactions and their interaction with the environment may influence the grain yield of variety mixtures relative to their component varieties. For this purpose, six variety mixtures of spring barley and 14 component varieties were grown in each of 17 trial environments. A total of 28 observed and a priori plant characteristics, including grain yield, disease severity and weed competitiveness, were derived for each component variety in each trial. The relationship between inter-varietal diversity of each characteristic and the mixing effect on grain yield was analysed. Additionally, various types of yield stability were estimated and compared among mixtures and component varieties. One mixture out-yielded all of its component varieties in almost half of the trial environments. Inter-varietal diversity in grain yield potential correlated significantly with mixing effect, as did straw length diversity when weighted with weed pressure. The grain yields of most mixtures were more stable across environments than their component varieties when accounting also for the general response to environmental productivity. Hence, most mixtures adapted slightly better to environmental productivity and were less sensitive to environmental stress than their component varieties. We conclude that the efficacy of variety mixtures may be enhanced by mixing relatively high-yielding varieties differing in responsiveness to environmental productivity