Browsing by Subject "Computersimulation"

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Development and applications of Plabsoft : a computer program for population genetic data analyses and simulations in plant breeding
(2008) Maurer, Hans Peter; Melchinger, Albrecht E.
Marker-assisted breeding approaches are promising tools for enhancement of the conventional plant breeding process. They have been successfully applied in many areas such as plant variety protection, classification of germplasm, assessment of genetic diversity, mapping of genes underlying important agronomic traits, and using the mapping information for selection decisions. Powerful and flexible bioinformatic tools are urgently required for a better integration of molecular marker applications and classical plant breeding methods. The objective of my thesis work was to develop and apply Plabsoft, a computer program for population genetic data analyses and simulations in plant breeding. The assumption of Hardy-Weinberg equilibrium is a cornerstone of many concepts in population and quantitative genetics. Therefore, tests for Hardy-Weinberg equilibrium are of crucial importance, but the assumptions underlying asymptotic chi-square tests are often not met in datasets from plant breeding programs. I developed and implemented in Plabsoft a new algorithm for exact tests of Hardy-Weinberg equilibrium with multiple alleles. The newly derived algorithm has considerable computational advantages over previously described algorithms and extends substantially the range of problems that can be tested. Knowledge about the amount and distribution of linkage disequilibrium (LD) in breeding populations is of fundamental importance to assess the prospects for gene mapping with whole-genome association studies. To analyze LD in breeding populations, I implemented various LD measures in Plabsoft and developed a new significance test for these LD measures. The routines were employed to analyze LD in 497 elite maize lines from a commercial hybrid breeding program, which were fingerprinted by 81 simple sequence repeat (SSR) markers covering the entire genome. Strong LD was detected and, therefore, whole-genome association studies were recommended as promising. However, LD between unlinked loci will most likely result in a high rate of false positives. The prediction of hybrid performance with DNA markers facilitates the identification of superior hybrids. The single marker models used so far do not take into account the correlation between allele frequencies at linked markers. To overcome this problem, the concept of haplotype blocks was proposed. I developed and implemented in Plabsoft three alternative algorithms for haplotype block detection suitable for plant breeding. The algorithms were applied for the haplotype-based prediction of the hybrid performance of 270 hybrids, the parents of which were fingerprinted with 20 amplified fragment length polymorphism (AFLP) primer combinations. Employing haplotypes resulted in an improved prediction of hybrid performance compared with single marker models. Consequently, haplotype-based prediction methods have a high potential to improve substantially the efficiency of hybrid breeding programs. Computer simulations can be employed to solve population genetic problems in plant breeding, for which the simplifying assumptions underlying the classical population genetic theory do not hold true. However, before the start of my thesis no flexible simulation software was available. I developed algorithms for simulation of single breeding steps and entire plant breeding programs and implemented these in Plabsoft. The routines allow the simulation of plant breeding programs as they are conducted in practice. The simulation routines of Plabsoft were validated by simulating two marker-assisted backcross programs in rice conducted by the International Rice Research Institute (IRRI). In the simulations, the frequency distributions of the proportion of recurrent parent genome in the backcross populations were assessed. The simulation results were in good agreement with the experimental data. Therefore, computer simulations are a useful tool for pre-test estimation of selection response in marker-assisted backcrossing. The application of Plabsoft was exemplified by two studies in maize. In the first study, the expected LD decay in the intermating generations of two recurrent selections programs was determined with simulations. This application demonstrates the use of Plabsoft to solve problems for which analytical results are not available. In the second study, the forces generating and maintaining LD in a hybrid maize breeding program were investigated with computer simulations. This application demonstrates the capability of modeling complex long-term breeding programs as performed in practice. The studies of my thesis provide an example for the broad range of possible applications of Plabsoft. In addition to the presented studies, Plabsoft has so far been employed in about 40 further studies, which corroborates the usefulness of Plabsoft for integrating new genomic tools in applied plant breeding programs.
Inhomogenität in Getreidesaatgutpartien : Ursachen und Konsequenzen für die Saatgutprobenahme
(2009) Schmohl, Sven; Kruse, Michael
The objective of this research was to quantify inhomogeneity and evaluate its formation in cereal seed lots. The results were used to compile proposals for a better in seed sampling schemes and to give recommendations to avoid inhomogeneity formation during seed processing. For this purpose, the extent and structure of the variation in the seed quality criteria, purity, other seed count, germination, thousand seed mass and size grading were determined within seed lots as well as their change during seed processing. Commercial seed lots of oat, wheat and barley were sampled from the delivery point to the bagging of the lots. All primary samples, in total 1944, were analyzed separately. The evaluation of the inhomogeneity was done by either an H-test or a R-test according to the ISTA rules. Additionally, for each seed quality criteria at each station of seed processing the results of the primary samples were analysed by means of regression analyses to detect systematic gradients. From a total of 57 stations, 56 showed significant inhomogeneity in at least one seed quality criteria. There were significant differences between the seed quality criteria and the crop species in terms of composition as well as extent of inhomogeneity. In the unprocessed seed lots the proportion of stations with significant inhomogeneity were between 14 and 100 % for thousand seed mass, 33 and 100 % for germination, 50 and 100 % for size grading, 57 and 100 % for purity and between 0 and 75 % for other seed count. After cleaning, the proportion of stations with significant inhomogeneity were between 17 and 55 % for size grading, 14 and 100 % for thousand seed mass, 0 and 43 % for purity and between 50 - 67 % for germination. During the seed processing the initially stochastic dispersion of the seed quality criteria size grading and purity at the delivery point were increasingly replaced by systematic gradients. In case of thousand seed mass, systematic gradients were already present at the delivery point. However, the determination of the observed gradients increased during the processing. In the processed seed lots the seed quality criteria thousand seed mass and purity with 74 % and 72 % respectively showed most frequently systematic gradients at the sampling stations, followed by seed grading with 59 % and germination with 29 %. Other seed count showed rarely systematic gradients with less than 5 % of the stations. In the processed seed lots the systematic gradients entailed inhomogeneity in up to 100 % of the stations for germination, in up to 60 % for thousand seed mass and in up to 33 % for size grading and purity. In the case of other seed count the systematic gradients did not cause inhomogeneity, however for the most part because the lots were almost free from other seeds. The main reasons for the formation of gradients, and thus for the formation of inhomogeneity, are segregation effects in combination with core flow during filling and discharging silos. Additionally, in the case of the germination the mechanical load of the seeds during the processing is an important factor for the formation of inhomogeneity. Therefore, besides the use of suitable conveying devices and the limitation of lot size, the use of suitable silos in respect to the prevention of core flow and the evasion of unnecessary interim storage are important steps for the avoidance of inhomogeneity. The frequent occurrence of systematic gradients in processed and unprocessed seed lots recommends a systematic or stratified sampling scheme. In case of systematic sampling the primary samples are drawn in constant time intervals. In case of stratified sampling the primary samples have to be drawn within constant periods of time, whereas the time within the intervals is at random. These sampling schemes and the random sampling scheme were evaluated in computer simulations in terms of their accuracy and efficiency. The simulations were using the data collected from the cereal seed lots. The systematic and the stratified sampling of only 10 primary samples results in the same accuracy of the submitted sample as 30 primary samples collected at random according to the present ISTA rules. In case of interference between the systematic and stratified sampling scheme and the systematic gradients, a further decrease of the number of primary samples could lead to a strong impair of the accuracy of the submitted sample. Therefore in terms of these sampling schemes a further reduction of sampling intensity is not advisable. On the basis of the results obtained from commercial seed lots produced in one seed processing plant of one enterprise, inhomogeneity and its causes in cereal seed lots could be studied in detail. From the experimental data of commercial seeds lots conclusions for the further improvement of sampling procedures could be compiled.
Models for the representation of ecological systems? The validity of experimental model systems and of dynamical simulation models as to the interaction with ecological systems
(2001) Haag, Daniel; Kaupenjohann, Martin
Models guide the investigation of ecological phenomena and the managemant of man-environment interactions. Based on six papers, this thesis critically examines characteristic features, limitations and the scientific and societal role of experimental model systems (as well-tried instruments of knowledge production) and of dynamical simulation models (as representatives of relatively recent computer models). Experimental model systems are described as materially and conceptually closed systems with a limited number of parameters. They consist of a material component which is encoded into a formal (numerical) system through the measurement of defined parameters. The transfer of statements derived from model systems to natural systems is critically discussed. Dynamical systems - the paradigm for the representation of ecosystems - permit the simultaneous handling of a large number of parameters. Dynamical systems are conceptually closed systems and are based on the notion of an abstract state (focussing on 'being'). I contrast this view with an image of ecosystems as conceptually open systems ('becoming') which emphasizes the evolutionary openness of ecological systems, the internal production of novelty, and the emergence of system level properties. Taking the nitrogen cycle and its human alterations as an example, model concepts and limitations to the derivation of cause-effect-relationships in ecological systems are illustrated. Acknowledging the limited predictive capacity of simulation models and the intrinsic perspectivity of the identification of 'relevant' phenomena and parameters and drawing on new forms of knowledge production (as described by science studies), a modified role for model building and for simulation models - particularly with respect to science for policy - is sketched.
Optimizing the development of seed-parent lines in hybrid rye breeding
(2001) Tomerius, Alexandra-Maria; Geiger, Hartwig H.
In hybrid rye breeding, seed-parent and pollinator lines are developed from two divergent gene pools. Line development comprises selection for line performance per se followed by selection for combining ability to the opposite gene pool. Cytoplasmic-genic male sterility (CMS) is employed as hybridizing mechanism. This study deals with model calculations aiming to optimize and compare alternative schemes of seed-parent line development in hybrid rye breeding on the basis of their expected selection gain per year in an index comprising the most important breeding objectives. Prediction of selection gains rests on current estimates of quantitative-genetic and economic parameters. The schemes are optimized for the number of candidates, testers to assess testcross performance, test locations, and replicates at the individual selection stages. Optimization is carried out assuming a fixed annual budget. Five schemes are investigated which differ in the basic genetic material assumed, in the type of test units and the number of selection stages for line and testcross selection, and in the length. The standard scheme employs second cycle material. First, S2-lines are evaluated per se. Selection for combining ability is then carried out at two stages employing testcross progenies of the CMS analogues of the candidate lines in backcross generations BC1 resp. BC2. The first alternative scheme employs an additional stage of BC1L-testcross selection. Another scheme is suited for developing seed-parent lines from broader-based population material. In addition to these 'conventional' methods, a scheme using doubled haploid lines is investigated as well as a scheme in which testcross progenies are produced by means of a gametocide instead of CMS. The optimum dimensioning and relative efficiency of the schemes is investigated for various genetical and economical situations.