Browsing by Subject "Marker"

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Entwicklung, Charakterisierung und Kartierung von Mikrosatellitenmarkern bei der Zuckerrübe (Beta vulgaris L.)
(2001) Dörnte, Jost; Geiger, Hartwig H.
Simple sequence repeats (SSRs) or microsatellites were isolated from a sugarbeet (Beta vulgaris L.) genomic phage library. The size-fractionated library was screened for the occurrence of the motifes (GA)n, (GT)n, (TGA)n, (AGA)n and (CCG)n. The motifes (GA)n and (GT)n were found to occur most frequently in the sugarbeet genome (every 225 kb). In contrast, the trimer motifes were half as frequent (every 527 kb). A total of 217 microsatellite sequences were found in the sequenced clones. Most of the repeats were imperfect and/or compound. Sequence comparison revealed that 23% of the clones wich containing the (GT)n motif are variants of a previously described satellite DNA (SCHMIDT et al. 1991). Of 102 primer pairs tested on sugarbeet DNA, 71 gave a single product in the expected size. On 23 sugarbeet samples 64 of the 71 SSR-markers reveald length polymorphisms. The number of detected alleles per marker ranged from 2 to 13 (average 4,9) and the PIC-values ranged from 0,17 to 0,86 (average 0,58). A cluster analysis of the 23 samples confirms the pedigree data. The developed SSR markers were compared with RFLP and AFLP markers. Therefore nine sugarbeet lines, each with five single plants per line, were analysed. The SSR analyse shows the lowest similarity between the nine lines. The similarity inside the lines revealed no differences between the marker assays. Thirtythree SSR markers were genetically mapped into the RFLP framework maps of 2 F2-populations. The markers are randomly distributed over eight linkage groups of sugar beet.
Factors influencing the accuracy of genomic prediction in plant breeding
(2017) Schopp, Pascal; Melchinger, Albrecht E.
Genomic prediction (GP) is a novel statistical tool to estimate breeding values of selection candidates without the necessity to evaluate them phenotypically. The method calibrates a prediction model based on data of phenotyped individuals that were also genotyped with genome-wide molecular markers. The renunciation of an explicit identification of causal polymorphisms in the DNA sequence allows GP to explain significantly larger amounts of the genetic variance of complex traits than previous mapping-based approaches employed for marker-assisted selection. For these reasons, GP rapidly revolutionized dairy cattle breeding, where the method was originally developed and first implemented. By comparison, plant breeding is characterized by often intensively structured populations and more restricted resources routinely available for model calibration. This thesis addresses important issues related to these peculiarities to further promote an efficient integration of GP into plant breeding.
Genome-wide prediction of testcross performance and phenotypic stability for important agronomic and quality traits in elite hybrid rye (Secale cereale L.)
(2016) Wang, Yu; Miedaner, Thomas
Genomic selection offers a greater potential for improving complex, quantitative traits in winter rye than marker-assisted selection. Prediction accuracies for grain yield for unrelated test populations have, however, to be improved. Nevertheless, they are already favorable for selecting phenotypic stability of quality traits.
Improvement of breeding strategies for the trait vase life in cut carnations (Dianthus caryophyllus L.)
(2018) Boxriker, Maike; Piepho, Hans-Peter
Carnation (Dianthus caryophyllus L.) is one of the ten most famous cut flowers worldwide. A single big flower characterizes standard carnations, while mini car-nations possess multiple flowers per stem. Vase life (VL) is one of the most im-portant breeding objectives in carnations due to the need of long transportation times and direct influence on the costumers. But VL is a complex trait with several effects influencing it. Two-phase traits like VL are traits where the assessment is done in a second phase, in the laboratory and the plants are cultivated in the greenhouse, the first phase. Many experiments have a two-phase character, but little research has been conducted to develop experimental designs in the second phase. To improve breeding efficiency, molecular markers and genomic selection is used in agriculture science but it is so far not common in ornamental breeding. The goal of this thesis was the implementation of SNP-based molecular markers for the trait VL to improve selection of long-lasting, transportable cut carnations. For marker association, 1,500 carnation genotypes were screened for VL behav-ior in an experimental design in both phases. Response to selection was used to assess efficiency. The second-phase experimental design was more important for precise data analyses. This highlights the research need on this topic. Fur-thermore, it was possible to suggest row-column designs for VL trials. Row-column designs are more flexible in the case of positional effects compared with one-dimensional blocking and can be easily analyzed like an α-design. The easiest way to design the following phases are to apply the design one-to-one. The carnation types, mini and standard, showed an influence on VL. The mini carnations last 0.5 d longer than the standard carnations. The same conclusion was drawn based on the molecular data. Transcriptome data was generated with two different sequencing methods. By independent analysis of both carnation types, different results than via the analysis of the whole data set were found. This indicates that the analysis of carnations should be done separately for each carnation type. Association of the phenotypic and genotypic data was so far not possible. As an alternative to molecular markers, genetic correlations for the use as indirect selection for the trait VL and others for breeding relevant traits was calculated. For the first time, bivariate analysis was conducted in two-phase ex-periments. The genotypic correlation between VL and FD was high, but indirect selection would be less effective than direct selection. However, the information can provide an indication of the performance and the effort to measure FD is small. The calculated high heritability of VL and found differences in VL of up to 15 d between the best and worst genotypes showed the potential of improving the population mean by using improved selection strategies like marker-assisted selection or auxiliary traits and the use of statistical methods like experimental designs in all phases of the experiment. The influence of carnation type was shown with this thesis and indicates that the implementation of molecular markers must be done independently for each car-nation type. The importance of experimental designs in multi-phase experiments was highlighted and statistical analysis by mixed models and a bivariate analysis of different traits was performed. Until now, no molecular marker for VL was identified but in a further research project, this will be solved by generating more genotypic data and the construction of a genetic map.
Mapping stem rust and leaf rust resistances in winter rye (Secale cereale L.)
(2023) Gruner, Paul; Miedaner, Thomas
Rye (Seale cereale L.) is one of the few cross-pollinating small-grain cereals and is mainly used for bread baking, biogas production and as animal feed. In its largest cultivation area (Northern, Central and Eastern Europe, including the Russian Federation) two major rust diseases, stem rust (SR) caused by Puccinia graminis f. sp. secalis and leaf rust (LR) caused by Puccinia recondita, can cause severe yield losses. Whereas LR can be found in most rye growing areas every year, SR is occurring less regularly, but can become epidemic in some years. The general occurrence of stem rust in Germany is becoming more regular, especially when hot summers provide optimum conditions for the growth and the spread of this fungus. Resistant cultivars can be a successful way to control both diseases, but SR is not assessed in the (German) variety registration and still several cultivars can be found that are susceptible or medium resistant for LR. Before the studies of this thesis were conducted, no marker-associated SR resistance gene locus was known and only six LR resistance loci had been reported. Rust resistances can be classified into all-stage resistances (ASR), that are usually caused by single R-genes and adult-plant resistances (APR), that are characterized by smaller (quantitative) effects and can only be observed in the adult-plant stage and thus make field tests mandatory. This thesis aimed on identifying resistant genotypes and respective resistance loci for SR and LR resistances in the rye genome. Two different material groups were used: biparental populations composed of inbred lines and populations composed of self-incompatible single plants. In total ten biparental populations and two additional testcross populations were studied, each constituting 68-90 genotypes. Self-incompatible populations were genetic resources from the Russian Federation, Austria and the United States of America and had 68-74 single plants each. Inbred lines were assessed in multi-environmental field trials (4-6 environments per population) and to guarantee high disease pressure, SR was artificially inoculated in contrast to naturally occurring LR in all environments. In addition, two different kind of seedling tests, one based on inoculations of entire seedling plants and one based on inoculation of detached leaves, were used to assess SR resistance. Mixed linear models were used to analyze the phenotypic data from field experiments and (mixed) cumulative logit models were used to analyze ordinal data resulting from seedling tests. Due to small sample size of a single detached leaf per genotype and isolate in self-incompatible populations, the results based on cumulative modes were cross checked with a non-parametric test. Both, progenies from biparental populations and single plants from self-incompatible populations were genotyped with single nucleotide polymorphism (SNP) based markers (Illumina iSelect 10K SNP chip or DArTseqTM) and appropriate statistical tests for phenotype-marker association were applied. This was achieved by extending phenotypic models with additive and dominant marker effects and their respective interaction with the environment or the isolates. Two marker-associated SR ASR loci (Pgs1, Pgs3.1) could be identified in biparental populations that were responsible for (large) qualitative differences between resistant and susceptible plants in the field and/or seedling stage. Additionally, 14 quantitative trait loci (QTLs) were shown to be responsible for SR APR. For LR, except one QTL found at similar position compared to a previous study, two new genes (Pr7, Pr8) and three QTLs were identified. Self-incompatible rye populations were used for the first time for association mapping and three SR resistance loci (Pgs1 - Pgs3) could be identified. Two thereof were also found within biparental mapping populations by means of QTL mapping and this was considered as prove of this new method. Throughout all studies, the natural cross-pollinating character of rye had to be considered in choosing appropriate methods and for developing rust resistant rye hybrids. This thesis includes breeding material from the largest European rye breeding companies and experiments were conducted in close cooperation with them. The characterization of breeding material for SR and LR infection, development of (new) mapping approaches, detection of resistance loci and marker candidates in the rye genome and finally the discussion of selection strategies provides a solid basis for breeders to develop the most durable SR and LR resistant rye cultivars. For scientists, new research topics could be, for example, the cloning of rye genes or a more thorough understanding of pathogen dynamics to finally achieve durable resistance in future.
Prediction of hybrid performance in maize using molecular markers
(2008) Schrag, Tobias; Melchinger, Albrecht E.
Maize breeders develop a large number of inbred lines in each breeding cycle, but, owing to resource constraints, evaluate only a small proportion of all possible crosses among these lines in field trials. Therefore, predicting the performance of hybrids by utilising the data available from related crosses to identify untested but promising hybrids is extremely important. The objectives of this thesis research were to develop and evaluate methods for marker-based prediction of hybrid performance (HP) in unbalanced data as typically generated in commercial maize hybrid breeding programs. For HP prediction, a promising approach uses the sum of effects across quantitative trait loci (QTL) as predictor. However, comparison of this approach with established prediction methods based on general combining ability (GCA) was lacking. In addition, prediction of specific combining ability (SCA) is also possible with this approach, but was so far not used for HP prediction. The objectives of the first study in this thesis were to identify QTL for grain yield and grain dry matter content, combine GCA with marker-based SCA estimates for HP prediction, and compare marker-based prediction with established methods. Hybrids from four Dent × Flint factorial mating experiments were evaluated in field trials and their parental inbreds were genotyped with amplified fragment length polymorphism (AFLP) markers. Efficiency for prediction of hybrids, of which both parents were testcross evaluated (Type 2), was assessed by leave-one-out cross-validation. The established GCA-based method predicted HP better than the approach exclusively based on markers. However, with greater relevance of SCA, combining GCA with marker-based SCA estimates was superior compared with HP prediction based on GCA only. Linkage disequilibrium between markers was expected to reduce the prediction efficiency due to inflated QTL effects and reduced power. Thus, in the second study, multiple linear regression (MLR) with forward selection was employed for HP prediction. In addition, adjacent markers in strong linkage disequilibrium were combined into haplotype blocks. An approach based on total effects of associated markers (TEAM) was developed for multi-allelic haplotype blocks. Genome scans to search for significant QTL involve multiple testing of many markers, which increases the rate of false-positive associations. Thus, the TEAM approach was enhanced by controlling the false discovery rate. Considerable loss of marker information can be caused by few missing observations, if the prediction method depends on complete marker data. Therefore, the TEAM approach was improved to cope with missing marker observations. Modification of the cross-validation procedure reflected, that often only a subset of parental lines is crossed with all lines from the opposite heterotic group in a factorial mating design. The prediction approaches were evaluated with the same field data as in the previous study. The results suggested that with haplotype blocks instead of original marker data, similar or higher efficiencies for HP prediction can be achieved. Marker-based HP prediction of inter-group crosses between lines, which were marker genotyped but not testcross evaluated, was not investigated hitherto. Heterosis, which considerably contributes to maize grain yield, was so far not incorporated into marker-based HP prediction. Combined analyses of field trials from multiple experiments of a breeding program provide valuable data for HP prediction. With a mixed linear model analysis of such unbalanced data from nine factorial mating experiments, best linear unbiased prediction (BLUP) values for HP, GCA, SCA, line per se performance, and heterosis of 400 hybrids were obtained in the third study. The prediction efficiency was assessed in cross-validation for prediction of hybrids, of which none (Type 0) or one (Type 1) parental inbred was testcross evaluated. An extension of the established HP prediction method based on BLUP of GCA and SCA, but not using marker data, resulted in prediction efficiency intermediate for Type 1 and very low for Type 0 hybrids. Combining line per se with marker-based heterosis estimates (TEAM-LM) mostly resulted in the highest prediction efficiencies of grain yield and grain dry matter content for both Type 0 and Type 1 hybrids. For the heterotic trait grain yield, the highest prediction efficiencies were generally obtained with marker-based TEAM approaches. In conclusion, this thesis research provided methods for the marker-based prediction of HP. The experimental results suggested that marker-based HP prediction is an efficient tool which supports the selection of superior hybrids and has great potential to accelerate commercial hybrid breeding programs in a very cost-effective manner. The significance of marker-based HP prediction is further enhanced by recent advances in production of doubled haploid lines and high-throughput technologies for rapid and inexpensive marker assays.
Untersuchung der Informativität neuer Mikrosatellitenloci beim Kamel
(2001) Evdotchenko, Dmitri; Geldermann, Hermann
The goal of the investigations was it to use new primers for the representation of polymorphic microsatellite loci in different camel species and to examine new microsatellite loci for Informativity. Some polymorphic loci should be used for the investigation of the genetic differentiation of different dromedary races from Kenya and a bactrian race from Sibiria. For the investigations samples from two species of the old world camels (Camelus bactrianus and Camelus dromedarius) and two species of the new world camels (Llama pacos and Llama glama) were available. As DNA source full blood or leukocyte was used. The representation of the microsatellite loci was carried out with the help of the PCR and following fragment length analysis by means of an automated DNA-Sequencer (A.L.F.). The number of the alleles, their fragment lengths as well as the frequencies of allels and genotypes were computed per locus and taken as original data for estimation of invormativeness. Primer pairs for 34 sequenced loci were tested. 25 of this loci showed specific PCR amplifications with bactrian and dromedary and were therefore included into the further investigations. For instance one third of the loci were found as monomorph, the remaining loci were polymorph. 9 from 17 polymorphic loci showed more than ten alleles in all examined species. The genetic distances between the examined species, computed by means of new microsatellite loci, refer to clear differences between old and new world camels. With the investigations of some dromedary races from Kenya it was shown that the genetic distances estimated on the basis the new marker loci correlated with geographical distances between the races. The investigations supplied thus new informative markers for different genetic analysis in camel. The markers could be also important for the camel breeding (e.g. parentage testing).