Browsing by Subject "Kartierung"

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Development and fine mapping of markers closely linked to the SCMV resistance loci Scmv1 and Scmv2 in European maize (Zea mays L.)
(2002) Dußle, Christina M.; Melchinger, Albrecht E.
Sugarcane mosaic virus (SCMV) is an important disease in European maize cultivars (Zea mays L.). Because of its non-persistent transmission by aphid vectors, it is not possible to control SCMV directly. Therefore, cultivation of resistant maize varieties is an efficient way to control SCMV infections. The overall objectives of this study were the genetic analysis of SCMV resistance in cross F7 x FAP1360A and the identification of closely linked markers to the SCMV resistance genes Scmv1 on chromosome 6 and Scmv2 on chromosome 3 for map-based cloning and marker-assisted selection (MAS). The technical objectives were to (1) identify in particular the location of Scmv1 and Scmv2 on chromosomes 3 and 6 in cross F7 x FAP1360A, (2) estimate the gene action of the alleles present at these loci, (3) enrich the SCMV resistance regions surrounding Scmv1 and Scmv2 with amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers by applying a modified targeted bulked segregant analysis, tBSA, (4) convert AFLP markers into codominant, simple PCR-based markers as a tool for MAS and map-based cloning of Scmv1 and Scmv2 and, (5) assess resistance gene analogues (RGAs) as potential candidate genes for Scmv1 and Scmv2. Quantitative trait loci (QTL) mapping SSR markers revealed the presence of two QTL on chromosome 6 (Scmv1a and Scmv1b) and one QTL on chromosome 3 (Scmv2). tBSA identified 24 AFLP and 25 SSR markers adjacent to either Scmv1 or Scmv2. AFLP marker E35M62-1, closely linked to Scmv1 on chromosome 6, was successfully converted into an indel marker. For chromosome 3, AFLP marker E33M61-2 was converted into a CAPS marker. Both converted AFLP markers mapped to the same chromosome region as their original AFLP markers. Development of CAPS of the RGAs and mapping in relation to SCMV resistance genes Scmv1 and Scmv2 identified pic19 and pic13 as potential candidates for these resistance genes. In this study, useful markers were developed for applications in MAS. Because inheritance of SCMV resistance is strongly affected by the environment, MAS enables the selection of resistant individuals independently of field experiments. Furthermore, MAS can assist breeders to identify resistant individuals before flowering and to pyramid resistance genes in elite inbred lines. Another benefit of these closely linked markers is their application for map-based cloning. Final evidence, whether there are one or more genes clustered on chromosomes 3 and 6, conferring resistance against SCMV, can only be solved after cloning these genes.
Dissection of the genetic architecture of stalk mechanical strength and in vivo haploid induction in maize
(2016) Hu, Haixiao; Melchinger, Albrecht E.
Stalk lodging causes yield losses in maize cultivation ranging from 5 to 20% annually worldwide and stalk mechanical strength is widely accepted as an indirect indicator for its measurement. QTL mapping can reveal the genetic basis of stalk strength and provide information about markers suitable for marker-assisted selection (MAS). Constantly increasing market demands urge maize geneticists and breeders not only to enhance the field performance of new hybrids, but also to improve the breeding process. During the last decade, advances in the double haploid (DH) technology based on in vivo haploid induction (HI) shifted the breeding paradigm and greatly accelerated the breeding process in maize. Further spread of DH technology urgently demands a simple but efficient way for developing new inducers, which could be achieved by introducing the mandatory QTL/gene(s) of HI to advanced breeding lines. Therefore, the main goal of my thesis was to dissect the genetic architecture of stalk strength and detect the mandatory genomic region(s) of HI using genome-wide molecular markers. Several methods have been developed and applied in the literature to evaluate stalk mechanical strength, among which the rind penetrometer resistance (RPR) is a simple, rapid and non-destructive measurement during data collection, whereas stalk bending strength (SBS) is more closely associated with stalk lodging in the field. According to common knowledge in the mechanics of materials, SBS is reflected by the maximum load exerted to breaking (Fmax), the breaking moment (Mmax) and the critical stress (σmax). Thus, to have a complete understanding of the genetic architecture of stalk strength in maize, RPR and SBS (measured by Fmax, Mmax and σmax) were used to characterize stalk strength in our study. Utilizing a segregating population with 216 recombinant inbred lines, our analysis showed that stalk strength traits, RPR and SBS, have high heritability, ranging from 0.75 to 0.91. Nine QTL and one epistatic interaction between QTL were detected for RPR. Two, three and two QTL were detected for Fmax, Mmax and σmax, respectively. All QTL showed minor effects and only one QTL on chromosome 10 had overlapping support intervals between RPR and SBS. Co-locations of QTL and high positive correlations between stalk strength traits and other stalk traits suggested presence of pleiotropism and a complex genetic architecture of stalk strength. Owing to lack of major QTL, MAS solely based on molecular markers was found to be less effective than classical phenotypic selection for stalk strength. However, for SBS we observed considerably higher proportions of genetic variance explained by a genomic selection approach than obtained in QTL mapping with cross validation. Therefore, genomic selection might be a promising tool to improve the efficiency of breeding for stalk strength. All QTL mapping studies conducted hitherto for unraveling the genetic architecture of HI rate detected a major QTL, termed qhir1, in bin 1.04. Dong et al. (2013) further narrowed down this QTL to a 243 kb region. Considering the complex genetic architecture of HI and genetic background noise possibly affecting fine mapping of qhir1, we attempted to validate these results with an alternative approach before embarking on map-based gene isolation. Utilizing 51 maize haploid inducers and 1,482 non-inducers collected worldwide, we were able to investigate the genetic diversity between inducers and non-inducers and detect genomic regions mandatory for HI. The genetic diversity analyses indicated that the inducer group was clearly separated from other germplasm groups and had high familial relatedness. Analyzing our data by a case-control association approach failed because the segregation of HI was heavily confounded with population structure. Moreover, selective sweep approaches commonly used in the literature that are designed for capturing selective sweeps in a long-term evolutionary context failed due to high familial relatedness among inducers. To solve this problem, we developed a novel genome scan approach to detect fixed segments among inducers. With this approach, we detected a segment, termed qhir12, 4.0 Mb in length, within the support interval of the qhir1. This segment was the longest genomic segment detected by our novel approach and was entirely absent in all non-inducers analyzed. However, qhir12 has no overlap with the fine mapping region of Dong et al. (2013), termed qhir11. This indicates that the genomic region harboring the mandatory gene of HI should be confirmed by further experiments to corroborate its existence and identify its location in the maize genome.
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.
Gene mining in doubled haploid lines from European maize landraces with association mapping
(2014) Strigens, Alexander Carl Georg; Melchinger, Albrecht E.
Since the introduction of maize into Europe, open-pollinated varieties of flint maize were cultivated across the continent. Natural selection promoted adaptation to the climatic conditions prevailing in the different regions. With the advent of hybrid breeding in Europe during the 1950’s, some of the genes responsible for the specific adaptations of the landraces to abiotic and biotic stress were captured in the first developed inbred lines, but most of their genetic diversity is still untapped. Development of inbred lines out of this material by recurrent selfing is very tedious due to strong inbreeding depression. In contrast, the doubled-haploid (DH) technology allows producing fully homozygous lines out of landraces in only one step. This allows their precise characterization in replicated trials and identification of new genes by genome wide association (GWA) mapping. In this study we genotyped a set of 132 DH lines derived from European Flint landraces and 364 elite European flint (EU-F), European dent (EU-D) and North-American dent (NA-D) inbred lines with 56,110 single nucleotide polymorphism (SNP) markers. The lines were evaluated in field trials for morphologic and agronomic traits and GWA mapping was performed to identify underlying quantitative trait loci (QTL). In particular, our objectives were to (1) develop a robust method for quantifying early growth with a non-destructive remote-sensing platform, (2) evaluate the importance of early growth performance of inbred lines with regard to their testcross performance, (3) determine the potential of GWA mapping to identify genes underlying early growth and cold tolerance related traits, (4) evaluate the phenotypic and genotypic diversity recovered in the DH lines derived from the landraces, (5) estimate the effect of the DH method on the recovered genetic diversity, (6) identify new genes by GWA mapping in the DH lines derived from landraces, and (8) discuss the potential of DH lines derived from landraces to improve the genetic diversity and performance of elite maize germplasm. A phenotyping platform using spectral reflectance and light curtains was used to perform repeated measurements of biomass and estimate relative growth rates (RGR) of the DH and inbred lines, as well as of two testcrosses of 300 dent inbred lines. The DH lines derived from the landraces Schindelmeiser and Gelber Badischer had the highest RGR followed by EU-F lines, DH lines derived from Bugard, EU-D lines and, finally, NA-D lines. For inbred lines, whole plant dry matter yield (DMY) was positively correlated with RGR (r = 0.49), whereas this relation was weaker in the testcrosses (r = 0.29). RGR of the inbred lines correlated with RGR of their testcrosses (r = 0.42), but it had no influence on testcross DMY. A set of 375 EU-F, EU-D and NA-D lines were further evaluated in growth chambers under chilling (16/13°C) and optimal (27/25°C) temperatures. Photosynthetic and early growth performance were estimated for each treatment and an adaptation index (AI) built as the chilling to optimal performance ratio. Nineteen QTL were identified by GWA mapping for trait performance and AI. Candidate genes involved in ethylene signaling, brassinolide, and lignin biosynthesis were found in their vicinity. Several QTL for photosynthetic performance co-located with previously reported QTL and the QTL identified for shoot dry wieght under optimal conditions co-located with a QTL for RGR. Comparison of the DH lines derived from landraces with the EU-F lines showed that genotypic variances in single DH populations were greater than in the EU-F breeding population. A high average genetic distance among the DH lines derived from the same landrace as well as a rapid decay of linkage disequilibrium suggests a high effective population size of the landraces. Because no systematic phenotypic differences were observed between the landraces and synthetic landraces obtained by intermating the corresponding DH lines, the expected purge of lethal recessive alleles during the DH production did neither improve grain yield performance nor affect the recovered genetic diversity. Performing GWA in the DH lines derived from landraces as well as the EU-F, and EU-D lines allowed the identification of 49 QTL for 27 traits. A larger set of DH lines derived from more landraces might solve problems arising from population structure and allow a much higher power for the detection of new alleles. In conclusion, the introgression of DH lines derived from landraces into the elite breeding material would strongly broaden its genetic base. However, grain yield performance was 22% higher in EU-F lines than in the DH lines derived from landraces. Selection of the best DH lines would allow partially bridging this yield gap and marker-assisted selection may allow introgression of positive QTL without introducing negative features by linkage drag.
QTL mapping and genomic prediction of complex traits based on high-density genotyping in multiple crosses of maize (Zea mays L.)
(2013) Stange, Michael; Melchinger, Albrecht E.
Most important agronomic traits like disease resistance or grain yield (GY) in maize show a quantitative trait variation and, therefore, are controlled by dozens to thousands of quantitative trait loci (QTL). Mapping of these QTL is well established in plant genetics to elucidate the genetic architecture of quantitative traits and to detect QTL for knowledge-based breeding. Nowadays, high-density genotyping is routinely applied in maize breeding and offers a huge number of SNP markers used in association mapping and genomic selection (GS). This enables also the construction of high-density linkage maps with marker densities of 1 cM or even higher. Nevertheless, QTL mapping studies were until recently mostly based on low-density maps. This raises the question if high-density maps are an overkill for QTL mapping, or in contrast, if important QTL mapping parameters would profit from them. High-density maps could also be beneficial for dissection of the complex trait GY into its components 100-kernel weight (HKW) and kernel number (KN). Analysis of these less complex traits may help to unravel the genetic architecture and improve the predictive ability for complex traits. However, an open question is whether consideration of component traits and epistatic interactions in QTL mapping models are beneficial for predicting the performance of untested genotypes for the complex trait GY. In this thesis, high-density linkage maps were constructed for biparental maize populations of doubled haploid (DH) lines and applied in different QTL linkage mapping approaches. In detail, the objectives of this study were to (1) investigate the effect of high-density versus low-density linkage maps in QTL mapping of important QTL mapping parameters and to analyze the resolution of closely linked QTL with experimental data and computer simulations, (2) map QTL for HKW, KN, and GY with high-density maps and to analyze epistatic interactions, (3) compare the prediction accuracy for GY with different QTL mapping models, and (4) answer the question how the composition of the test set (TS) influences the accuracy in genomic prediction of progenies from individual crosses. This thesis was based on five interconnected biparental populations with a total of 699 DH lines evaluated in field experiments for GER resistance related traits as well as for HKW, KN, and GY. All DH lines were genotyped with the Illumina MaizeSNP50 Bead Chip and high-density linkage maps were constructed separately for each population. For evaluation of high-density versus low-density maps on QTL mapping parameters, three linkage maps with marker densities of 1, 2, and 5 cM were constructed, starting from the full linkage map with 7,169 markers mapped in the largest population (N=204). QTL mapping was performed with all three marker densities in the experimental population for GER resistance related traits and for yield related traits, as well as in a simulation study with different population sizes. In the simulation study, independent QTL with additive effects explaining 0.14 to 7.70% of the expected phenotypic variance, as well as linked QTL with map distances of 5 and 10 cM, were simulated. Results showed that high-density maps had only minor effects on the QTL detection power and the proportion of genotypic variance explained. In contrast, support interval length decreased with increasing marker density, indicating an increasing precision of QTL localization. The precision of QTL effect estimates was measured as deviation between the reference additive effects and the estimated QTL effects. It gained from an increase in marker density, especially for small and medium effect QTL. Increasing the marker density from 5 to 1 cM was advantageous for separately detecting linked QTL in coupling phase with both linkage distances. In conclusion, this study showed that QTL mapping parameters relevant for knowledge-based breeding profited from an increase in marker density. For QTL mapping of the complex trait GY and the components HKW and KN, three QTL mapping models were applied to the four largest populations, of which two models were based on the component traits HKW and KN. All models included tests for epistatic interactions. The results showed that heritability was slightly higher for the component traits compared to the complex trait. The average length of support intervals of detected QTL was short with 12 cM, indicating high precision of QTL localization. Co-located QTL with same parental origin of favorable alleles were detected within populations for different traits and between populations for same traits, reflecting common QTL across populations. However, to finally confirm these common QTL, multi-population QTL mapping should be conducted. Based on the detected QTL, predictions for GY showed that epistatic models did not outperform the respective additive models. Nevertheless, component trait based models can be advantageous for identification of favorable allele combinations for multiplicative traits. For all five populations, the comparison of genetic similarities reflected the crossing scheme with full-sib families, half-sib families and unrelated families. The evaluation of prediction accuracies for different scenarios depended on the composition of the TS. Highest prediction accuracies were observed for DH lines within full-sib families, medium values if full-sib DH lines were replaced by half-sib DH lines, and lowest values if the TS comprised of DH lines from unrelated crosses. In conclusion, I found high-density linkage maps to be advantageous for linkage mapping in biparental DH populations by improving important QTL mapping parameters. Higher costs for high-density genotyping are by far compensated by these advantages. Dissecting the complex trait GY into its component traits HKW and KN by component trait based QTL mapping models revealed a complex genetic network of GY. Future research should focus on high-density consensus maps applied in multi-population QTL mapping to take advantage of the improved QTL detection power and to confirm common QTL across populations.
Quantitative trait loci (QTL) mapping in multi-line crosses of European maize
(2012) Steinhoff, Jana; Reif, Jochen Christoph
Multiple-line crosses (MC) have been proposed as promising mapping resource for quantitative trait loci (QTL) detection for agronomic important traits. In contrast to mapping populations derived from a single biparental population, MC can increase the statistical power of QTL detection, the accuracy of QTL location and of QTL effect estimates. Additionally, MC-QTL mapping has the advantage of using data routinely collected in plant breeding programs. The objectives of this study were to (i) assess the reliability of the maize genetic consensus map by comparing it to its six single population linkage maps, (ii) exploit the benefits of a combined analysis by applying two MC-QTL mapping models and to compare the results to single-population analyses, and (iii) investigate the genetic architecture of grain yield, grain moisture, adaptation, and flowering time in elite maize. The experiment comprised six populations with 109 to 150 individuals, resulting from crosses of elite maize breeding material. The germplasm was provided by Syngenta Seeds, Bad Salzuflen, Germany. The 788 genotypes were genotyped with 857 SNP markers. After constructing genetic linkage maps of the six single populations, the genotypic information of the single populations was integrated in a consensus map and its reliability was tested for QTL studies. The average distance between adjacent markers was 1.84 cM suggesting that the marker density is not a limiting factor for QTL analyses. Moreover, we observed medium to high heritabilities for all traits. Consequently, the quality of both genotypic and phenotypic data should allow QTL detection with substantial power. We applied two different MC-QTL mapping models on the data assuming fixed allele effects. The disconnected model estimates QTL effects nested within populations, whereas the connected model takes into account the relationship between the populations. Both models outperformed the single population analyses with regard to QTL detection rate, variance explained by the detected QTL, and the size of the confidence intervals. In all analyses, the disconnected model outperformed the connected model in terms of number of QTL and size of confidence intervals. This superiority seems to be caused by the high background dependencies of QTL effects in connected crosses, which was revealed by a modified diallel analysis of the QTL effects. We investigated the genetic architecture of grain yield, grain moisture, adaptation to maturity zones, and flowering time. Our findings suggest that all traits exhibit a complex genetic architecture with an absence of large QTL effects. Some of the studied traits appear to be influenced by epistasis, interactions between loci. In particular, for flowering time, the two-dimensional scan for epistatic interactions suggested the presence of digenic epistasis. The absence of QTL with large effects suggests that marker-assisted selection is not an appropriate tool to breed for adapted maize hybrids with improved grain yield. Consequently, more suitable approaches for complex traits such as genomic selection should be applied. The joint analyses across populations resulted in higher QTL detection power and resolution compared to single population analyses. Thus, for traits with a less complex genetic architecture, MC-QTL mapping is a powerful tool for the identification of robust diagnostic markers.
Untersuchungen zur Ertragskartierung während der Getreideernte mit dem Mähdrescher
(1997) Reitz, Peter
Die Getreideernte in den Industrieländern wird heute ausschließlich mit dem Mähdrescher durchgeführt. Durch eine gleichzeitige Ertragskartierung werden die Voraussetzungen für eine teilflächenspezifische Feldbewirtschaftung geschaffen. Aus den geokartierten Ertragsdaten lassen sich Rückschlüsse über kleinräumige Unterscheide in den Wachstumsbedingungen innerhalb eines Feldes ziehen. In der vorliegenden Arbeit werden die theoretischen Grundlagen zur Ertragskartierung und ein Verfahren zum Betrieb des Mähdreschers mit geokodierten Teilflächendaten entwickelt und untersucht. Zu deren Realisierung werden Module für die Erfassung, Übertragung, Verarbeitung und Umsetzung geokodierter Teilflächendaten benötigt.