Browsing by Subject "QTL mapping"

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Assessment of phenotypic, genomic and novel approaches for soybean breeding in Central Europe
(2022) Zhu, Xintian; Würschum, Tobias
Soybean is the economically most important leguminous crop worldwide and serves as a main source of plant protein for human nutrition and animal feed. Europe is dependent on plant protein imports and the EU protein self-sufficiency, which is an issue that has been on the political agenda for several decades, has recently received renewed interest. The protein imports are mainly in the form of soybean meal, and soybean therefore appears well-suited to mitigate the protein deficit in Europe. This, however, requires an improvement of soybean production as well as an expansion of soybean cultivation and thus breeding of new cultivars that combine agronomic performance with adaptation to the climatic conditions in Central Europe. The objective of this thesis was to characterize, evaluate and devise approaches that can improve the efficiency of soybean breeding. Breeding is essentially the generation of new genetic variation and the subsequent selection of superior genotypes as candidates for new cultivars. The process of selection can be supported by marker-assisted or genomic selection, which are both based on molecular markers. A first step towards the utilization of these approaches in breeding is the characterization of the genetic architecture underlying the target traits. In this study, we therefore performed QTL mapping for six target traits in a large population of 944 recombinant inbred lines from eight biparental families. The results showed that some major-effect QTL are present that could be utilized in marker-assisted selection, but in general the target traits are quantitatively inherited. For such traits controlled by numerous small-effect QTL, genomic selection has proven as a powerful tool to assist selection in breeding programs. We therefore also evaluated the genomic prediction accuracy and found this to be high and promising for the six traits of interest. In conclusion, these results illustrated the potential of genomic selection for soybean breeding programs, but a potential limitation of this approach are the costs required for genotyping with molecular markers. Phenomic selection is an alternative approach that uses near-infrared or other spectral data for prediction instead of the marker data used for its genomic counterpart. Here, we evaluated the phenomic predictive ability in soybean as well as in triticale and maize. Phenomic prediction based on near-infrared spectroscopy (NIRS) of seeds showed a comparable or even slightly higher predictive ability than genomic prediction. Collectively, our results illustrate the potential of phenomic selection for breeding of complex traits in soybean and other crops. The advantage of this approach is that NIRS data are often available anyhow and can be generated with much lower costs than the molecular marker data, also in high-throughput required to screen the large numbers of selection candidates in breeding programs. Soybean is a short-day plant originating from temperate China, and thus adaptation to the climatic conditions of Central Europe is a major breeding goal. In this study, we established a large diversity panel of 1,503 early-maturing soybeans, comprising of European breeding material and accessions from genebanks. This panel was evaluated in six environments, which revealed valuable genetic variation that can be introgressed into our breeding programs. In addition, we deciphered the genetic architecture of the adaptation traits flowering time and maturity. Taken together, the findings of this study show the potential of several phenotypic, genomic and novel approaches that can be integrated to improve the efficiency of soybean breeding and thus hold great promise to assist the expansion of soybean cultivation in Central Europe through breeding of adapted and agronomically improved cultivars.
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.
Phänotypische und molekulare Analyse von Kreuzungsnachkommen auf Resistenz gegen Ährenfusariosen bei Triticale (x Triticosecale Wittmack)
(2011) Großmann, Maren; Großmann, Maren
Fusarium head blight (FHB) is an epidemic disease of cereals but disease control still is insufficiently possible. Resistance breeding can be addressed as one approach to reduce the mycotoxin contents. Since 2006 the European Union had strict rules governing the values for Desoxinivalenol (DON) in food products. The extraordinary loads through mycotoxins in triticale, which are caused by FHB, lead to large reductions in grain yield and quality. Beyond the fact that it can cause health issues in animals, especially in pig feed, it may induce financial burdens for farming industries. Resistance against FHB is inherited quantitatively with mainly additive effects and therefore is only recorded by complex field experiments. Molecular markers accelerate resistance breeding and enable specific introgressions of favorable QTL. The main topic of this thesis is to show the application possibilities of molecular markers for the investigation of FHB resistance in triticale. In detail this study aims to analyze factors leading to a minimized mycotoxin accumulation in perennial field trials at several locations. Furthermore genetic maps of two different crossing populations were compiled and QTL mapping for ear appearance, plant height, DON content and FHB resistance was implemented. For all populations significant varieties had been displayed for all characteristics. The average values for FHB rate were between 8 and 43 % depending on year and location. The heritability?s showed high values for each population (h2 = 0.7 ? 0.82). The substantial genotype-environment-interaction pointed out the importance of field experiments. Furthermore no significant correlation was obtained between ear appearance and plant height. Due to the fact that the correlation factor between DON-content and FHB rate was very low (r = 0.32) to moderate (r = 0,65). Therefore no assumption about the DON-content subjected to the FHB rate could be made. The mapping of both populations LASKO x ALAMO and LASKO x TRIMESTER has been accomplished with SSR- and DArT-markers. The rate of polymorphism could be increased from 7 - 12 % respectively to 9 - 18 %. Genetic maps were constructed with length of 1.815 and 1.407 cM. They indicated 5.19 and 4.54 cM in their average marker distances. Throughout the QTL mapping several QTL were detected (6 QTL for ear appearance, 4 QTL for plant height, 1 QTL for DON-content and 4 QTL for FHB rate). These QTL explained 8 to 66 % of the phenotypical variance. In addition crossing populations of LASKO x TRIMESTER showed 2 QTL for ear appearance, 1 for plant height and 2 QTL for FHB resistance, which could explain 3 to 41 % of the phenotypical variance. This was also observed in several other QTL-surveys for wheat. Prospectively using molecular markers and genetically engineered methods will increase the research and development of resistant varieties and lead to a reduced mycotoxin accumulation. So far neither genetic maps nor any QTL studies for FHB resistance or DON-content in triticale have been published. Due to the fact that resistance is transmitted by several genes numerous artificial inoculations have to be carried out during breeding. Additive gene effects are useful to combine several resistance genes from different parents. Established methods in plant breeding such as recurrent selection, phenotypical and marker-based selection are successfully in use to reduce FHB- symptoms and to reduce the mycotoxin value but these methods have to be improved. The results of this thesis are promising for a superior resistance breeding in the future.
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.
Studying stem rust and leaf rust resistances of self-fertile rye breeding populations
(2022) Gruner, Paul; Witzke, Anne; Flath, Kerstin; Eifler, Jakob; Schmiedchen, Brigitta; Schmidt, Malthe; Gordillo, Andres; Siekmann, Dörthe; Fromme, Franz Joachim; Koch, Silvia; Piepho, Hans-Peter; Miedaner, Thomas
Stem rust (SR) and leaf rust (LR) are currently the two most important rust diseases of cultivated rye in Central Europe and resistant cultivars promise to prevent yield losses caused by those pathogens. To secure long-lasting resistance, ideally pyramided monogenic resistances and race-nonspecific resistances are applied. To find respective genes, we screened six breeding populations and one testcross population for resistance to artificially inoculated SR and naturally occurring LR in multi-environmental field trials. Five populations were genotyped with a 10K SNP marker chip and one with DArTseqTM. In total, ten SR-QTLs were found that caused a reduction of 5–17 percentage points in stem coverage with urediniospores. Four QTLs thereof were mapped to positions of already known SR QTLs. An additional gene at the distal end of chromosome 2R, Pgs3.1, that caused a reduction of 40 percentage points SR infection, was validated. One SR-QTL on chromosome 3R, QTL-SR4, was found in three populations linked with the same marker. Further QTLs at similar positions, but from different populations, were also found on chromosomes 1R, 4R, and 6R. For SR, additionally seedling tests were used to separate between adult-plant and all-stage resistances and a statistical method accounting for the ordinal-scaled seedling test data was used to map seedling resistances. However, only Pgs3.1 could be detected based on seedling test data, even though genetic variance was observed in another population, too. For LR, in three of the populations, two new large-effect loci (Pr7 and Pr8) on chromosomes 1R and 2R were mapped that caused 34 and 21 percentage points reduction in leaf area covered with urediniospores and one new QTL on chromosome 1R causing 9 percentage points reduction.