Browsing by Subject "Züchtung"

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Advancing soybean adaptation to Central European growth conditions with novel breeding tools
(2020) Jähne, Felix; Würschum, Tobias
According to the European Soy Monitor 2018 (European Soy Monitor, 2018), there is a wide discrepancy in the EU between market demands and general sustainability aims regarding soybean products. Europe needs to take action, if it wants to maintain its protein demands and at the same time requests a reduction in the destruction of globally important tropical and subtropical ecosystems. One step towards more sustainable soybean products lies in the increase of domestic production which has the potential to decrease soybean imports from areas of unsustainable cultivation. An augmented EU production of soybeans can be achieved for example by increasing the yield potential of soybeans in areas where successful cultivation already takes place or by expanding the cultivation area to more northern parts of Central Europe. Breeding for new, improved and adapted soybean cultivars that meet those terms, is a key activity towards that aim. This dissertation elucidates three different ways how the adaptation of soybeans to the climatic and photoperiodic conditions of Central Europe can be assisted and even accelerated: 1) By using off-season climate-controlled LED chambers to enable a speed breeding single seed descent approach. A 10 h light regime, rich in blue and deprived of far-red light emission is capable to significantly reduce and synchronise the generation time of soybeans. It was possible to shorten the life cycle for a panel of 8 soybean cultivars from different maturity groups to 77 days. This allows several generations of soybeans to be grown within one year. For the short day crops rice and amaranth on the other hand, different light quality parameters were favoured. In those crops mean flowering time was accelerated when far-red light was included in the light protocol. This underlines the importance of a crop-specific light regime in order to realise the full potential of LED-based speed breeding single seed descent. 2) By including experiments in climate-control chambers in combination with molecular tools (i.e. genomic prediction) to advance cold tolerance in soybeans. This quantitatively inherited key trait is necessary to adapt soybeans to colder regions and consequently extend growing areas of this crop to higher latitudes in Europe. In the biparental soybean population Merlin × Sigalia (103 recombinant inbred lines) three QTL for cold tolerance during pod onset were found on chromosomes 7, 11 and 13. The relatively small proportion of genotypic variance for this trait explained by these QTL underlines the quantitative nature of cold tolerance. Genomic prediction was shown to be a promising approach to select for cold stress tolerance. Scenarios with different test set sizes and prediction models were evaluated. In scenarios with smaller test set sizes prediction accuracies increased if known and confirmed QTL were included in the prediction model. 3) By incorporating citizen science into the breeding process. The citizen science project ‘1000 Gärten’ from 2016 approached this topic. Phenotypic data from soybean cultivars and breeding lines were collected by citizen scientists in 2492 gardens throughout Germany which generated a unique dataset. Among many other results this study was able to show that in 2016 and within the early maturity segment of soybeans the factor temperature influenced flowering and maturity to a higher degree than photoperiod although day length differed by over an hour between the north and the south of Germany during the time of flowering. It was shown that this admittedly challenging tool can realise a significant impact not only regarding the possibility of a highly multi-environmental screening of breeding material but also by connecting plant breeding, agriculture and potential future costumers in order to raise awareness and acceptance of a crop in larger parts of the society - a factor that may not be highlighted enough when a new crop is introduced to our agriculture. These approaches should not be seen as an alternative to classical plant breeding, but rather considered as valuable additional tools that can contribute to conventional breeding of soybeans, as well as other crops. If applied, the presented tools may assist plant breeding to pave Europe’s way towards a greener and more sustainable future that is urgently needed.
Analyse komplexer Merkmale beim Schwein mittels SNP-Chip Genotypen, Darmmikrobiota- und Genexpressionsdaten
(2017) Maushammer, Maria; Bennewitz, Jörn
In the present scientific research, SNP chip genotypes, gut microbiota and gene expression data were used for analysing complex traits in a Piétrain population. These data were collected from around 200 performance tested sows and were used for genetic and microbial analyses of complex trait as well as for structural and functional meat quality traits. The gut microbiome plays a major role in the immune system development, state of health and energy supply of the host. Quantitative-genetic methods were applied to analyse the interrelationship between pig gut microbiota compositions, complex traits (daily gain, feed conversion and feed intake) and pig genomes. The specific aims were to characterize the gut microbiota of the pigs, to analyse the effects of host genetics on gut microbial composition, and to investigate the role of gut microbial composition on the host’s complex traits. The pigs were genotyped with a standard 60K SNP chip. Microbial composition was characterized by 16S rRNA gene amplicon sequencing technology. Ten out of 51 investigated bacterial genera showed a significant host heritability, ranging from 0.32 to 0.57. Conducting genome wide association analysis showed associations of 22 SNPs and six bacterial genera. The potential candidate genes identified are involved in the immune system, mucosa structure and secretion of digestive juice. These results show, that parts of the gut microbiota are heritable and that the gut microbiome can be seen as quantitative trait. Microbial mixed linear models were applied to estimate the microbiota variance for each of the investigated traits. The fraction of phenotypic variance explained by the microbial variance was 0.28, 0.21, and 0.16 for daily gain, feed conversion, and feed intake, respectively. The SNP data and the microbiota data were used to predict the phenotypes of the traits using both, genomic best linear unbiased prediction (G-BLUP) and microbial best linear unbiased prediction (M-BLUP) methods. The prediction accuracies of G-BLUP were 0.35, 0.23, and 0.20 for daily gain, feed conversion, and feed intake, respectively. The corresponding prediction accuracies of M-BLUP were 0.41, 0.33, and 0.33. Thus, the gut microbiota can be seen as an explaining variable for complex traits like daily gain, feed conversion and feed intake. In addition, in combination with meat quality traits, transcript levels of muscle tissue were analysed at time of slaughtering. This study should give an insight into the biological processes involved in meat quality characteristics. The aims were to functionally characterise differentially expressed genes, to link the functional information with structural information obtained from GWAS, and to identify potential candidate genes based on these results. An important meat quality trait is the intramuscular fat content, since it affects the juiciness, the taste and the tenderness of the meat. Another important trait is drip loss which causes not only a loss of weight but also a loss of important proteins. Both traits have an impact on the consumer acceptance of fresh meat products. For each of the two traits, eight discordant sibling pairs were selected out of the Piétrain sample and were used for genome-wide gene expression analyses. Thirty five and 114 genes were identified as differentially expressed and trait correlated genes for intramuscular fat content and drip loss, respectively. On the basis of functional annotation, gene groups belonging to the energy metabolism of the mitochondria, the immune response and the metabolism of fat, were associated with intramuscular fat content. Gene groups associated with protein ubiquitination, mitochondrial metabolism, and muscle structural proteins were associated with drip loss. Furthermore, genome-wide association analyses were carried out for these traits and their results were linked to the genome-wide expression analysis by functional annotation. In this context, intramuscular fat was related to muscle contraction, transmembrane transport and nucleotide binding. Drip loss was characterized by the endomembrane system, the energy generation of cells, and phosphorus metabolic processes. Three and four potential candidate genes were identified for intramuscular fat content and drip loss, respectively.
Assessing the genetic variation of phosphate efficiency in European maize (Zea mays L.)
(2022) Weiß, Thea Mi; Würschum, Tobias
Why should plant breeders in Central Europe care about phosphate efficiency? Soil phosphorus levels have mostly reached high to very high levels over the last decades in intensively farmed, livestock-rich regions. However, the European Union demands a restructuring of the agricultural production systems through setting ambitious goals envisaged in the Farm to Fork Strategy. By 2030, fertilizer use should be reduced by 20 %, nutrient losses by at least 50 %. As a consequence, farmers have to be even more efficient with crop inputs, among them the globally limited resource of phosphorus fertilizers, while maintaining high yields. Plant breeding means thinking ahead. Therefore, phosphate-efficient varieties should be developed to help farmers meet this challenge and reduce the need for additional fertilizers. One prerequisite to reach this target is that genotypic variation for the relevant traits is available. Moreover, approaches that assist selection by accurate but also time- and resource-efficient prediction of genotypes are highly valuable in breeding. Finally, the choice of the selection environment and suitable trait assessment for the improvement of phosphate efficiency under well-supplied conditions, need to be elaborated. In this dissertation, a diverse set of maize genotypes from ancient landraces to modern hybrids was investigated for phosphate efficiency-related traits under well-supplied P soil conditions. Multi-environmental field trials were conducted in 2019 and 2020. The reaction to different starter fertilizer treatments of the 20 commercially most important maize hybrids grown in Germany was studied. In the hybrid trial, the factor environment had a significant effect on the impact of starter fertilizers. Especially in early developmental stages genotypes showed a different response to the application of starter fertilizers. On the overall very well-supplied soils, we observed no significant genotype-by-starter fertilizer interaction. Nonetheless, we identified hybrids, which maintained high yields also if no starter fertilizer was provided. Thus, it seems that sufficient variation is available to select and breed for phosphate efficiency under reduced fertilizer conditions. Furthermore, the concept of phenomic prediction, based on near-infrared spectra instead of marker data to predict the performance of genotypes, was applied to 400 diverse lines of maize and compared to genomic prediction. For this, we used seed-based near-infrared spectroscopy data to perform phenomic selection in our line material, which comprised doubled haploid lines from landraces and elite lines. We observed that phenomic prediction generally performed comparable to genomic prediction or even better. In particular, the phenomic selection approach holds great potential for predictions among different groups of breeding material as it is less prone to artifacts resulting from population structure. Phenomic selection is therefore deemed a useful and cost-efficient tool to predict complex traits, including phosphorus concentration and grain yield, which together form the basis to determine phosphate efficiency. Lastly, 20 different indicators for phosphate efficiency were calculated, the genetic variation of the different measures present in this unique set of lines was quantified, and recommendations for breeding were derived. Of the different measures for phosphate efficiency reported in literature, Flint landraces demonstrated valuable allelic diversity with regard to phosphate efficiency during the seedling stage. Due to the highly complex genetic architecture of phosphate efficiency-related traits, a combination of genomic and phenotypic selection appears best suited for their improvement in breeding. Taken together, phosphate efficiency, including its definition and meaning, is largely dependent on the available phosphorus in the target environment as well as the farm type, which specifies the harvested produce and thereby the entire phosphorus removal from the field. In conclusion, future maize breeding should work in environments that are similar to the future target environments, meaning reduced fertilizer inputs and eventually lower soil P levels. Our results demonstrate that breeding of varieties, which perform well without starter fertilizers is feasible and meaningful under the well-supplied conditions prevalent in Central Europe. For the improvement of the highly complex trait phosphate efficiency through breeding we recommend to apply genomic and phenomic prediction along with classical phenotypic screening of genotypes and by this making our food systems more resilient towards upcoming challenges in agriculture.
Breeding for resistance to Fusarium ear diseases in maize and small-grain cereals using genomic tools
(2021) Gaikpa, David Sewordor; Miedaner, Thomas
The world’s human and livestock population is increasing and there is the need to increase quality food production to achieve the global sustainable development goal 3, zero hunger by year 2030 (United Nations, 2015). However, biotic stresses such as Fusarium ear infections pose serious threat to cereal crop production. Breeding for host plant resistance against toxigenic Fusarium spp. is a sustainable way to produce more and safer cereal crops such as maize and small-grain winter cereals. Many efforts have been made to improve maize and small-grain cereals for ear rot (ER) and Fusarium head blight (FHB) resistances, using conventional and genomic techniques. Among small-grain cereals, rye had the shortest maturity period followed by the descendant, hexaploid triticale while both wheat species had the longest maturity period. In addition, rye and triticale were more robust to Fusarium infection and deoxynivalenol accumulation, making them safer grain sources for human and animal consumption. However, a few resistant cultivars have been produced by prolonged conventional breeding efforts in durum wheat and bread wheat. High genetic variation was present within each crop species and can be exploited for resistance breeding. In this thesis, the genetic architecture of FHB resistance in rye was investigated for the first time, by means of genome-wide association study (GWAS) and genomic prediction (GP). GWAS detected 15 QTLs for Fusarium culmorum head blight severity, of which two had major effects. Both weighted and unweighted GP approaches yielded higher prediction abilities than marker-assisted selection (MAS) for FHB severity, heading stage and plant height. Genomics-assisted breeding can shorten the duration of breeding rye for FHB resistance. In the past decade, genetic mapping and omics were used to identify a multitude of QTLs and candidate genes for ear rot resistances and mycotoxin accumulation in maize. The polygenic nature of resistance traits, high genotype x environment interaction, and large-scale phenotyping remain major bottlenecks to increasing genetic gains for ear rots resistance in maize. Phenotypic and molecular analyses of DH lines originating from two European flint landraces (“Kemater Landmais Gelb”, KE, and “Petkuser Ferdinand Rot”, PE) revealed high variation for Gibberella ear rot (GER) severity and three agronomic traits viz. number of days to female flowering, plant height and proportion of kernels per cob. By employing multi-SNP GWAS method, we found four medium-effect QTLs and many small-effect (10) QTLs for GER severity in combined DH libraries (when PCs used as fixed effects), none co-localized with the QTLs detected for the three agronomic traits analyzed. However, one major QTL was detected within KE DH library for GER severity. Two prioritized SNPs detected for GER resistance were associated with 25 protein-coding genes placed in various functional categories, which further enhances scientific knowledge on the molecular mechanisms of GER resistance. Genome-based approaches seems promising for tapping GER resistance alleles from European maize landraces for applied breeding. After several cycles of backcrossing and sufficient selection for agronomic adaptation traits, the resistant lines identified in this thesis can be incorporated into existing maize breeding programs to improve immunity against F. graminearum ear infection. Breeding progress can be faster using KE landrace than PE. A successful validation of QTLs identified in this thesis can pave way for MAS in rye and marker-assisted backcrossing in maize. Effective implementation of genomic selection requires proper design of the training and validation sets, which should include part of the current breeding population.
Breeding winter durum wheat for Central Europe : assessment of frost tolerance and quality on a phenotypic and genotypic level
(2015) Sieber, Alisa-Naomi; Würschum, Tobias
Durum wheat (Triticum durum) is a tetraploid wheat that is used for pasta and other semolina products. Quality standards for semolina requested by the pasta industry are very high. Different characteristics should come with the cereal as raw material for an optimal end product. Vitreosity, the glassy and amber quality feature of durum wheat kernels, is an indicator for high semolina yield. The complex protein-starch matrix of glassy kernels breaks the grain into the typical semolina granulate instead of flour during milling. Humid conditions, like late summer rains in Central Europe, have a huge effect on this characteristic, changing this matrix irreversibly. Such processes in the kernel are less understood and challenge plant breeders to find genotypes with improved vitreosity. A set of F5 winter durum wheat lines (Chapter 2) was used to investigate the relationship between protein content and vitreosity as well as the impact of humidity on the stability of the trait. A method to evaluate the mealy part in kernels was improved and enabled to test for the influence of humidity on vitreosity. Furthermore, it was revealed that the vitreosity of a durum wheat kernel depends on the protein content up to a specific threshold as well as on the genotypic potential to form the complex endosperm matrix. The ability to maintain this kernel quality under humid conditions also highly depends on the genetics of a variety. In the Mediterranean region, durum wheat is grown as autumn-sown spring type. The mild winters as well as rain during spring allow the plants to develop well, and the dry summers enable an early harvest in June. Durum wheat production in Central Europe, on the other hand, is confronted with harsh winters and recurring severe frosts. The lack of a sufficient frost tolerance in combination with high quality, forces farmers to use the spring type with a spring sowing. Growing winter durum instead of spring durum wheat, would allow an autumn sowing. Using the winter type in this growing area, could have several advantages like an increased yield and stability due to a prolonged growing time. Further, the constant soil coverage would prevent soil erosion and the growth vigor of winter durum has advantages against weeds. The success of winter durum breeding depends on frost tolerance as a key factor for varieties with excellent winter survival. Discontinuous occurrence of frosts across years and protective snow coverage, however, limit the phenotypic selection for this trait under field conditions. Greenhouses or climate chambers could be used as alternative to test under the necessary conditions, but those fully-controlled tests are time consuming and labor-intensive. The ‘Weihenstephaner Auswinterungsanlage’ are wooden boxes with movable glass lids used as a semi-controlled test. Plants are exposed to all seasonal conditions, including frost stresses, in this test, but they can be protected from snow coverage. While this method is already successfully used to test for frost tolerance in bread wheat, the application in durum wheat has not been evaluated yet. The frost tolerance scorings of winter durum elite lines (F5 and F6) based on the ‘Weihenstephaner Auswinterungsanlage’ were compared to the field evaluation (Chapter 3). It was demonstrated that this semi-controlled test produces reliable and highly heritable (h2 = 0.83-0.86) frost tolerance data. The correlation of those results compared with the field data (r = 0.71) suggests this semi-controlled test as an indirect selection platform. Since it is now possible to test cost-efficient at early stages for frost tolerance, the next challenge was to determine whether the kernel quality or the grain yield suffers from an increased frost tolerance. In a survey with F5 winter durum elite lines, no negative association between frost tolerance and quality or other important agronomic traits could be found in European breeding material (Chapter 4). In order to support classical plant breeding, which relies predominantly on phenotypic data and parental information, molecular markers can be taken into account. Molecular markers can provide an in-depth look into the genetic architecture of traits, enable the determination of the relatedness of genotypes, identify the genetic variation in a population, or can assess the effect of geographic selection preferences. Furthermore, it is possible to assist knowledge-based selection. This improves plant breeding programs on a genetic level. The population structure in spring durum has already been examined with molecular methods in several studies. Winter durum, on the other hand, was only analyzed as a small group as part of spring durum studies or in groups of landraces. A highly diverse and unique panel of 170 winter durum and 14 spring durum lines was analyzed using a genotyping-by-sequencing (GBS) approach. A total of 30,611 markers, well distributed across the chromosomes, were obtained after filtering for marker quality. A principal coordinate analysis and a cluster analysis were applied. Together they revealed the absence of a major population structure (Chapter 5). The lines, however, grouped in a certain way, depending on their origin, associated with decreasing quality and increasing frost tolerance moving from South to Continental Europe. These groups allow breeders to conduct targeted crosses to further improve the frost tolerance in the Central European material. Another possibility is to build heterotic groups for hybrid breeding. The linkage disequilibrium (LD) decay was within 2-5 cM, indicating a high diversity in winter durum. The high marker density together with the extent of LD observed in this analysis allows to perform high-resolution association mapping in the present winter durum panel. The 30,611 markers and additional markers for candidate genes in frost tolerance were used to assess the genetic architecture of frost tolerance in durum wheat (Chapter 6). A major QTL was identified on chromosome 5A, likely being Frost Resistance-A2 (Fr-A2). Additional analysis of copy number variation (CNV) of CBF-A14 at Fr-A2 support this conclusion. CBF-A14 CNV explains about 90% of the proportion of genotypic variance. Two markers found in the QTL region were combined into a haploblock and enabled to capture the genetic variance of this QTL. Furthermore, the frequency of the QTL allele for frost tolerance shows a latitudinal gradient which is likely associated with winter conditions. In summary, the selection tools for vitreosity and frost tolerance provided in this study create a platform for winter durum breeding to select for high quality genotypes with excellent winter survival utilizing phenotypic as well as genotypic information.
Deciphering the potential of large-scale proteomics to improve product quality and nutritional value in different wheat species
(2022) Afzal, Muhammad; Longin, Friedrich
Wheat (Triticum aestivum) is one of the most important staple crops globally, which provides on average ~20% of the dietary intake of protein, starch and further important ingredients like fiber, minerals, vitamins, and essential amino acids for humans. Besides common wheat, there exist further wheat species with global to only local importance, i.e., durum, spelt, emmer and einkorn. Common wheat and durum are relatively widely cultivated whereas the other three species are cultivated only in specific regions. Apart from other functions, wheat proteins largely influence the end-use quality of products such as bread and pasta quality. Furthermore, wheat proteins can induce inflammatory reactions in humans such as celiac disease, wheat allergy and non-celiac wheat sensitivity. Thus, proteome profiles of different wheat species and cultivars within these species are of high relevance for stakeholders along the wheat supply chain. Proteomic technology has made breakthrough advancements in the recent times capable of quantifying thousands of proteins in 1.5–2 hours. Also, the wheat reference genome has been published and extended recently. These developments are extremely helpful in studying the wheat proteome at a high resolution. However, the modern large-scale proteomics has yet neither been applied to perform comparative investigation of the proteomes of different wheat species nor to study the proteomes of different types of breads and flours nor to study its application in the context of plant breeding. Therefore, we utilized modern large-scale proteomics to fill these gaps within the framework of this PhD work. First of all, an optimized data analysis pipeline was designed to deal with big proteomics data. This was necessary to estimate a multitude of quantitative genetics parameters for each protein and perform a comparative investigation of the proteomes. Optimization included implementation of data filtering based on the quantification of a protein in a given proportion of the samples, cultivars and environments. Different tests such as test for normal distribution of each protein in the context of statistical modelling and test to check the equality of variance between groups to apply the appropriate t-test were incorporated into a semi-automated workflow. In parallel, we adjusted and improved the lab methodology to deal with hundreds of samples within a short time period. We introduced a novel hybrid liquid chromatography-mass spectrometry (LC-MS) approach that combines quantification concatamer (QconCAT) technology with short microflow LC gradients and data-independent acquisition (DIA). The proposed approach measures the proteome by label-free quantification (LFQ) while concurrently providing accurate QconCAT-based absolute quantification of the key amylase/trypsin inhibitors (ATIs). These methods were then applied to compare different wheat species based on dozens of cultivars grown at multiple locations. First, we compared common wheat and spelt and identified 3,050 proteins overall. Of total proteins, 1,555 proteins in spelt and 1,166 in common wheat were only detected in a subset of the field locations. There were 1,495 and 1,604 proteins in spelt and common wheat, respectively, which were consistently expressed across all test locations in at least one cultivar. Finally, there were 84 and 193 unique proteins for spelt and common wheat, respectively, as well as 396 joint proteins, which were significantly differentially expressed between the two species. Using potentially allergenic proteins – annotated as amylase/trypsin inhibitors, serpins, and wheat germ agglutinin – we calculated an equally weighted “allergen index” that largely varied across cultivars ranging from –13.32 to 10.88 indicating the potential to select for cultivars with favorable proteome profiles. Next, we examined the proteomes of six different flours (wholegrain and superfine flours) and 14 different bread types (yeast and sourdough fermented breads and common wheat breads plus/minus bread improver) from common wheat, spelt and rye. Proteins that could cause allergies were functionally classified and comparatively measured by LFQ in flours and breads. Our findings showed that allergenic proteins were more prevalent in common wheat and spelt than rye and were not specifically degraded during bread manufacturing. In terms of abundance of the allergenic proteins, there was almost no difference between spelt and common wheat and the type of grain is likely more important for allergenicity than milling or traditional fermentation techniques. In a further study, we generated the flour reference proteomes for five wheat species, identifying at least 2,540 proteins in each species. More than 50% of the proteins significantly differed between species. Particularly, einkorn expressed 5.4 and 7.2 times less allergens and amylase/trypsin inhibitors than common wheat, respectively, emerging as a potential alternative cereal crop for people with sensitivities to cereal allergens. Lastly, we studied the application of large-scale proteomics for plant breeding. We found a significant impact of the environmental factors on protein expression. Only a fraction of proteins was stably expressed in all environments in at least one cultivar. Environmental influence was observed not only in the form of absolute expression or suppression of a certain protein at one or more environments but also in the form of low heritability (H2). High coefficients of variation across wheat cultivars indicate that the protein profiles of different cultivars vary considerably. Although, heritability was low for many proteins, we were able to identify hundreds of proteins with H²>0.5 – including key proteins for baking quality and human health. It should be possible to specifically manipulate the expression of functionally important proteins with high heritability by selecting and breeding for superior wheat cultivars along the wheat supply chain. Nevertheless, a successful implementation in plant breeding programs needs an improvement in the speed of protein quantification methods and in the validation of protein functions and annotations. In a nutshell, high number of proteins can be quantified in cereal grains utilizing cutting-edge proteomics techniques, opening new avenues for their use in the wheat supply chain. We generated lists of intriguing candidate proteins for further investigations on wheat sensitivity, and proteins with high heritability and important biological functions. Current research work has significant implications for the scientific and business communities across multiple disciplines including breeding, agriculture, cereal technology, nutritional science, health, and medicine. Political decision-makers and stakeholders in the food supply chain can benefit from the findings of this PhD project.
Design of breeding strategies for energy maize in Central Europe
(2012) Grieder, Christoph; Melchinger, Albrecht E.
The area of maize (Zea mays L.) grown for production of biogas has tremendously increased in Germany during the past decade. Thus, breeding companies have a keen interest to develop special varieties for this new market segment. A high methane yield per area (MY), which depends multiplicatively on dry matter yield (DMY) and methane fermentation yield (MFY), is required to ensure the efficiency of biogas maize cultivation. However, information on the targeted biogas maize ideotype is still missing and estimates of relevant quantitative genetic parameters for representative material are required to design optimum breeding strategies. We conducted a large field experiment to assess the relevant traits in biogas maize, their variation, and associations among them. In detail, our objectives were to (1) determine MFY and its production kinetics as well as the chemical composition, (2) examine the relationship of MFY and traits related to its kinetics with plant chemical composition and silage quality traits like in vitro digestible organic matter (IVDOM) and metabolizable energy concentration (MEC); (3) examine the potential of near infrared spectroscopy (NIRS) for prediction of traits related to methane production; (4) evaluate a large population of inbred lines and their testcrosses under field conditions for agronomic and quality traits; (5) estimate variance components and heritabilities (h2) of traits relevant to biogas production; (6) study correlations among traits as well as between inbred line per se (LP) and testcross performance (TP); and (7) draw conclusions for breeding maize as a substrate for biogas production. For this purpose, a representative set of 285 dent inbred lines from diverse origins and their 570 testcross progenies with two adapted flint testers was produced. Both material groups were evaluated in field experiments conducted in six environments (three locations, two years) in Germany. For analysis of MFY, samples of a diverse core set of 16 inbred lines and their 32 testcrosses were analyzed using the Hohenheim Biogas Yield Test, a discontinuous, laboratory fermentation assay. The kinetics of methane production was assessed by non-linear regression. Estimates of h2 for MFY measured after short fermentation time (3 days) were high, but genotypic variance and, therefore, also h2 decreased towards the end of the fermentation period (35 days). This was presumably the consequence of a nearly complete degradation of all chemical components during the long fermentation period. This interpretation was supported by strong correlations of MFY with chemical components, IVDOM and MEC for the early, but not the late fermentation stages. Based on the samples in the core set, NIRS calibrations were developed for MFY, parameters related to the kinetics of methane production, and chemical composition. With a coefficient of determination from validation (R2V) of 0.82, accuracy of prediction was sufficiently high for the maximum methane production rate, which is related to the early fermentation phase, but not satisfactory for the time needed to reach 95% of a sample?s final MFY (R2V = 0.51). In agreement with the trend of h2, performance of NIRS to predict MFY on day 35 (R2V = 0.77) was lower than for MFY on day 3 (R2V = 0.85), but still at a satisfactory level, as was the case for concentrations of different chemical components. Hence, NIRS proved to be a powerful tool for prediction of MFY and chemical composition in the main experiment. For TP, estimates of variance components from the main experiments revealed that general combining ability (GCA) was the major source of variation. The very tight correlation of MY with DMY but not with MFY indicated that variation in MY was primarily attributable to differences in DMY. Compared to MEC, MFY showed a weaker association with chemical composition. Genotypic correlation (rg) of MFY was strongest with non-degradable lignin (-0.58). Correlation of MFY with starch was not significant and indicated a lower importance of high cob proportions for biogas maize than for forage maize. Hence, to improve MY, selection should primarily focus on increasing DMY. Results for LP in the main experiment largely confirmed results from testcrosses and favor selection for high dry matter yielding genotypes with less emphasis on ear proportion. Estimates of rg between LP and GCA were highest (> 0.94) for maturity traits (days to silking, dry matter concentration) and moderate (> 0.65) for DMY and MY. Indirect selection for GCA on basis of LP looks promising for maturity traits, plant height, and to some extent also for DMY.
Experimental and simulation studies on introgressing genomic segments from exotic into elite germplasm of rye (Secale cereale L.) by marker-assisted backcrossing
(2005) Susic, Zoran; Geiger, Hartwig H.
The introgression of exotic germplasm is a promising approach to increase the genetic diversity of elite rye breeding materials. Even though exotic germplasm may contain genomic segments that can improve oligo- and polygenically inherited traits, it has not been intensively utilized in modern rye breeding due to its agronomically inferior phenotypes and low performance level. Introgression of exotic germplasm requires techniques that would minimize negative side effects attributable to genetic interactions between recipient and donor. This appears achievable by the introgression library approach involving the systematic transfer of donor chromosome (DC) segments from an agriculturally unadapted source (donor) into an elite line (recipient, recurrent parent). A set of introgression lines (ILs) is thus developed, in which introgression is restricted to one or a few short DC segments. Ideally, the introgressed DC segments are evenly distributed over the whole recipient genome and the total genome of the exotic donor is comprised in the established set of ILs. The systematic development of an introgression library in rye has not been described yet. The main objectives of this study were to i) establish two rye introgression libraries by marker-assisted backcrossing, comprising of ILs each harbouring one to three DC segments and jointly covering most of the donor genome (DG), and ii) apply computer simulations to develop a highly effective and cost-efficient marker-assisted introgression strategy for the creation of introgression libraries in rye. A cross between a homozygous elite rye inbred line L2053-N (recurrent parent) and a heterozygous Iranian primitive rye population Altevogt 14160 (donor) was used as base material to generate the two libraries (F and G). Repeated backcrossing (BC) and subsequent selfing (S) until generation BC2S3 were chosen as the introgression method. The AFLP and SSR markers were employed to select individuals carrying desired DC segments, starting from generation BC1 to generation BC2S2. The chromosomal localization of DC segments, the number of DC segments per IL, and the proportion of recurrent parent genome were used as criteria to select parent individuals. This procedure resulted in the first two rye introgression libraries worldwide, comprising 40 BC2S3 ILs per library and covering 72% of the total DG in library F and 63% in library G (jointly approximately 80%). Most of the established ILs harboured one to three homozygous DC segments (on average 2.2 in both libraries), with a mean length of 18.3 cM in library F and 14.3 cM in library G. Computer simulations were conducted using the software PLABSIM version 2 to evaluate and optimize strategies for developing an introgression library in rye. Simulations were based on map-length estimates obtained from genotyping the BC1 generation of population F (7 chromosome pairs, genome size 665 cM). Six strategies differing in the number of BC and S generations were analysed, by setting the restrictions of sufficient DG coverage and RPG recovery. The medium-long BC3S1 strategy proved to be the most recommendable. It allows to achieve close to 100% DG coverage with moderate progeny sizes (19 individual per IL) in the individual generations and an acceptable total number of marker data points (52700), thus providing a good compromise between the cost and speed of an introgression procedure. Longer strategies are somewhat more cost-efficient but too time-demanding. The reverse is true for shorter strategies. An optimal allocation of resources is achieved by starting an introgression strategy with a small BC1 population (between 60 and 200 individuals) and stepwise increasing the progeny size per IL from about 15 to about 25-35 individuals in the succeeding generations. Targeting longer DC segments and using genetic maps with lower marker density allow a remarkable reduction in resources. This approach, however, possesses shortcomings when implementation in breeding is considered. The longer DC segments more likely carry i) unfavourable loci as well, ii) more than one gene controlling the trait in question, or iii) many additional loci affecting other traits. The major disadvantage of genetic maps with large marker distances is the unknown information about possible double cross-overs within marker intervals. All above-mentioned disadvantages may cause problems in the process of identification and isolation of genes controlling the trait of interest. Thus, a lower initial effort for the establishment of an introgression library will later on require additional efforts for using the ILs in breeding and genomics. Since the results of the simulation study became available after the marker-assisted establishment of the two rye introgression libraries had been finished, the dimensioning of the experimental study deviated from the optimum dimensioning determined in the simulation study: i) The BC2S2 introgression strategy was used in the empirical approach, whereas the BC3S1 strategy proved to be most recommendable in the simulation study. ii) The BC1 population sizes of libraries F and G (68 and 69, respectively) were far below the optimum value (200) determined in the simulation study for the chosen BC2S2 strategy. iii) The mean progeny sizes per IL from generation BC2 onwards varied between 7 and 21, whereas the optimum progeny size would have been two to three times higher. iv) The total number of analysed individuals (690 in library F, 684 in library G) was considerably lower than the optimum determined in the simulation study (3440). As a consequence, the coverage of the donor genome in the two libraries was incomplete and most ILs harboured more than a single DC segment. The potential application of the results of the simulation study would have increased the value of the developed ILs (higher DG coverage, lower number of DC segments per IL) considerably, despite limited resources. The effects of the introgressed DC segments on agronomically important qualitative and quantitative traits still need to be examined in multi-environmental field experiments. Introgression lines with beneficial DC segments may directly be used in practical hybrid rye breeding programs. Moreover, such ILs may be further backcrossed to create near isogenic lines (NILs) each carrying a single marker-characterized short DC segment. These NILs are an ideal starting point for high-resolution mapping and for the isolation and functional characterisation of candidate genes. The two rye introgression libraries and the results of the simulation study mark important milestones for the targeted exploitation of exotic rye germplasm and provide a promising opportunity to proceed towards functional genomics in rye.
Extensions of genomic prediction methods and approaches for plant breeding
(2013) Technow, Frank; Melchinger, Albrecht E.
Marker assisted selection (MAS) was a first attempt to exploit molecular marker information for selection purposes in plant breeding. The MAS approach rested on the identification of quantitative trait loci (QTL). Because of inherent shortcomings of this approach, MAS failed as a tool for improving polygenic traits, in most instances. By shifting focus from QTL identification to prediction of genetic values, a novel approach called 'genomic selection', originally suggested for breeding of dairy cattle, presents a solution to the shortcomings of MAS. In genomic selection, a training population of phenotyped and genotyped individuals is used for building the prediction model. This model uses the whole marker information simultaneously, without a preceding QTL identification step. Genetic values of selection candidates, which are only genotyped, are then predicted based on that model. Finally, the candidates are selected according their predicted genetic values. Because of its success, genomic selection completely revolutionized dairy cattle breeding. It is now on the verge of revolutionizing plant breeding, too. However, several features set apart plant breeding programs from dairy cattle breeding. Thus, the methodology has to be extended to cover typical scenarios in plant breeding. Providing such extensions to important aspects of plant breeding are the main objectives of this thesis. Single-cross hybrids are the predominant type of cultivar in maize and many other crops. Prediction of hybrid performance is of tremendous importance for identification of superior hybrids. Using genomic prediction approaches for this purpose is therefore of great interest to breeders. The conventional genomic prediction models estimate a single additive effect per marker. This was not appropriate for prediction of hybrid performance because of two reasons. (1) The parental inbred lines of single-cross hybrids are usually taken from genetically very distant germplasm groups. For example, in hybrid maize breeding in Central Europe, these are the Dent and Flint heterotic groups, separated for more than 500 years. Because of the strong divergence between the heterotic groups, it seemed necessary to estimate heterotic group specific marker effects. (2) Dominance effects are an important component of hybrid performance. They had to be included into the prediction models to capture the genetic variance between hybrids maximally. The use of different heterotic groups in hybrid breeding requires parallel breeding programs for inbred line development in each heterotic group. Increasing the training population size with lines from the opposite heterotic group was not attempted previously. Thus, a further objective of this thesis was to investigate whether an increase in the accuracy of genomic prediction can be achieved by using combined training sets. Important traits in plant breeding are characterized by binomially distributed phenotypes. Examples are germination rate, fertility rates, haploid induction rate and spontaneous chromosome doubling rate. No genomic prediction methods for such traits were available. Therefore, another objective was to provide methodological extensions for such traits. We found that incorporation of dominance effects for genomic prediction of maize hybrid performance led to considerable gains in prediction accuracy when the variance attributable to dominance effects was substantial compared to additive genetic variance. Estimation of marker effects specific to the Dent and Flint heterotic group was of less importance, at least not under the high marker densities available today. The main reason for this was the surprisingly high linkage phase consistency between Dent and Flint heterotic groups. Furthermore, combining individuals from different heterotic groups (Flint and Dent) into a single training population can result in considerable increases in prediction accuracy. Our extensions of the prediction methods to binomially distributed data yielded considerably higher prediction accuracies than approximate Gaussian methods. In conclusion, the developed extensions of prediction methods (to hybrid prediction and binomially distributed data) and approaches (training populations combining heterotic groups) can lead to considerable, cost free gains in prediction accuracy. They are therefore valuable tools for exploiting the full potential of genomic selection in plant breeding.
Genome-wide association mapping of molecular and physiological component traits in maize
(2013) Riedelsheimer, Christian; Melchinger, Albrecht E.
Genome-wide association (GWA) mapping emerged as a powerful tool to dissect complex traits in maize. Yet, most agronomic traits were found to be highly polygenic and the detected associations explained together only a small portion of the total genetic variance. Hence, the majority of genetic factors underlying many agronomically important traits are still unknown. New approaches are needed for unravelling the chain from the genes to the phenotype which is still largely unresolved for most quantitative traits in maize. Instead of further enlarging the mapping population to increase the power to detect even smaller QTL, this thesis research aims to present an alternative route by mapping not the polygenic trait of primary interest itself, but genetically correlated molecular and physiological component traits. As such components represent biological sub-processes underlying the trait of interest, they are supposed to be genetically less complex and thus, more suitable for genetic mapping. Using large diversity panels of maize inbred lines, this approach is demonstrated with (i) biomass yield by using metabolites and lipids as molecular component traits and with (ii) chilling sensitivity by using physiological component traits such as photosynthesis parameters derived from chlorophyll fluorescence measurements. In a first step, we developed a sampling and randomization scheme which allowed us to obtain metabolic and lipid profiles from large-scale field trials. Both profiles were found to be inten- sively structured reflecting their functional grouping. They also showed repeatabilities higher than in comparable profiles obtained in previous studies with the model plant Arabidopsis under controlled conditions. By applying GWAS with 56,110 SNPs to metabolites and lipids, large-scale genetic associations explaining more than 30 % of the genetic variance were detected. Confounding with structure was found to be a problem of less extent for molecular components than for agronomic traits like flowering time. The lipidome was also found to show a multilevel control architecture similar as employed in controlling complex mechanical systems. In several instances, direct links between candidate genes underlying the detected associations and agronomic traits could be established. An example is cinnamoyl-CoA reductase, a key enzyme in the lingin biosynthesis pathway. It was found to be a candidate gene underlying a major QTL found for several intermediates in the lignin biosynthesis pathways. These intemediates were in turn found to be correlated with plant height, lignin content, and dry matter yield at the end of the vegetation period. The different signs of these correlations indicated that the relationships between pathway intermediates and the final product is not simple. Directly modeling complex traits with individual component traits may therefore require consideration of feedback loops and other interdependencies. Such connections were however found difficult to be established with physiological components underlying chilling sensitivity. The main reasons for this were the weak correlations between physiological components under controlled conditions and chilling sensitivity in the field as well as high levels of genotype × environment interactions caused by the complex and environment- dependent responses of maize after perception of chilling temperatures. The approach explored in this thesis research uses component traits to gain biological insights about the genetic control of biomass yield and chilling sensitivity evaluated in diverse populations of still manageable sizes. We showed that GWAS with 56k SNPs can identify large additive effects for component traits correlated with these traits. For mapping epistatic interactions and rare variants, classical linkage mapping with biparental populations will be a reasonable complementary approach. However, controlling and modeling genotype × environment interactions remains an important issue for understanding the genetic basis of especially chilling sensitivity. If the goal is merely to predict the phenotypic value in a given set of en- vironments, black-box genomic selection methods with either SNPs, molecular profiles, or a combination of both, are very promising strategies to achieve this goal.
Gibberella ear rot resistance in European maize : genetic analysis by complementary mapping approaches and improvement with genomic selection
(2022) Han, Sen; Melchinger, Albrecht E.
During the last decades, implementation of molecular markers such as single nucleotide polymorphisms (SNPs) has transformed plant breeding practices from conventional phenotypic selection to marker-assisted selection (MAS) and genomic selection (GS) that are more precise, faster and less resource-consuming. In this dissertation, we investigated these three selection approaches for improving the polygenic trait Gibberella ear rot (GER) resistance in maize (Zea mays L.), which is an important fungal disease in Europe and North America leading to reduced grain yield and grain contaminated with mycotoxins such as deoxynivalenol (DON) and zearalenone (ZON). Three different sets of materials were evaluated in multiple environments and analyzed for different objectives. In the first study, five flint doubled-haploid (DH) families (with size 43 to 204) inter-connected at various levels through common parents, were generated in an incomplete half-diallel design with four parental lines developed by the University of Hohenheim. Significant genotypic variances and generally high heritabilities were observed for all three traits (i.e., GER, DON and days to silking (DS)) in all families, implying good prospects for resistance breeding and phenotypic selection against GER across different environments in European maize germplasm. Genetic correlations were extremely tight between DON and GER and moderately negative for DS with DON or GER, suggesting that indirect selection against GER would be efficient to reduce DON, but maturity should be considered in GER resistance breeding. Using a high-density consensus map with 2,472 marker loci, we compared classical bi-parental mapping of QTL (quantitative trait locus/loci) with multi-parental QTL mapping conducted with joint families and using four different biometric models. Multi-parental QTL mapping models identified all and even further QTL than the bi-parental QTL mapping model conducted within each family. Interestingly, QTL for DON and GER were mostly family-specific, yet multiple families had several common QTL for DS. Many QTL displayed large additive effects and most favorable alleles originated from the highly resistant parent. Interactions between detected QTL and genetic background (family) were rare and had comparatively small effects. Multi-parental QTL mapping models generally did not yield higher prediction accuracy than the bi-parental QTL mapping model for all traits. In the second study, two diversity panels consisting of 130 elite European dent and 114 flint lines, respectively, from the University of Hohenheim were evaluated and subject to a genome-wide association study within each pool. Similar to the first study, highly significant genotypic and genotype × environment interaction variances were observed for GER, DON and DS. Heritabilities were moderately high for GER and DON and high for DS in both pools. Estimated genomic correlations between pools were close to zero for DON and DS, and slightly higher for GER. The detected QTL for DON were all specific to each heterotic pool and none of them was in common with previously detected QTL. Furthermore, no QTL was detected for GER and DS in both pools. Genomic prediction (GP) across pools yielded low or even negative prediction accuracy for all traits. When the training set (TS) size was increased by combining lines from both heterotic pools, the combined-pool GP approaches had no higher prediction accuracy than the within-pool GP approach. Different from expectation, method BayesB did not outperform genomic best linear unbiased prediction (GBLUP). In the third study, we analyzed two backcross (BC) families derived from a resistant and a susceptible recurrent parent. Both BC populations differed substantially in their means for all traits, suggesting that the two recurrent parents have different QTL alleles for GER resistance. Relatively high correlations were observed between DON and ZON concentrations measured by immunoassays and GER visual severity scoring and NIRS (near-infrared spectroscopy) within each BC population. Thus, the mycotoxin content in grain can reliably be reduced by directional selection for GER severity and NIRS measurements that are less expensive and less laborious. In conclusion, GER resistance in European maize germplasm can be effectively improved through breeding with resistant donor lines. GER visual severity scoring and NIRS measurements were found to be reliable predictors for DON and ZON concentrations in grain. We observed that QTL for GER and DON are mostly specific to a few families or a limited number of materials, whereas QTL for DS are more commonly shared between families. The multi-parental QTL mapping approach is complementary to the classical bi-parental QTL mapping in that the latter has generally higher power to identify rare but large-effect QTL for traits such as GER and DON, whereas the former is superior in detecting common but small-effect QTL for traits such as DS. Composing the TS with materials more closely related to the prediction set and increasing the TS size generally resulted in higher prediction accuracy for MAS and GS, irrespective of the trait and statistical model.
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.
Improvements of the doubled haploid technology in maize
(2019) Molenaar, Willem; Melchinger, Albrecht E.
The in vivo doubled haploid (DH) technology in maize carries many advantages over traditional line development by recurrent selfing and has played an integral role in numerous breeding programs since the early 21st century. A bottleneck in the DH technology is still the success rate of chromosome doubling treatment, which has a strong influence on the costs of DH production. Currently, only a minority (~10%) of treated D0 haploid plants result in DH lines. Improvement in the chromosome doubling step of DH production would not only make DH lines cheaper, but could also change the optimum allocation of resources in hybrid breeding. In addition, the development of treatments using alternative doubling agents to colchicine, which is toxic to humans, would improve worker safety and simplify waste disposal issues for developing countries to benefit from the DH technology. Initiating such developments is the goal of this thesis. In a first step, we evaluated anti-mitotic herbicides with different modes of action as alternatives to colchicine for reducing the toxicity of chromosome-doubling treatment and for potentially increasing the success rates. In a series of experiments, we evaluated anti-mitotic herbicides with different modes of action in different concentrations and combinations. Based on the results of the initial experiments, we chose a specific concentration of amiprophos-methyl for evaluation in combination with varying concentrations of pronamide in a further experiment. This revealed the optimal concentration of pronamide in combination with the chosen concentration of amiprophos-methyl. However, this less-toxic treatment showed slightly lower success rates and slightly higher costs per DH line as compared to the standard colchicine treatment. In a second step after evaluating anti-mitotic herbicides for seedling treatment, we evaluated gaseous treatments using nitrous oxide (N2O), an anti-mitotic gas, in varying concentrations and combinations with air and pure oxygen. In two years of evaluation, we found an N2O treatment which had similar success rates as colchicine. The major benefit of such treatment is that this gas can simply be released into the atmosphere, eliminating the difficulty of proper chemical waste disposal, which is difficult to secure in developing countries. The only requirement is a treatment chamber, in contrast to the laboratory facilities required for handling colchicine. In a third step, we evaluated the potential of spontaneous chromosome doubling (SCD) as an alternative to chemical treatment-based chromosome doubling. Although previous studies found significant genetic variation and high heritability for SCD, a classical quantitative genetic analysis, elucidating the type of gene action governing this trait, and a selection experiment for improving SCD was missing in the literature. We found a predominance of additive genetic effects compared to epistatic effects, and a large selection gain after three cycles of recurrent selection for SCD to levels far beyond those reached by standard colchicine treatment. This indicates the great potential of SCD to improve the DH technology. The approximately ten-fold increase in spontaneous chromosome doubling rate (SDR) reached in our recurrent selection experiment marks a paradigm shift in the chromosome doubling step of DH production in maize. DH production efficiency can be greatly increased by the vast improvement in SDR, and production can be further simplified to enable even higher throughput. Instead of chromosome doubling treatment, which involves much handling of seedlings, haploid seeds from germplasm with a high innate ability to produce seed set without chemical treatment can be simply seeded in the DH nursery, eliminating the most costly production steps. Thus, this thesis has provided new opportunities to increase worker safety and reduce toxic waste in DH production, and further provided a proof of concept for genetic improvement of spontaneous chromosome doubling, which has great prospects for increasing the efficiency of DH production in maize.
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.
Optimizing community-based breeding for indigenous goat breeds in Ethiopia
(2016) Belete, Tatek Woldu; Valle Zárate, Anne
Ziegen sind für arme Kleinbauern in rauen und trockenen Regionen wesentliche Quellen für Fleisch, Milch, Dünger, Einkommen und soziale Sicherheit. Die Zahl der Ziegen in Äthiopien stieg im letzten Jahrzehnt deutlich schneller an als die Zahl der Schafe und Rinder. Trotz des derzeitig starken Anstiegs, ist der Beitrag der Ziegen zur nationalen Fleischproduktion sowie zu den Exporteinnahmen gering. Zusätzlich blieb die Schlachtausbeute der lokalen Ziegen im letzten Jahrzehnt unter dem ostafrikanischen und dem Weltdurchschnitt. Langsame Wachstumsraten der Ziegen, hohe Sterblichkeitsraten und geringe Verkaufsraten zählen zu den größten Herausforderungen für die kleinbäuerliche Ziegenhaltung in Äthiopien. Ein vielversprechender Ansatz, um einige dieser Einschränkungen zu überwinden, ist die Gestaltung eines nachhaltigen, dörflichen Zuchtprogramms (CBBP), das sowohl lokale Rassen als auch Merkmalspräferenzen der Landwirte und regionale Zuchtorganisationen berücksichtigt. Unverzichtbar für die Gestaltung und Umsetzung der CBBPs ist einerseits das Verständnis der vielfältigen Funktionen der Ziegen über die verschiedene Produktionssysteme hinweg und die Identifizierung der Zuchtzielmerkmale und deren relative ökonomische Bedeutung andererseits. Zur Bestimmung der Zuchtzielmerkmale und der Feststellung des jeweiligen ökonomischen Wertes wurden bislang Choice Experiments (CE) eingesetzt. Derzeit sind jedoch nur begrenzt Informationen, die ein umfassendes Verständnis der Merkmalspräferenzen aus Sicht der Produzenten und des Marktes bieten, verfügbar. Nachhaltige Programme für eine genetische Verbesserung fokussieren zusätzlich nicht nur auf die technische Umsetzbarkeit, sondern analysieren auch die organisatorischen Aspekte des Züchtungsschemas unter bestimmten Rahmenbedingungen. Das übergeordnete Ziel dieser Studie ist es, zur Gestaltung eines optimierten dörflichen Ziegenzuchtprogramms, welches die vielfältigen Funktionen der Ziegen, die Merkmalspräferenzen der Produzenten, die Marktanforderungen, die organisatorischen Rahmenbedingungen und die vielfältigen Ziegenproduktionssysteme berücksichtigt, beizutragen. Die spezifischen Ziele sind (i) die Bestimmung der Faktoren, die den Beitrag der Ziegenhaltung zum ökonomischen Erfolg und der Nahrungsmittelvielfalt des Haushaltes in drei Ziegenproduktionssystem beeinflussen, (ii) die Evaluierung der Ziegenzuchtziele und der ökonomischen Werte der Merkmale, basierend auf offenbarten und angegebenen Präferenzen und (iii) die Bestimmung der wichtigsten Interessensvertreter, organisatorischen Netzwerke und weiteren Organisationselementen und deren Einfluss auf die Einrichtung und das erfolgreiche Betreiben einer dörflichen Ziegenzüchtung. Die Studie wurde in den Bezirken Abergele, Konso und Meta Robi in Äthiopien durchgeführt. Diese repräsentieren aride agro-pastorale (AAP), semi-aride agro-pastorale (SAAP) und gemischte Ackerbau-Viehhaltungs-Systeme des Hochlands (HMCL). Die Interviews umfassten 180 Haushalte, die mittels teilstrukturierter Fragebögen durchgeführt wurden. Die Befragung zielte auf das Einkommen und die Kosten der bedeutendsten landwirtschaftlichen Aktivitäten sowie die Ernährungsvielfalt der Haushalte ab. Bruttogewinn (GM) und Nettogewinn (unter Berücksichtigung materieller und immaterieller Vorteile) wurden als Indikatoren für den ökonomischen Erfolg der Ziegenhaltung verwendet. Zur Analyse der Faktoren, die den ökonomischen Erfolg der Ziegenhaltung beeinflussen, wurde ein lineares gemischtes Modell verwendet. Eine ordinale Regression wurde zur Prognose der Effekte der sozioökonomischen Variablen auf die Ernährungsvielfalt der Haushalte benutzt. Mittels eines Choice Experiments, das 360 Ziegenhalter umfasste, wurden deren Merkmalspräferenzen über die verschiedenen Ziegenproduktionssysteme hinweg bestimmt. Um die offenbarten Präferenzen (RP) der Käufer für Ziegenmerkmale zu verstehen, wurden außerdem Marktdaten von 796 Ziegenverkäufen erfasst. Zusammenhänge zwischen Eigenschaften und Preise der Ziegen wurden durch hedonische Modellierungen bewertet, während ökonomische Werte der Merkmale inklusive des CE durch ein Conditional Logit (CL) Modell beurteilt wurden. Der Teilnutzwert eines Merkmals gibt die relative Wichtigkeit eines Merkmals an. Er wurde basierend auf den impliziten Preisen, die Landwirte für eine Verbesserung des Merkmals bereit waren zu bezahlen (WTP) berechnet. Die Ökonometrie-Software NLOGIT 4.0 wurde zur Analyse der CE und RP Daten verwendet. Die Organisation kleinbäuerlicher Ziegenzucht von dörflicher bis zu nationaler Ebene wurde auf Basis von sechs Fokusgruppen-Diskussionen mit 68 Ziegenhaltern, Befragungen wichtiger Akteure (aus zehn öffentlichen und sieben privaten Instituten) und der sozialen Netzwerkeanalyse (SNA) der Ziegenhaltung und Marketingstrukturen ermittelt. Die Daten aus den Befragungen wichtiger Akteure wurden mittels deskriptiver Statistik analysiert. Social Network Visualizer (SocNetV) wurde zur Visualisierung der sozialen Netzwerkstrukturen verwendet. Ziegenhalter die in einer rauen Region leben, repräsentiert durch das AAP System, hatten signifikant geringere Ziegenverkäufe als diejenigen in SAAP und HMCL Systemen. Die Wechselwirkung zwischen Herdengröße und Produktionssystem beeinflusste signifikant (P<0.001) den Nettogewinn der Ziegenhaltung. Die Steigerung des Nettogewinns durch die Haltung größerer Herden war im AAP System, aufgrund größerer materieller und immaterieller Vorteile der Ziegen in diesem System, höher. Im Gegensatz dazu hatten Ziegenhalter im HMCL System höhere Ziegenverkaufsraten und tendierten dazu Zicklein (< 1 Jahr) eher zu verkaufen als ausgewachsene Ziegen. Der Effekt der Herdengröße als Einflusswert für die Ernährungsvielfalt des Haushaltes war in keinem der untersuchten Produktionssystemen signifikant. Dennoch wurde eine signifikante, positive Korrelation zwischen dem Einkommen aus der Ziegenhaltung und der Ernährungsvielfalt in AAP Systemen festgestellt, die auf eine indirekte Rolle der Ziegenhaltung für die Ernährungssicherheit hinweist. Ergebnisse der offenbarten und angegebenen Präferenzstudien zeigten, dass Ziegenhalter in allen Produktionssystemen großen Nutzen von großen Körpergrößen der Ziegen ableiten und Käufer einheitlich höhere Preise für Ziegen mit höherem Körpergewicht bezahlten. Im AAP System wurden hohe ökonomische Werte für Anpassungsmerkmale wie Krankheitsresistenz sowohl für Böcke als auch für Zicken bestimmt. Ziegenzüchter in diesem System waren bereit, für Böcke mit hohem Krankheitsresistenzvermögen nahezu dreimal so viel zu bezahlen wie Züchter in SAAP und HMCL Systemen. Dieses Merkmal wurde jedoch in der Selektion von weiblichen Zuchtziegen im HMCL System nicht als maßgeblicher Faktor betrachtet. Ziegenhalter im HMCL System waren bereit für Zicken mit hoher Zwillingsrate mehr zu bezahlen als Ziegenhalter in den AAP und SAAP Systemen. Ergebnisse der Zuchtorganisationsanalyse zeigten, dass eigene und dörfliche Herden die Hauptquellen für die Ziegenzüchtung in allen Regionen sind. Im AAP System haben jedoch auch NGOs und Forschungszentren Zuchtziegen für die Ziegenhalter gestellt. Die ermittelten bäuerlichen Organisationen, die mit Ziegenhaltung und Marketing verknüpft sind, beinhalteten auch multifunktionale Genossenschaften sowie bäuerliche Entwicklungsgruppen und Netzwerke. Die multifunktionalen Genossenschaften im AAP System waren in mehr Marketingaktivitäten eingebunden als in den SAAP und HMCL Systemen. Wichtige Akteure wie Forschungsinstitute und NGOs fehlten im HMCL System. Die SNA zeigte, dass die Beratungsbeamten der Gebiete die höchsten Werte für Grad und Verbundenheit der Zentralität haben, was auf deren vertrauensvolle Beziehung mit den Ziegenhaltern und die beste Erreichbarkeit hindeuten. Die höheren materiellen und immateriellen Vorteile der Ziegen im AAP System verbunden mit höheren ökonomischen Werten, aufgrund der höheren Bewertung der Anpassungsmerkmale, weisen auf die Notwendigkeit der Einbeziehung von Überlebensmerkmalen zusätzlich zu den Leistungsmerkmalen hin für die Formulierung der Zuchtziele in rauen, trockenen Regionen. In den gemischten Pflanzenbau-Viehhaltungs-Systemen ist die Erzeugung von Bareinnahmen durch erhöhte Ziegenverkaufsraten die herausragende Priorität der Ziegenhalter und die Zwillingsrate der Ziegen hat einen hohen Stellenwert. In diesem System sollte die Verbesserung der Fortpflanzungsfähigkeit und die Steigerung der Anzahl der vermarktungsfähigen Ziegen anvisiert werden. Jedoch erschweren die geringe institutionelle Präsenz und die unwesentliche ökonomische Rolle der Ziegen in HMCL und SAAP Systemen die Umsetzung des CBBP wohingegen die aktive institutionelle Unterstützung und die besseren Vermarktungsmöglichkeiten in den AAP Systemen ein Ziegen CBBP vielversprechender macht. Vor allem Beratungsbeamte der Bezirke sollten aufgrund ihrer herausragenden Rolle in den sozialen Netzwerken eine Rolle als Wegbereiter und Verbindungsperson bei der Gründung und im Betreiben der CBBPs übernehmen.
Optimum schemes for hybrid maize breeding with doubled haploids
(2011) Wegenast, Thilo; Melchinger, Albrecht E.
In hybrid maize breeding, the doubled haploid technique is increasingly replacing conventional recurrent selfing for the development of new lines. In addition, novel statistical methods have become available as a result of enhanced computing facilities. This has opened up many avenues to develop more efficient breeding schemes and selection strategies for maximizing progress from selection. The overall aim of the present study was to compare the selection progress by employing different breeding schemes and selection strategies. Two breeding schemes were considered, each involving selection in two stages: (i) developing DH lines from S0 plants and evaluating their testcrosses in stage one and testcrosses of the promising DH lines in stage two (DHTC) and (ii) early testing for testcross performance of S1 families before production of DH lines from superior S1 families and then evaluating their testcrosses in the second stage (S1TC-DHTC). For both breeding schemes, we examined different selection strategies, in which variance components and budgets varied, the cross and family structure was considered or ignored, and best linear unbiased prediction (BLUP) of testcross performance was employed. The specific objectives were to (1) maximize through optimum allocation of test resources the progress from selection, using the selection gain (ΔG) or the probability to select superior genotypes (P(q)) as well as their standard deviations as criteria, (2) investigate the effect of parental selection, varying variance components and budgets on the optimum allocation of test resources for maximizing the progress from selection, (3) assess the optimum filial generation (S0 or S1) for DH production, (4) compare various selection strategies - sequential selection considering or ignoring the cross and family structure - for maximizing progress from selection, (5) examine the effect of producing a larger number of candidates within promising crosses and S1 families on the progress from selection, and (6) determine the effect of BLUP, where information from genetically related candidates is integrated in the selection criteria, on the progress from selection. For both breeding schemes, the best strategy was to select among all S1 families and/or DH lines ignoring the cross structure. Further, in breeding scheme S1TC-DHTC, the progress from selection increased with variable sizes of crosses and S1 families, i.e., larger numbers of DH lines devoted to superior crosses and S1 families. Parental cross selection strongly influenced the optimum allocation of test resources and, consequently, the selection gain ΔG in both breeding schemes. With an increasing correlation between the mean testcross performance of the parental lines and the mean testcross performance of their progenies, the superiority in progress from selection compared to randomly chosen parents increased markedly, whereas the optimum number of parental crosses decreased in favor of an increased number of test candidates within crosses. With BLUP, information from genetically related test candidates resulted in more precise estimates of their genotypic values and the progress from selection slightly increased for both optimization criteria ΔG and P(q), compared with conventional phenotypic selection. Analytical solutions to enable fast calculations of the optimum allocation of test resources were developed. This analytical approach superseded matrix inversions required for the solution of the mixed model equations. In breeding scheme S1TC-DHTC, the optimum allocation of test resources involved (1) 10 or more test locations at both stages, (2) 10 or fewer parental crosses each with 100 to 300 S1 families at the first stage, and (3) 500 or more DH lines within a low number of parental crosses and S1 families at the second stage. In breeding scheme DHTC, the optimum number of test candidates at the first stage was 5 to 10 times larger, whereas the number of test locations at the first stage and the number of DH lines at the second stage was strongly reduced compared with S1TC-DHTC. The possibility to reduce the number of parental crosses by selection among parental lines is of utmost importance for the optimization of the allocation of test resources and maximization of the progress from selection. Further, the optimum allocation of test resources is crucial to maximize the progress from selection under given economic and quantitative-genetic parameters. By using marker information and BLUP-based genomic selection, more efficient selection strategies could be developed for hybrid maize breeding.
Optimum strategies to implement genomic selection in hybrid breeding
(2022) Marulanda Martinez, Jose Joaquin; Melchinger, Albrecht E.
To satisfy the rising demand for more agricultural production, a boost in the annual expected selection gain (ΔGa) of traits such as grain yield and especially yield stability has to be rapidly achieved. Hybrid breeding has contributed to a notable increment in performance for numerous allogamous species and has been proposed as a way to match the increased demand for autogamous cereals such as rice, wheat, and barley. An additional tool to increase the rate of annual selection gain is genomic selection (GS), a method to assess the merit of an individual by simultaneously accounting for the effects associated with hundreds to thousands of DNA markers. Successful integration of GS and hybrid breeding should go beyond the study of GS prediction accuracy and focus on the design of breeding strategies, for which GS maximizes ΔGa and optimizes the allocation of resources. The main goal of this thesis was to examine strategies for optimum implementation of GS in hybrid breeding with emphasis on estimation set design to perform GS within biparental populations and on the optimization of hybrid breeding strategies through model calculations. One strategy, GSrapid, with moderate nursery selection, one stage of GS, and one stage of phenotypic selection, reached the greatest ΔGa for single trait selection regardless of the budget, costs, variance components, and accuracy of genomic prediction. GSrapid was also the most efficient strategy for the simultaneous improvement of two traits regardless of the correlation between traits, selection index chosen, and economic weights assigned to each trait. The success of this strategy relies principally on the reduction of breeding cycle length and marginally on the increase in selection intensity. Moving from traditional breeding strategies based on phenotypic selection to strategies using GS for single trait improvement in hybrid breeding could lead not only to increments in ΔGa but also to large savings in the budget. The implementation of nursery selection in breeding strategies boosted the importance of efficient systems for inbred generation accompanied by improvements in the methods of hybrid seed production for experimental tests. When it comes to multiple trait improvement, the choice between optimum and base selection indices had minor impact on the net merit. However, considerable differences for ΔGa of single traits were observed when applying optimum or base indices if the variance components of the traits to be improved differed. The role of the economic weights assigned to each trait was determinant and small variations in the weights led to a remarkable genetic loss in one of the traits. The optimum design of estimation sets to perform GS within biparental populations should be based on phenotypic data, rather than molecular marker data. This finding poses major challenges for GS-based strategies aiming to select the best new inbreds within second cycle breeding populations, as breeding cycle length might not be reduced. Then, the ES design to optimize GS within biparental populations would have a defined application on the exploitation of within-family variation by increasing selection intensity in biparental populations with the largest potential of producing high-performing inbreds. Based on the results of this thesis, future challenges for the optimum implementation of GS in hybrid breeding strategies include (i) reductions in breeding cycle length and increments in selection intensity by refinements of DH technology or implementation of speed breeding, (ii) improvements in the methods for hybrid seed production, facilitating the reallocation of resources to the production of more candidates tested during the breeding cycle, and (iii) precise estimation of economic weights, reflecting the importance of the traits for breeding programs and farmers, and maximizing long term ΔGa for the most relevant traits.
Pedigreeanalysen zur Beschreibung der populations- und quantitativgenetischen Situation von baden-württembergischen Lokalrinderrassen
(2014) Hartwig, Sonja; Bennewitz, Jörn
The challenge of a conservation breeding program is to solve a conflict of goals: genetic variability and genetic autonomy should be maintained, and on time a certain amount of breeding progress has to be realized to ensure the ability to compete. The aim of the present study was to analyse the situation concerning the targets mentioned above for traditional cattle breeds of Baden-Württemberg. Furthermore, methods for the consolidation and development of these breeds should be reconsidered. In chapter 1 the organisation of a breeding program for small cattle breeds is discussed. The challenge of such a program is the conservation of agrobiodiversity, culture and traditions and the progress of traditional local breeds. Number and extend of these breeds declined due to the increasing popularity of high-yielding breeds. Additionally, some of the local breeds are used in different branches of production compared to their original usage. Breeding programs have to be fitted. The establishment of individual adapted breeding methods is required for a sophisticated solution of the conflict mentioned above. Federal support is requested. Nowadays the implementation of genomic selection is not yet practicable for small breeds. But future opportunities should be analysed. The establishment of performance tests concerning breed specific product and efforts is demanded to improve these characteristics. In the following genetic variability of Vorderwald, Hinterwald and Limpurg cattle was examined. In chapter 2 for each breed two reference populations were defined that enable to observe the development over the years. Animals within the reference population comply with restrictions concerning racial origin and completeness of pedigree. Effective population size and the effective number of founders, and ancestors were estimated. The interpretation of the results was done with regard to the history of the breeds. The absolute population size of Vorderwald cattle is the biggest one. The number of Hinterwald cattle is intermediate; Limpurg cattle have the smallest population size. Whereas the management of Hinterwald cattle seemed to maintain genetic variability, the management of Vorderwald cattle was not that target-orientated. With an effective population size greater than 100 there is enough genetic variability within Vorderwald and Hinterwald. In contrast the values of Limpurg cattle are too low. Besides genetic variability, genetic autonomy and breeding progress are the targets of a conservation breeding program. Cross-breeding was carried out to mitigate the risk of inbreeding depression and to improve the performance of local breeds. However, breeding activities for local breeds were not as intensive and target oriented as for popular high yielding breeds. While the gap between the performance of high-yielding and local breeds increase, genetic autonomy of local breeds declined due to migrant influences. Chapter 3 examined the importance of migrant breed influences for the realization of breeding progress of beef traits of Vorderwald and Hinterwald cattle. The results show that there is a high amount of migrant contributions and their effects on performance are substantial for most traits. Breeding values adjusted for the effects of the migrant breeds showed little genetic trend for beef traits. The subject of chapter 4 is the development of milk yield and the associated migrant influences. Yield deviations for milk, fat, and protein content were analysed. Migrant contributions to Vorderwald cattle were high and even rose in the latest past. All the effects of foreign breeds were positive and in most cases highly significant. Most influential breed was Montbéliard. The influences of migrant breeds were substantial for the development of milk performance. However, the trend of milk yield traits for both breeds was positive even without foreign breeds’ influences. In comparison the number of analysed Hinterwald cows was small due to the reason that just a few Hinterwald husbandries take part at the official milk performance recording. Migrant breed contributions were moderate and nearly constant over the time. The most influential migrant breed was the Vorderwald cattle. The development of milk yield shows a flat trend. Influences of migrant breeds were low. The thesis ends with a general discussion.
Phenotypic and genomics-assisted breeding of soybean for Central Europe : from environmental adaptation to tofu traits
(2022) Kurasch, Alena; Würschum, Tobias
Soybean (Glycine max Merr.) is one of the major crops in the world providing an important source of protein and oil for food and feed; however it is still a minor crop in Central Europe. Soybean cultivation can play an important role in a more sustainable agricultural system by increasing local and regional protein production in Europe. The demand for locally produced soybean products is still growing in Europe. The key for a successful establishment of soybean cultivation in Europe is adaptation of soybean varieties to the Central European growing conditions. For the latitudinal adaptation to long-day conditions in Central to Northern Europe, an adapted early flowering and maturity time is of crucial importance for a profitable cultivation. The key traits flowering and maturity are quantitatively inherited and mainly affected by photoperiod responsiveness and temperature sensitivity. The most important loci for an early flowering and maturity are E1-E4 and the various allelic combinations condition soybean flowering and maturity time and therefore strongly contribute to the wide adaptability (Jiang et al., 2014; Tsubokura et al., 2014; M. Xu et al., 2013). Besides the main usage as protein source for animal feeding, soybean is also a very valuable source for human consumption. Tofu is enjoying ever greater popularity in Europe, as it is one of the best sources of plant protein with additional health benefits, rich in essential amino acids, beneficial lipids, vitamins, and minerals, as well as other bioactive compounds, such as isoflavones, soyasaponin, and others, (Lima et al., 2017; Zhang et al., 2018). Thus, plant breeding has to provide not only well-adapted varieties with good agronomic and quality properties, but also provide varieties well-suited to the further processing into soymilk and tofu. Therefore, a good knowledge about the breeding target, how to assess it and how it is inherited is crucial. The conducted studies covered a broad range of aspects relevant to improve a soybean breeding program. By combining environmental analysis, E-gene analysis, genomic approaches (QTL mapping and genomic prediction), and tofu phenotyping, breeder decisions become more accurate and targeted in the way of selection thereby increasing the genetic gain. In addition, combining the results of the different aspects helps to optimize the resources of a breeding program. Increasing the knowledge about the different aspects from environment to tofu QTL enables a breeder to be more precise and focused. But the more targeted and specific, the more complex a breeding program gets, which requires adequate tools to handle all the different information in a meaningful and efficient way to enable a quick and precise breeding decision.
Phenotypic and genotypic assessment of traits with relevance for hybrid breeding in European winter wheat
(2015) Langer, Simon Martin; Würschum, Tobias
Hybrid breeding in wheat has recently received increased interest, especially in Europe, and large public and private projects investigating hybrid wheat breeding have been launched. Hybrid breeding has been a great success story for allogamous crops and is seen as a promising approach to increase the yield potential in wheat. Wheat covers more of the world’s surface than any other food crop and is the second main staple crop for human consumption. It can be produced under widely varying conditions and is grown all around the globe, yet, yield gain has declined and is lagging behind the needs of the constantly growing human population. Future challenges in wheat breeding such as the establishment of hybrid varieties and the adaptation of breeding germplasm to increasing stresses caused by climatic changes also in Europe require knowledge-based improvements of relevant traits and phenotyping approaches suited for applied high-throughput plant breeding. A major limitation for the establishment and the production of hybrid wheat is the lack of a cost-efficient hybrid seed production system. This requires the generation of parental ideotypes which maximize the cross-fertilization capability. Male parents should have an extended time of flowering, extrude anthers and widely shed large amounts of viable pollen. Females need increased receptivity for male pollen by opening the glumes and extruding stigmatic hair. Furthermore, male plants should be taller than females and a synchronized timing of flowering between the two parents is also of utmost importance. Employing a set of European elite winter wheat lines, we developed and evaluated phenotyping methods for important floral and flowering traits with relevance for improved cross-pollination (Publication I). We observed high heritabilities for important traits such as ‘pollen mass’ (h2=0.72) and ‘anther extrusion’ (h2=0.91). In addition, genotypic variances were significant which warrants further breeding success. Positive correlations were found among important flowering and floral characteristics which enables the improvement of outcrossing by indirect selection. ‘Pollen mass’ for example, was associated with ‘anther extrusion’, ‘anther length’ and ‘plant height’. Our findings suggest the utility of the developed phenotyping approaches for applied plant breeding and the potential of the traits to assist in the design of the male ideotype for increased cross-fertilization. We investigated the genetic architecture of flowering time and plant height (Publication II and III). A panel of 410 European winter wheat varieties was genotyped by a genotyping-by-sequencing approach and in addition, analyzed for the effects of specific candidate genes. The major factor affecting flowering time was the photoperiod regulator Ppd-D1 (58.2% of explained genotypic variance) followed by Ppd-B1 copy number variation (3.2%). For plant height, the two candidate loci Rht-D1 (37.0%) and Rht-B1 (14.0%) had the largest effects on the trait but contrary to reports in the literature did not contribute to flowering time control. In addition, we identified several small effect QTL and epistatic QTL responsible for fine-adjustments of these two traits. Population structure and genetic relatedness in European elite wheat lines was assessed using different types of markers (Publication IV). Results for relatedness differed for the marker types but consistently showed the absence of a major population structure. Regarding the large wheat genome our results revealed that a high number of markers is necessary as there are regions with only low coverage. Concordantly, we were not able to identify the major flowering locus Ppd-D1 without targeted candidate gene analysis. Observations on the findings on population structure could be confirmed in Publication II and III and in addition, the geographical distribution of important flowering time and plant height genes displayed the historical development of wheat breeding in Europe. This information on genetic relatedness among lines can also be employed to assist the establishment of hybrid wheat.