Landessaatzuchtanstalt

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Appreciable genetic correlation between inbred lines and testcrosses facilitates breeding for resistance to Fusarium head blight in hybrid rye (Secale cereale)
(2021) Miedaner, Thomas; Rose, Marvin; Overbeck, Franziska; Koch, Silvia; Gruner, Paul; Eifler, Jakob
Hybrid breeding is based on selection of inbred lines in early generations. A sufficient genetic correlation between inbred lines and testcrosses is, however, the prerequisite for a higher selection gain in the hybrids. Therefore, we investigated this crucial parameter for Fusarium head blight (FHB) resistance on 60 inbred lines each of the heterotic groups Petkus and Carsten and their corresponding crosses with two testers each at four (inbred lines) or six (testcrosses) environments (location × year combinations). FHB severity measured as percentage of infected spikelets per plot was used as resistance trait, and a correction was made by using flowering time as covariate. Variances for genotype and genotype–environment interaction were high, and the heritability was estimated .84 and .74 for the line per se performance (Petkus and Carsten) and .71 and .78 for the general combining ability (GCA). For both inbred lines and testcrosses, negative correlations with plant height were found ranging from −.20 to −.51. FHB severity was considerably higher for the inbred lines than for the testcrosses. Genetic variance was lower for testcrosses, and dominance effects of the testers and heterosis may be key factors reducing the general infection level of three‐way hybrids. The effect of the tester (i.e., difference between testers) was very small and only significant for the Carsten group. The variance for specific combining ability (SCA) was very small, too. This, and high genetic correlations between line per se and GCA (r = .82 for Petkus and r = .72 for Carsten), does allow or even favour the selection based on line per se performance. Still, in the last generation before the official trials, testcrosses should also be tested for FHB resistance and mycotoxin contents to reliably improve food and feed quality in rye.
Multi‐parental QTL mapping of resistance to white spot of maize (Zea mays) in southern Brazil and relationship to QTLs of other foliar diseases
(2021) Kistner, María Belén; Galiano‐Carneiro, Ana Luísa; Kessel, Bettina; Presterl, Thomas; Miedaner, Thomas
Maize white spot (MWS) is one of the most important foliar diseases in Brazil causing significant yield losses. Breeding genotypes with MWS resistance is the most sustainable alternative for managing such losses; however, their genetic control is poorly understood. Our objectives were to identify genomic regions controlling MWS resistance and to explore the presence of common regions controlling resistance to MWS, grey leaf spot (GLS) and northern corn leaf blight (NCLB). We performed a multi‐parental QTL mapping for MWS and GLS resistance with a total of 474 testcrosses and phenotypic data collected in southern Brazil. Six QTLs for MWS resistance on bins 1.03, 1.04, 6.02, 8.05, 1.03, and 10.06 were detected. These findings were compared with previously reported QTLs for NCLB in the same populations, and a common QTL region (bin 8.05) controlling MWS and NCLB resistances was identified. Our findings contribute to a better understanding of MWS resistance by revealing three QTLs (bin 6.02, 1.03, and 10.06), to the best of our knowledge, not yet described in the literature, that are valuable for improving MWS resistance and one promising candidate region for multiple disease resistance.
Genetic dissection of phosphorus use efficiency in a maize association population under two P levels in the field
(2021) Li, Dongdong; Wang, Haoying; Wang, Meng; Li, Guoliang; Chen, Zhe; Leiser, Willmar L.; Weiß, Thea Mi; Lu, Xiaohuan; Wang, Ming; Chen, Shaojiang; Chen, Fanjun; Yuan, Lixing; Würschum, Tobias; Liu, Wenxin
Quantitative-genetic evaluation of resistances to five fungal diseases in a large triticale diversity panel (×Triticosecale)
(2022) Miedaner, Thomas; Flath, Kerstin; Starck, Norbert; Weißmann, Sigrid; Maurer, Hans Peter
The man-made cereal triticale was fully resistant to the biotrophic diseases powdery mildew, leaf rust, yellow rust, and stem rust from its introduction in Europe in the mid-1970s until about 1990. In the following years, new races that were able to infect at least some triticale genotypes developed in all four pathogen populations, and resistance breeding came into focus. Here, we analyzed 656 winter triticale cultivars from 12 countries for resistance to these biotrophic diseases and Fusarium head blight (FHB) at up to 8 location-year combinations (environments). FHB ratings were corrected for plant height and heading stage by comparing three statistical methods. Significant (p < 0.001) genetic variances were found for all resistances with moderate to high entry-mean heritabilities. All traits showed a normal distribution, with the exception of stem rust, where the ratings were skewed towards resistance. There were no substantial correlations among the five disease resistances (r = −0.04 to 0.26). However, several genotypes were detected with multi-disease resistance with a disease rating below average for all five diseases simultaneously. In future, such genotypes must be selected primarily to cope with future challenges of less pesticide use and global climate change.
Genome-wide association mapping of prostrate/erect growth habit in winter durum wheat
(2020) Marone, Daniela; Rodriguez, Monica; Saia, Sergio; Papa, Roberto; Rau, Domenico; Pecorella, Ivano; Laidò, Giovanni; Pecchioni, Nicola; Lafferty, Julia; Rapp, Matthias; Longin, Friedrich H.; De Vita, Pasquale
By selecting for prostrate growth habit of the juvenile phase of the cycle, durum wheat cultivars could be developed with improved competitive ability against weeds, and better soil coverage to reduce the soil water lost by evaporation. A panel of 184 durum wheat (Triticum turgidum subsp. durum) genotypes, previously genotyped with DArT-seq markers, was used to perform association mapping analysis of prostrate/erect growth habit trait and to identify candidate genes. Phenotypic data of plant growth habit were recorded during three consecutive growing seasons (2014–2016), two different growth conditions (field trial and greenhouse) and two sowing periods (autumn and spring). Genome-wide association study revealed significant marker-trait associations, twelve of which were specific for a single environment/year, 4 consistent in two environments, and two MTAs for the LSmeans were identified across all environments, on chromosomes 2B and 5A. The co-localization of some MTAs identified in this study with known vernalization and photoperiod genes demonstrated that the sensitivity to vernalization and photoperiod response are actually not only key components of spring/winter growth habit, but they play also an important role in defining the magnitude of the tiller angle during the tillering stage. Many zinc-finger transcription factors, such as C2H2 or CCCH-domain zinc finger proteins, known to be involved in plant growth habit and in leaf angle regulation were found as among the most likely candidate genes. The highest numbers of candidate genes putatively related to the trait were found on chromosomes 3A, 4B, 5A and 6A. Moreover, a bioinformatic approach has been considered to search for functional ortholog genes in wheat by using the sequence of rice and barley tiller angle-related genes. The information generated could be used to improve the understanding of the mechanisms that regulate the prostrate/erect growth habit in wheat and the adaptive potential of durum wheat under resource-limited environmental conditions.
Genetic architecture underlying the expression of eight α-amylase trypsin inhibitors
(2021) El Hassouni, Khaoula; Sielaff, Malte; Curella, Valentina; Neerukonda, Manjusha; Leiser, Willmar; Würschum, Tobias; Schuppan, Detlef; Tenzer, Stefan; Longin, C. Friedrich H.
Amylase trypsin inhibitors (ATIs) are important allergens in baker’s asthma and suspected triggers of non-celiac wheat sensitivity (NCWS) inducing intestinal and extra-intestinal inflammation. As studies on the expression and genetic architecture of ATI proteins in wheat are lacking, we evaluated 149 European old and modern bread wheat cultivars grown at three different field locations for their content of eight ATI proteins. Large differences in the content and composition of ATIs in the different cultivars were identified ranging from 3.76 pmol for ATI CM2 to 80.4 pmol for ATI 0.19, with up to 2.5-fold variation in CM-type and up to sixfold variation in mono/dimeric ATIs. Generally, heritability estimates were low except for ATI 0.28 and ATI CM2. ATI protein content showed a low correlation with quality traits commonly analyzed in wheat breeding. Similarly, no trends were found regarding ATI content in wheat cultivars originating from numerous countries and decades of breeding history. Genome-wide association mapping revealed a complex genetic architecture built of many small, few medium and two major quantitative trait loci (QTL). The major QTL were located on chromosomes 3B for ATI 0.19-like and 6B for ATI 0.28, explaining 70.6 and 68.7% of the genotypic variance, respectively. Within close physical proximity to the medium and major QTL, we identified eight potential candidate genes on the wheat reference genome encoding structurally related lipid transfer proteins. Consequently, selection and breeding of wheat cultivars with low ATI protein amounts appear difficult requiring other strategies to reduce ATI content in wheat products.
Long-term breeding progress of yield, yield-related, and disease resistance traits in five cereal crops of German variety trials
(2021) Laidig, Friedrich; Feike, T.; Klocke, B.; Macholdt, J.; Miedaner, Thomas; Rentel, D.; Piepho, Hans-Peter
Plant breeding and improved crop management generated considerable progress in cereal performance over the last decades. Climate change, as well as the political and social demand for more environmentally friendly production, require ongoing breeding progress. This study quantified long-term trends for breeding progress and ageing effects of yield, yield-related traits, and disease resistance traits from German variety trials for five cereal crops with a broad spectrum of genotypes. The varieties were grown over a wide range of environmental conditions during 1988–2019 under two intensity levels, without (I1) and with (I2) fungicides and growth regulators. Breeding progress regarding yield increase was the highest in winter barley followed by winter rye hybrid and the lowest in winter rye population varieties. Yield gaps between I2 and I1 widened for barleys, while they shrank for the other crops. A notable decrease in stem stability became apparent in I1 in most crops, while for diseases generally a decrasing susceptibility was found, especially for mildew, brown rust, scald, and dwarf leaf rust. The reduction in disease susceptibility in I2 (treated) was considerably higher than in I1. Our results revealed that yield performance and disease resistance of varieties were subject to considerable ageing effects, reducing yield and increasing disease susceptibility. Nevertheless, we quantified notable achievements in breeding progress for most disease resistances. This study indicated an urgent and continues need for new improved varieties, not only to combat ageing effects and generate higher yield potential, but also to offset future reduction in plant protection intensity.
Optimum breeding strategies using genomic and phenotypic selection for the simultaneous improvement of two traits
(2021) Marulanda, Jose J.; Mi, Xuefei; Utz, H. Friedrich; Melchinger, Albrecht E.; Würschum, Tobias; Longin, C. Friedrich H.
Selection indices using genomic information have been proposed in crop-specific scenarios. Routine use of genomic selection (GS) for simultaneous improvement of multiple traits requires information about the impact of the available economic and logistic resources and genetic properties (variances, trait correlations, and prediction accuracies) of the breeding population on the expected selection gain. We extended the R package “selectiongain” from single trait to index selection to optimize and compare breeding strategies for simultaneous improvement of two traits. We focused on the expected annual selection gain (ΔGa) for traits differing in their genetic correlation, economic weights, variance components, and prediction accuracies of GS. For all scenarios considered, breeding strategy GSrapid (one-stage GS followed by one-stage phenotypic selection) achieved higher ΔGa than classical two-stage phenotypic selection, regardless of the index chosen to combine the two traits and the prediction accuracy of GS. The Smith–Hazel or base index delivered higher ΔGa for net merit and individual traits compared to selection by independent culling levels, whereas the restricted index led to lower ΔGa in net merit and divergent results for selection gain of individual traits. The differences among the indices depended strongly on the correlation of traits, their variance components, and economic weights, underpinning the importance of choosing the selection indices according to the goal of the breeding program. We demonstrate our theoretical derivations and extensions of the R package “selectiongain” with an example from hybrid wheat by designing indices to simultaneously improve grain yield and grain protein content or sedimentation volume.
Can we abandon phosphorus starter fertilizer in maize? Results from a diverse panel of elite and doubled haploid landrace lines of maize (Zea mays L.)
(2022) Roller, Sandra; Weiß, Thea M.; Li, Dongdong; Liu, Wenxin; Schipprack, Wolfgang; Melchinger, Albrecht E.; Hahn, Volker; Leiser, Willmar L.; Würschum, Tobias
The importance of phosphorus (P) in agriculture contrasts with the negative environmental impact and the limited resources worldwide. Reducing P fertilizer application by utilizing more efficient genotypes is a promising way to address these issues. To approach this, a large panel of maize (Zea mays L.) comprising each 100 Flint and Dent elite lines and 199 doubled haploid lines from six landraces was assessed in multi-environment field trials with and without the application of P starter fertilizer. The treatment comparison showed that omitting the starter fertilizer can significantly affect traits in early plant development but had no effect on grain yield. Young maize plants provided with additional P showed an increased biomass, faster growth and superior vigor, which, however, was only the case under environmental conditions considered stressful for maize cultivation. Importantly, though the genotype-by-treatment interaction variance was comparably small, there is genotypic variation for this response that can be utilized in breeding. The comparison of elite and doubled haploid landrace lines revealed a superior agronomic performance of elite material but also potentially valuable variation for early traits in the landrace doubled haploid lines. In conclusion, our results illustrate that breeding for P efficient maize cultivars is possible towards a reduction of P fertilizer in a more sustainable agriculture.
The performance of phenomic selection depends on the genetic architecture of the target trait
(2021) Zhu, Xintian; Maurer, Hans Peter; Jenz, Mario; Hahn, Volker; Ruckelshausen, Arno; Leiser, Willmar L.; Würschum, Tobias
Genomic selection is a powerful tool to assist breeding of complex traits, but a limitation is the costs required for genotyping. Recently, phenomic selection has been suggested, which uses spectral data instead of molecular markers as predictors. It was shown to be competitive with genomic prediction, as it achieved predictive abilities as high or even higher than its genomic counterpart. The objective of this study was to evaluate the performance of phenomic prediction for triticale and the dependency of the predictive ability on the genetic architecture of the target trait. We found that for traits with a complex genetic architecture, like grain yield, phenomic prediction with NIRS data as predictors achieved high predictive abilities and performed better than genomic prediction. By contrast, for mono- or oligogenic traits, for example, yellow rust, marker-based approaches achieved high predictive abilities, while those of phenomic prediction were very low. Compared with molecular markers, the predictive ability obtained using NIRS data was more robust to varying degrees of genetic relatedness between the training and prediction set. Moreover, for grain yield, smaller training sets were required to achieve a similar predictive ability for phenomic prediction than for genomic prediction. In addition, our results illustrate the potential of using field-based spectral data for phenomic prediction. Overall, our result confirmed phenomic prediction as an efficient approach to improve the selection gain for complex traits in plant breeding.
Do we need to breed for regional adaptation in soybean? - Evaluation of genotype-by-location interaction and trait stability of soybean in Germany
(2023) Döttinger, Cleo A.; Hahn, Volker; Leiser, Willmar L.; Würschum, Tobias
Soybean is a crop in high demand, in particular as a crucial source of plant protein. As a short-day plant, soybean is sensitive to the latitude of the growing site. Consequently, varieties that are well adapted to higher latitudes are required to expand the cultivation. In this study, we employed 50 soybean genotypes to perform a multi-location trial at seven locations across Germany in 2021. Two environmental target regions were determined following the latitude of the locations. Adaptation and trait stability of seed yield and protein content across all locations were evaluated using Genotype plus Genotype-by-Environment (GGE) biplots and Shukla’s stability variance. We found a moderate level of crossing-over type genotype-by-location interaction across all locations. Within the environmental target regions, the genotype-by-location interaction could be minimised. Despite the positive correlation (R = 0.59) of seed yield between the environmental target regions and the same best-performing genotype, the genotype rankings differed in part substantially. In conclusion, we found that soybean can be grown at a wide range of latitudes across Germany. However, the performance of genotypes differed between the northern and southern locations, with an 18.8% higher mean yield in the south. This in combination with the observed rank changes of high-performing genotypes between both environmental target regions suggests that selection targeted towards environments in northern Germany could improve soybean breeding for those higher latitude regions.
The antioxidant potential of various wheat crusts correlates with AGE content independently of acrylamide
(2023) Wächter, Kristin; Longin, Carl Friedrich H.; Winterhalter, Patrick R.; Bertsche, Ute; Szabó, Gábor; Simm, Andreas
Epidemiological studies have indicated that the consumption of whole-grain products is associated with a reduced risk of cardiovascular diseases, type II diabetes, and cancer. In the case of bread, high amounts of antioxidants and advanced glycation end products (AGEs) are formed during baking by the Maillard reaction in the bread crust; however, the formation of potentially harmful compounds such as acrylamide also occurs. This study investigated the antioxidant responses of different soluble extracts from whole-grain wheat bread crust extracts (WBCEs) in the context of the asparagine, AGE, and acrylamide content. For that, we analyzed nine bread wheat cultivars grown at three different locations in Germany (Hohenheim, Eckartsweier, and Oberer Lindenhof). We determined the asparagine content in the flour of the 27 wheat cultivars and the acrylamide content in the crust, and measured the antioxidant potential using the induced expression of the antioxidant genes GCLM and HMOX1 in HeLa cells. Our study uncovered, for the first time, that the wheat crust’s antioxidant potential correlates with the AGE content, but not with the acrylamide content. Mass spectrometric analyses of WBCEs for identifying AGE-modified proteins relevant to the antioxidant potential were unsuccessful. However, we did identify the wheat cultivars with a high antioxidant potential while forming less acrylamide, such as Glaucus and Lear. Our findings indicate that the security of BCEs with antioxidative and cardioprotective potential can be improved by choosing the right wheat variety.
Generation of high oleic acid sunflower lines using gamma radiation mutagenesis and high-throughput fatty acid profiling
(2023) Rozhon, Wilfried; Ramirez, Veronica E.; Wieckhorst, Silke; Hahn, Volker; Poppenberger, Brigitte
Sunflower (Helianthus annuus L.) is the second most important oil seed crop in Europe. The seeds are used as confection seeds and, more importantly, to generate an edible vegetable oil, which in normal varieties is rich in the polyunsaturated fatty acid linoleic acid. Linoleic acid is biosynthesized from oleic acid through activity of the oleate desaturase FATTY ACID DESATURASE 2 (FAD2), which in seeds is encoded by FAD2-1, a gene that’s present in single copy in sunflowers. Defective FAD2-1 expression enriches oleic acid, yielding the high oleic (HO) acid trait, which is of great interest in oil seed crops, since HO oil bears benefits for both food and non-food applications. Chemical mutagenesis has previously been used to generate sunflower mutants with reduced FAD2-1 expression and here it was aimed to produce further genetic material in which FAD2-1 activity is lost and the HO trait is stably expressed. For this purpose, a sunflower mutant population was created using gamma irradiation and screened for fad2-1 mutants with a newly developed HPLC-based fatty-acid profiling system that’s suitable for high-throughput analyses. With this approach fad2-1 knock-out mutants could be isolated, which stably hyper-accumulate oleic acid in concentrations of 85-90% of the total fatty acid pool. The genetic nature of these new sunflower lines was characterized and will facilitate marker development, for the rapid introgression of the trait into elite sunflower breeding material.
The importance of Fusarium head blight resistance in the cereal breeding industry: Case studies from Germany and Austria
(2023) Miedaner, Thomas; Flamm, Clemens; Oberforster, Michael
Fusarium head blight (FHB) resistance in wheat and triticale has a high priority in the European Union because of the strict guidelines for the major mycotoxins deoxynivalenol (DON) and zearalenone (ZON) and the admission policy of the regulatory authorities. Potentially 70% of the arable land in Germany and about 60% in Austria can be affected by Fusarium. Although epidemics occur only in some years and/or some regions, DON and ZON are detected every year in varying amounts in wheat, rye and maize. Despite a high significance of FHB resistance in breeding companies, as validated by a recent survey, breeding progress in wheat is basically absent for FHB resistance in both countries. The main reasons are the complex inheritance of FHB resistance and the high proportions of the dwarfing allele Rht‐D1b in high‐yielding varieties promoting susceptibility. Despite this, some varieties with high FHB resistance (score 2–3 on the 1–9 scale) have been released that account, however, only for 11% and 18% of the multiplication area in Germany and Austria, respectively. For triticale, an official testing system for FHB resistance in terms of DON content exists in Germany and Austria, but not for the other cereals. Susceptibility to maize ear rot has been described in Austria, but not in Germany. Additionally, a testing system for stalk rot resistance in both countries should be established.
Spectroscopy‐based prediction of 73 wheat quality parameters and insights for practical applications
(2023) Nagel‐Held, Johannes; El Hassouni, Khaoula; Longin, Friedrich; Hitzmann, Bernd
Background and Objectives: Quality assessment of bread wheat is time-consuming and requires the determination of many complex characteristics. Because of its simplicity, protein content prediction using near-infrared spectroscopy (NIRS) serves as the primary quality attribute in wheat trade. To enable the prediction of more complex traits, information from Raman and fluorescence spectra is added to the NIR spectra of whole grain and extracted flour. Model robustness is assessed by predictions across cultivars, locations, and years. The prediction error is corrected for the measurement error of the reference methods. Findings: Successful prediction, robustness testing, and measurement error correction were achieved for several parameters. Predicting loaf volume yielded a corrected prediction error RMSECV of 27.5 mL/100 g flour and an R² of 0.86. However, model robustness was limited due to data distribution, environmental factors, and temporal influences. Conclusions: The proposed method was proven to be suitable for applications in the wheat value chain. Furthermore, the study provides valuable insights for practical implementations. Significance and Novelty With up to 1200 wheat samples, this is the largest study on predicting complex characteristics comprising agronomic traits; dough rheological parameters measured by Extensograph, micro-doughLAB, and GlutoPeak; baking trial parameters like loaf volume; and specific ingredients, such as grain protein content, sugars, and minerals.
Improving host resistance to Fusarium head blight in wheat (Triticum aestivum L.) and Gibberella ear rot in maize (Zea mays L.)
(2023) Akohoue, Félicien; Miedaner, Thomas
Fusarium head blight (FHB) in wheat and Fusarium (FER) and Gibberella ear rot (GER) in maize are major cereal diseases which reduce yield and contaminate kernels with several mycotoxins. In Europe, these diseases contribute to significant yield gaps and high mycotoxin risks across countries. However, existing management strategies related to agronomic practices are not fully effective, with some of them being cost-prohibitive. Enhancing host plant resistance is additionally required for managing the diseases more effectively and sustainably. Unfortunately, breeding for FHB resistance is challenged by complex interactions with morphological traits and the quantitative nature of the trait. In maize, available genetic resources have not been fully exploited to improve GER resistance in elite materials. In this work, we elucidated the complex interactions between FHB resistance and morphological traits, like plant height (PH) and anther retention (AR) in wheat. The effect of reduced height (Rht) gene Rht24 on AR and the contribution of genomic background (GB) to FHB resistance in semi-dwarf genotypes were also assessed. GB refers to all genomic loci, except major Rht genes, that affect the traits. To achieve this, 401 winter wheat cultivars were evaluated across five environments (location × year combination). All cultivars were genotyped using Illumina 25 K Infinium single-nucleotide polymorphism array. We performed correlation and path coefficient analysis, and combined single and multi-trait genome-wide association studies (GWAS). Our findings revealed significant genotypic correlations and path effects between FHB severity with PH and AR, which were controlled by several pleiotropic loci. FHB severity and PH shared both negatively and positively acting pleiotropic loci, while only positively acting pleiotropic loci were detected between FHB severity and AR. Rht-D1 is a major pleiotropic gene which exerted a negative effect on FHB resistance. These pleiotropic loci contribute to our understanding of the complex genetic basis of FHB resistance, and their exploitation can help to simultaneously select for FHB resistance with PH and AR. Contrary to Rht-D1b, Rht24b had no negative effect on FHB resistance and AR. This exhibits Rht24 as an important FHB-neutral Rht gene which can be integrated into breeding programs. Genomic estimated breeding values (GEBV) were calculated for each cultivar to assess GB. We observed highly negative GEBV for FHB severity within resistant wheat cultivars. Susceptible cultivars exhibited positive GEBV. Genomic prediction has a great potential and can be exploited by selecting for semi-dwarf winter wheat genotypes with higher FHB resistance due to their genomic background resistance. To tackle maize ear rot diseases, refined and stable quantitative trait loci (QTL) harboring candidate genes conferring resistances to FER and GER were identified. The effectiveness of introgression of two European flint landraces, namely “Kemater Gelb Landmais” (KE) and “Petkuser Ferdinand Rot” (PE) was evaluated. The prediction accuracy of using line performance as a predictor of hybrid performance for GER resistance was also evaluated within the two landraces. We applied a meta-QTL (MQTL) analysis based on 15 diverse SNP-based QTL mapping studies and performed gene expression analysis using published RNA-seq data on GER resistance. In total, 40 MQTL were identified, of which 14 most refined MQTL harbored promising candidate genes for use in breeding programs for improving FER and GER resistances. 28 MQTL were common to both FER and GER, with most of them being shared between silk (channel) and kernel resistances. This highlights the co-inheritance of FER and GER resistances as well as types of active resistance. Resistance genes can be transferred into elite cultivars by integrating refined MQTL into genomics-assisted breeding strategies. Afterwards, four GER resistant doubled haploid (DH) lines from both KE and PE landraces were crossed with two susceptible elite lines to generate six bi-parental populations with a total of 534 DH lines which were evaluated for GER resistance. GER severity within the six landrace-derived populations were reduced by 39−61% compared to the susceptible elite lines. Moderate to high genetic advance was observed within each population, and the use of KE landrace as a donor was generally more effective than PE landrace. This shows promise in enhancing resistance to GER in elite materials using the European flint landraces as donors. Furthermore, per se performance of 76 DH lines from both landraces was used to predict GER resistance of their corresponding testcrosses (TC). Moderate phenotypic and genomic prediction accuracy between TC and line per se performance was found for GER resistance. This implies that pre-selecting lines for GER resistance is feasible; however, TC should be additionally tested on a later selection stage to aim for GER-resistant hybrid cultivars.
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.
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.
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.
Molecular and phenotypic diversity in populations of Fusarium culmorum on cereal hosts
(2022) Castiblanco Vargas, Eveline Valheria; Miedaner, Thomas
Fusarium head blight is one of the most devastating diseases of cereals globally and responsible for large harvest losses, not only due to the reduction in productivity but also due to the contamination of the grain with mycotoxins. The major causal agent worldwide is Fusarium graminearum; in Europe also other Fusarium species, among them Fusarium culmorum (FC) play an important role. The interaction between Fusarium species and cereals has been categorized as quantitative according to previous phenotypic and genetic observations. We studied the molecular and phenotypic diversity of natural populations of FC and how they interact with four cereals (bread wheat, durum wheat, triticale, rye) as host. Specifically, we sought (i) to understand the interaction between host and isolate, and between isolate and environment using the variance partition approach offered by mixed models applied to analyze multi-environmental studies; (ii) to identify or validate the association of Fusarium genes previously assigned as candidates using field aggressiveness and deoxynivalenol (DON) production; and (iii) to compare the application and results of the candidate gene association mapping approach applied to the same population of FC isolates but with different phenotypic data obtained from inoculation in different hosts-bread wheat and rye. Phenotyping was based on multi-environmental field experiments where each plot of the host plant was artificially inoculated with spores of the respective isolate in accordance with the experimental design. Aggressiveness was visually quantified as the percentage of spikelets with symptoms per plot and was repeatedly evaluated over time. The content of the mycotoxin deoxynivalenol (DON) in the harvested grain was evaluated by double enzyme linked immunosorbent assays (ELISA). Genes previously reported in the literature as related to aggressiveness were selected for sequencing. Using the available F. graminearum genome sequence, specific primers were constructed to amplify and sequence the most variable regions of the respective genes. The partitioning of the phenotypic variance using mixed models, for a subpopulation of 38 FC isolates in four cereal hosts, allowed to disaggregate the magnitude of the genotypic and environmental variance, and the environmental variance in turn into its different components. The genotypic variance was significant, but was exceeded by the magnitude of the environmental variance and its interactions with genotype, showing that the role of plasticity in the pathosystem of Fusarium culmorum and its cereal hosts is highly important. In contrast, the variance associated with the host factor and the interactions with host were not significant, confirmed by high values of genetic correlation amogn host. This result supports the categorization of the cereal/Fusarium culmorum interaction as unspecific and quantitatively inherited also from the view of the pathogen. For the present study, plasticity was understood as the changes in the phenotype of the pathogen that could be attributed to changes induced by the environment. Our data revealed the year as factor with the highest influence on plasticity, meaning that the isolates with high performance values under humid conditions did not exhibit the same high values under dry conditions. Because the environmental conditions are erratic between the years, the lack of a constant selection pressure in the same direction reduces the probability of achieving a speciation event per environment. The phenotypic data of the DON content in harvested grain showed a high correlation with the aggressiveness data. An association mapping study with 17 candidate genes for aggressiveness using a population of 100 isolates of FC inoculated on bread wheat revealed the significant association of the HOG1 gene, explaining 10.29% of the genetic variance of aggressiveness and 6.05% of the genetic variance corresponding to the accumulation of DON in mature grain. HOG1 is a kinase-like protein involved in the communication within the oxidative metabolism of the fungus. In a similar study using the same population of FC isolates and the same candidate genes but rye as host, the gene CUT showed a significant association with aggressiveness, explaining 16.05% of the genetic variance. The CUT gene encodes a cutinase protein, belonging to the secretome and involved in the process of unleashing the membranes and cuticles of the host plant. Taken together, our results suggest that i) field trials of breeding for resistance to FC in cereals should be carried out in several years to properly account for the genotype-by-year interaction; ii) despite the fact that molecular communication may present some type of host specificity the high plasticity guarantees that the effects on the phenotype are very similar among the cereal hosts; and iii) the high genetic correlation of aggressiveness for different cereals invites to involve non-cereal crops in the rotation plans focused on Fusarium disease management.

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