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Haplotype blocks might carry additional information compared to single SNPs and have therefore been suggested for use as independent variables in genomic prediction. Studies in different species resulted in more accurate predictions than with single SNPs in some traits but not in others. In addition, it remains unclear how the blocks should be built to obtain the greatest prediction accuracies. Our objective was to compare the results of genomic prediction with different types of haplotype blocks to prediction with single SNPs in 11 traits in winter wheat. We built haplotype blocks from marker data from 361 winter wheat lines based on linkage disequilibrium, fixed SNP numbers, fixed lengths in cM and with the R package HaploBlocker. We used these blocks together with data from singleyear field trials in a cross-validation study for predictions with RR-BLUP, an alternative method (RMLA) that allows for heterogeneous marker variances, and GBLUP performed with the software GVCHAP. The greatest prediction accuracies for resistance scores for B. graminis, P. triticina, and F. graminearum were obtained with LD-based haplotype blocks while blocks with fixed marker numbers and fixed lengths in cM resulted in the greatest prediction accuracies for plant height. Prediction accuracies of haplotype blocks built with HaploBlocker were greater than those of the other methods for protein concentration and resistances scores for S. tritici, B. graminis, and P. striiformis. We hypothesize that the trait-dependence is caused by properties of the haplotype blocks that have overlapping and contrasting effects on the prediction accuracy. While they might be able to capture local epistatic effects and to detect ancestral relationships better than single SNPs, prediction accuracy might be reduced by unfavorable characteristics of the design matrices in the models that are due to their multi-allelic nature.

Improved wheat varieties have ameliorated our food production. Intensive cropping systems, as in Germany, achieve very high grain yields and thus contribute greatly to global food security. As diseases, especially fungal pathogens, pose major threats in winter wheat production, disease management is crucial to uphold high production levels and to avoid economic losses. Yet, the economic value of breeding varieties with increased resistance to fungal pathogens has not been analyzed with comprehensive data. Our analysis fills this gap by quantifying the economic effects of 50 years of resistance breeding for winter wheat production in Germany. Based on field trials and agronomic production data, we analyze how resistances have influenced the economic profitability of the crops. Thereby, we can isolate the pure breeding-induced effects of increased resistance to fungal pathogens, which cause leaf and stripe rust, powdery mildew, and Fusarium head blight. We calculated the gross margins of 176 varieties according to nitrogen and fungicide applications in field trials. Regression models show that resistance breeding had a strong positive and statistically significant effect on the gross margins of the varieties. In comparison, the specific meta-environment of the season had a larger effect, while the effect of high nitrogen as well as fungicide treatments was lower. The gross margin increased over time along with higher resistances. Simultaneously, the difference in gross margins between the fungicide-treated and untreated variants decreased, indicating an increased contribution of resistances to yield stability. Resistances have increased gross margins greatly, as the health levels of varieties remain high without the need for fungicide applications and thus production costs can be saved. We conclude that resistance breeding has increased the economic profitability and sustainability of crop production due to a reduction in the costs for fungicides. In fields of farmers, these positive effects of resistance breeding can be fully realized by an optimal variety choice and a variety- and situation-specific disease management. Such an agronomic practice would not only further improve winter wheat gross margins but also mitigate some of the pressures on agricultural productions, such as reduced disease management options and adverse climate change impacts.

Climate change impacts imply that the stabilization and improvement of agricultural production systems using technological innovations has become vital. Improvements in plant breeding are integral to such innovations. In the context of German crop breeding programs, the economic impact of exchanging genetic material has yet to be determined. To this end, we analyze in this impact assessment the economic effects on German winter wheat production that are attributable to exchanging parental material amongst breeders in the breeding process. This exchange is supported by the breeders’ exemption, which is an integral part of the German plant variety protection legislation. It ensures that breeders can freely use licensed varieties created by other breeders for their own breeding activities and aims to speed up the development of improved varieties. For our analysis, we created a unique data set that combines variety-specific grain yield, adoption, and pedigree information of 133 winter wheat varieties. We determined the parental pedigree of each variety to see if a variety was created by interbreeding varieties that are internal or external to its specific breeder. Our study is the first that analyzes the economic impact of exchanging genetic material in German breeding programs. We found that more than 90 % of the tested varieties were bred with exchanged parental material, whereby the majority had two external parents. Also, these varieties were planted on an 8.5 times larger area than the varieties that were bred with two internal parents. Due to lower adoption, these only contributed 11 % to the overall winter wheat production in Germany, even though they yielded more. We used an economic surplus model to measure the benefits of exchanging parental breeding material on German winter wheat production. This resulted in an overall estimated economic surplus of 19.2 to 22.0 billion EUR from production year 1972 to 2018. This implies tremendous returns to using the breeder’s exemption, which, from an economic perspective, is almost cost-free for the breeder. We conclude that the exchange of breeding material contributes to improving Germany’s agricultural production and fosters the development of climate-resilient production systems and global food security.

This is the experimental data set of Voss-Fels, et. al. (2019. Nature Plants). The first table (NP2019_MainExperiment_adjMeans.csv) presents the adjusted mean trait data of the full panel of 191 elite winter wheat cultivars in the main experiment. Data for each trait were considered independently for each of three cropping intensities. High, medium and low intensities represent HiN/HiF, HiN/NoF and LoN/NoF, respectively. Details are described in the supplementary Figure 2.The second table (NP2019_ValidationExperiment_adjMeans.csv) presents the adjusted mean yield of 52 elite winter wheat cultivars in the validation experiment., Contact: Dr. Tsu-Wei Chen (ORCID: 0000-0001-6698-563X), Leibniz Universität Hannover.

Nitrogen is essential for plant growth, and N fertilization allows farmers to obtain high yields and produce sufficient agricultural commodities. On the other hand, nitrogen losses potentially cause adverse effects to ecosystems and to human health. Increasing nitrogen use efficiency is vital to solve the conflict between productivity, to secure the demand of a growing world population, and the protection of the environment. To ensure this, genetic improvement is considered to be a paramount aspect toward ecofriendly crop production. Winter oilseed rape (Brassica napus L.) is the second most important oilseed crop in the world and is cultivated in many regions across the temperate zones. To our knowledge, this study reports the most comprehensive field-based data generated to date for an empirical evaluation of genetic improvement in winter oilseed rape varieties under two divergent nitrogen fertilization levels. A collection of 30 elite varieties registered between 1989 and 2014, including hybrids and open pollinated varieties, was tested in a two-year experiment in 10 environments across Germany for changes in seed yield and seed quality traits. Furthermore, nitrogen use efficiency was calculated. We observed a highly significant genetics-driven increase in seed yield per se and, thus, increased NUE at both nitrogen fertilization levels. On average, seed yield from modern open-pollinated varieties and modern hybrids was higher than from old open-pollinated varieties and old hybrids. The annual yield progress across all tested varieties was approximately 35 kg ha-1 year-1 at low nitrogen and 45 kg ha-1 year-1 under high nitrogen fertilization. Furthermore, in modern varieties an increased oil concentration and decreased protein concentration was observed. Despite the significant effects of nitrogen fertilization, a surprisingly low average seed yield gap of 180 kg N ha-1 was noted between high and low nitrogen fertilization. Due to contrary effects of N fertilization on seed yield per se and seed oil concentration an oil yield of 2.04 t ha-1 was measured at both N levels. Collectively, the data reveal that genetic improvement through modern breeding techniques in conjunction with reduced N fertilizer inputs has a tremendous potential to increase NUE of oilseed rape.

In den letzten Jahren ist eine gesteigerte Anbaufläche von Raps (Brassica napus), begründet durch eine Nachfragesteigerung nach Rapsöl für die Biodieselproduktion, in Deutschland und innerhalb der EU erkennbar. Dadurch stellen sich neue Herausforderungen für die Pflanzenzüchtung bezüglich Ölertrag und -qualität und insbesondere der Schrotqualität, um vor allem das Rapsschrotes, als Rückstand der Ölextraktion, als hochwertiges Eiweißfuttermittel in der Tierernährung vollwertig zu nutzen. Rapsschrot enthält ca. 40% Protein mit einer günstigen Aminosäuren-Zusammensetzung und hohen Anteilen essentieller Aminosäuren, wie z.B. Methionin und Cystein. Aufgrund eines relativ hohen Rohfasergehaltes und der Präsenz weiterer antinutritiver Sameninhaltsstoffe, wie z.B. Sinapin und kondensierte Tannine, kann herkömmliches Rapsschrot aber nur bedingt in der Fütterung von Nutztieren eingesetzt werden. Um nun die Verwendungsmöglichkeiten weiter zu steigern, müssen die Gehalte der wertmindernden Inhaltsstoffe, wie Rohfaser (u.a. Lignin, Hemicellulose und Cellulose) und anderer wertmindernder phenolischer Substanzen (u.a. Tannine und Sinapine), reduziert werden. Hinsichtlich der Reduktion solcher wertmindernder Inhaltsstoffe wird aus Sicht der Pflanzenzüchtung der Entwicklung gelb- bzw. hellsamiger Rapsgenotypen eine große Bedeutung beigemessen, indem die Rohfaser reduziert und die innere Samenqualität dadurch deutlich verbessert wird.In diesem Zusammenhang ist aber in der praktischen Pflanzenzüchtung die Erfassung möglichst vieler relevanter und antinutritiver Sameninhaltsstoffe, wie z.B. Rohfaser, mittels Hochdurchsatz-Analysemethoden eine notwendige Voraussetzung für die erfolgreiche Selektion neuer Rapsgenotypen mit verbesserter Schrotqualität. Das wesentliche Ziel der Arbeit bestand darin, durch die Entwicklung von Kalibrationen für die Nahinfrarot-Reflektionsspektroskopie (NIRS) der Faserfraktionen NDF (neutral detergent fibre), ADF (acid detergent fibre) und ADL (acid detergent lignin) für verschiedene Samenvolumina (10ml und 1ml) in intakten B. napus Samen, solche umfassenden Analysemethoden bereit zu stellen. Es konnte gezeigt werden, dass die NIRS-Kalibrationen für die Faserkomponenten, speziell für die ADL-Bestimmung, hinreichend genau sind und ein großes Potential für die züchterische Selektion von neuen Linien und Sorten, sowohl in jungen als auch in fortgeschrittenen Zuchtmaterial, mit verbesserter Schrotqualität aufweisen. Weiterhin wurden die neu entwickelten NIRS-Kalibrationen genutzt, um einerseits die vorhandene genetische Variation für die Faserkomponenten in unterschiedlichen für Samenfarbe bzw. Schrotqualität spaltenden Winterrapspopulationen zu analysieren. Andererseits dienten die erzielten phänotypischen Daten als Grundlage für quantitativ- und molekular-genetische Untersuchungen, um genauere Kenntnisse über die Vererbung sowie die genetischen Assoziation mit anderen Samenschalenmerkmalen, wie z.B. der Samenfarbe und den kondensierten Tanninen, in der Rapssaat zu erlangen.Aus den Untersuchungen wurde deutlich, dass ein starker Zusammenhang zwischen der Samenfarbe und den verschiedenen Faserkomponenten in B. napus existiert, und dass die niedrigsten Fasergehalte in hellsamigen Genotypen zu finden sind. Bemerkenswert sind aber auch die zu beobachtende breite Variation für, beispielsweise ADL, in schwarzsamigen Rapsgenotypen einerseits und die Identifizierung eines gemeinsamen Genombereiches auf dem B. napus-Chromosom A9, der die genetischen Zusammenhänge der verschiedenen Samenschalenmerkmale erklärt, andererseits. Die in dieser Arbeit erstellten Analysemethoden für die Faserfraktionen der Rapssaat und die gewonnenen Erkenntnisse über die genetischen Zusammenhänge von Sameninhaltsstoffen, die einen maßgeblichen Einfluss auf die Schrotqualität haben, stellen wertvolle Informationen für die Züchtung von in der Schrotqualität verbesserten Rapssorten dar, mit denen eine Steigerung der dualen Verwertbarkeit von Körnerölraps für die Ölgewinnung und die Tierfütterung realisierbar ist., Oilseed rape (Brassica napus) meal or cake is an important product for livestock nutrition. With constantly rising seed production in Europe due to higher demands for vegetable oil and biodiesel, an improvement of the seed meal quality is an increasingly important breeding aim in order to increase the overall economic value of the crop. Oilseed rape meal possesses about 40% protein with a favorable composition of amino acids, and high contents of essential amino acids like methionin and cystein. However the utilisation of rapeseed meal in animal nutrition is limited by its high content of undigestible and antinutritive fibre components and additionally high quantities of other phenolic compounds, such as sinapine and condensed tannins. Until now most efforts to select for improved meal quality have concentrated on the use of the yellow seed trait as a selection marker for reduced contents of fibre and condensed tannins. In modern breeding programs the use of high-throughput analysis for all relevant valuable and antinutritive seed compounds, such as fibre, is necessary for a successful selection of oilseed rape genotypes with an improved meal quality. In this regard the development of near infrared reflection spectroscopy (NIRS) calibration for fibre fractions NDF (neutral detergent fibre), ADF (acid detergent fibre) and ADL (acid detergent lignin) in different seed volumes (10ml and 1ml) of intact B. napus seeds was the main aim of this study. It could be shown that accurate calibrations were obtained for ADL, the major antinutritional fibre fraction in oilseed rape meal, and adequate calibrations for NDF and ADF in both seed volumes. The new developed calibrations demonstrate the power of NIRS for the selection of genotypes with an improved meal quality in early and advanced breeding generations.Evaluation of diverse B. napus germplasm with the new calibrations revealed a surprisingly broad variation of ADL content in dark-seeded oilseed rape, whereas the lowest fibre contents could be observed in yellow-seeded genotypes. Furthermore the obtained phenotypic data were used for genetic studies to investigate the inheritance and the association of seed fibre components with other seed coat traits, such as seed coat colour and other phenolic compounds. The results demonstrate that a major genome region on B. napus chromosome A9 is simultaneously influencing a number of seed coat traits.The new developed NIRS-calibrations for NDF, ADF and ADL as well as the obtained information about the inheritance of seed fibre and the genetic association of several antinutritive seed components represents an important breakthrough in breeding for improved nutritional quality of seed extraction meals from oilseed rape.