Grain yield trade-offs in spike-branching wheat can be mitigated by elite alleles affecting sink capacity and post-anthesis source activity.

Introducing variations in inflorescence architecture, such as the 'Miracle-Wheat' (Triticum turgidum convar. compositum (L.f.) Filat.) with a branching spike, has relevance for enhancing wheat grain yield. However, in the spike-branching genotypes, the increase in spikelet number is generally not translated into grain yield advantage because of reduced grains per spikelet and grain weight. Here, we investigated if such trade-offs might be a function of source-sink strength by using 385 recombinant inbred lines developed by intercrossing the spike-branching landrace TRI 984 and CIRNO C2008, an elite durum (T. durum L.) cultivar; they were genotyped using the 25K array. Various plant and spike architectural traits, including flag leaf, peduncle, and spike senescence rate, were phenotyped under field conditions for 2 consecutive years. On chromosome 5AL, we found a new modifier QTL for spike branching, branched headt3 (bht-A3), which was epistatic to the previously known bht-A1 locus. Besides, bht-A3 was associated with more grains per spikelet and a delay in flag leaf senescence rate. Importantly, favourable alleles, viz. bht-A3 and grain protein content (gpc-B1) that delayed senescence, are required to improve grain number and grain weight in the spike-branching genotypes. In summary, achieving a balanced source-sink relationship might minimize grain yield trade-offs in Miracle-Wheat.

No correlation between amylase/trypsin-inhibitor content and amylase inhibitory activity in hexaploid and tetraploid wheat species.

Wheat amylase/trypsin-inhibitors (ATI) are known triggers for wheat-related disorders. The aims of our study were to determine (1) the inhibitory activity against different α-amylases, (2) the content of albumins and globulins (ALGL) and total ATI and (3) to correlate these parameters in wholegrain flour of hexaploid, tetraploid and diploid wheat species. The amount of ATI within the ALGL fraction varied from 0.8% in einkorn to 20% in spelt. ATI contents measured with reversed-phase high-performance liquid chromatography (RP-HPLC) revealed similar contents (1.2-4.2 mg/g) compared to the results determined by LC-MS/MS (0.2-5.2 mg/g) for all wheat species except einkorn. No correlation was found between ALGL content and inhibitory activity. In general, hexaploid cultivars of spelt and common wheat had the highest inhibitory activities, showing values between 897 and 3564 AIU/g against human salivary α-amylase. Tetraploid wheat species durum and emmer had lower activities (170-1461 AIU/g), although a few emmer cultivars showed similar activities at one location. In einkorn, no inhibitory activity was found. No correlation was observed between the ATI content and the inhibitory activity against the used α-amylases, highlighting that it is very important to look at the parameters separately.

From farm to fork: future supply chains need to measure and trade nutrient content.

In the future, 8-10 billion people will need to be fed by our agriculture and food production system. Moreover, currently up to five billion people are already affected by malnutrition including undernutrition, inadequate consumption of micronutrients, and overweight. A healthy and sustainable diet will therefore play a pivotal role in our future, but most food products are traded and consumed based only on techno-functional or gustatory properties. We wish to stimulate a debate on the urgent need for multidisciplinary research and education to realize future diets with enhanced nutritional profiles. In particular, there is a need to better measure and understand the factors that influence the nutrients of food products along the global supply chains.

Reference proteomes of five wheat species as starting point for future design of cultivars with lower allergenic potential.

Wheat is an important staple food and its processing quality is largely driven by proteins. However, there is a sizable number of people with inflammatory reactions to wheat proteins, namely celiac disease, wheat allergy and the syndrome of non-celiac wheat sensitivity. Thus, proteome profiles should be of high importance for stakeholders along the wheat supply chain. We applied liquid chromatography-tandem mass spectrometry-based proteomics to establish the flour reference proteome for five wheat species, ancient to modern, each based on 10 cultivars grown in three diverse environments. We identified at least 2540 proteins in each species and a cluster analyses clearly separated the species based on their proteome profiles. Even more, >50% of proteins significantly differed between species - many of them implicated in products' quality, grain-starch synthesis, plant stress regulation and proven or potential allergic reactions in humans. Notably, the expression of several important wheat proteins was found to be mainly driven by genetics vs. environmental factors, which enables selection and refinement of improved cultivars for the wheat supply chain as long as rapid test methods will be developed. Especially einkorn expressed 5.4 and 7.2-fold lower quantities of potential allergens and immunogenic amylase trypsin inhibitors, respectively, than common wheat, whereas potential allergen content was intermediate in tetraploid wheat species. This urgently warrants well-targeted clinical studies, where the developed reference proteomes will help to design representative test diets.

Mineral and Phytic Acid Content as Well as Phytase Activity in Flours and Breads Made from Different Wheat Species.

Wheat is of high importance for a healthy and sustainable diet for the growing world population, partly due to its high mineral content. However, several minerals are bound in a phytate complex in the grain and unavailable to humans. We performed a series of trials to compare the contents of minerals and phytic acid as well as phytase activity in several varieties from alternative wheat species spelt, emmer and einkorn with common wheat. Additionally, we investigated the potential of recent popular bread making recipes in German bakeries to reduce phytic acid content, and thus increase mineral bioavailability in bread. For all studied ingredients, we found considerable variance both between varieties within a species and across wheat species. For example, whole grain flours, particularly from emmer and einkorn, appear to have higher mineral content than common wheat, but also a higher phytic acid content with similar phytase activity. Bread making recipes had a greater effect on phytic acid content in the final bread than the choice of species for whole grain flour production. Recipes with long yeast proofing or sourdough and the use of whole grain rye flour in a mixed wheat bread minimized the phytic acid content in the bread. Consequently, optimizing food to better nourish a growing world requires close collaboration between research organizations and practical stakeholders ensuring a streamlined sustainable process from farm to fork.

Large-scale genotyping and phenotyping of a worldwide winter wheat genebank for its use in pre-breeding.

Plant genetic resources (PGR) stored at genebanks are humanity's crop diversity savings for the future. Information on PGR contrasted with modern cultivars is key to select PGR parents for pre-breeding. Genotyping-by-sequencing was performed for 7,745 winter wheat PGR samples from the German Federal ex situ genebank at IPK Gatersleben and for 325 modern cultivars. Whole-genome shotgun sequencing was carried out for 446 diverse PGR samples and 322 modern cultivars and lines. In 19 field trials, 7,683 PGR and 232 elite cultivars were characterized for resistance to yellow rust - one of the major threats to wheat worldwide. Yield breeding values of 707 PGR were estimated using hybrid crosses with 36 cultivars - an approach that reduces the lack of agronomic adaptation of PGR and provides better estimates of their contribution to yield breeding. Cross-validations support the interoperability between genomic and phenotypic data. The here presented data are a stepping stone to unlock the functional variation of PGR for European pre-breeding and are the basis for future breeding and research activities.

Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement.

The great efforts spent in the maintenance of past diversity in genebanks are rationalized by the potential role of plant genetic resources (PGR) in future crop improvement-a concept whose practical implementation has fallen short of expectations. Here, we implement a genomics-informed prebreeding strategy for wheat improvement that does not discriminate against nonadapted germplasm. We collect and analyze dense genetic profiles for a large winter wheat collection and evaluate grain yield and resistance to yellow rust (YR) in bespoke core sets. Breeders already profit from wild introgressions but PGR still offer useful, yet unused, diversity. Potential donors of resistance sources not yet deployed in breeding were detected, while the prebreeding contribution of PGR to yield was estimated through 'Elite × PGR' F1 crosses. Genomic prediction within and across genebanks identified the best parents to be used in crosses with elite cultivars whose advanced progenies can outyield current wheat varieties in multiple field trials.

Hybrid wheat: quantitative genetic parameters and heterosis for quality and rheological traits as well as baking volume.

KEY MESSAGE: Heterosis effects for dough quality and baking volume were close to zero. However, hybrids have a higher grain yield at a given level of bread making quality compared to their parental lines. Bread wheat cultivars have been selected according to numerous quality traits to fulfill the requirements of the bread making industry. These include beside protein content and quality also rheological traits and baking volume. We evaluated 35 male and 73 female lines and 119 of their single-cross hybrids at three different locations for grain yield, protein content, sedimentation value, extensograph traits and baking volume. No significant differences (p < 0.05) were found in the mean comparisons of males, females and hybrids, except for higher grain yield and lower protein content in the hybrids. Mid-parent and better-parent heterosis values were close to zero and slightly negative, respectively, for baking volume and extensograph traits. However, the majority of heterosis values resulted in the finding that hybrids had higher grain yield than lines for a given level of baking volume, sedimentation value or energy value of extensograph. Due to the high correlation with the mid-parent values (r > 0.70), an initial prediction of hybrid performance based on line per se performance for protein content, sedimentation value, most traits of the extensograph and baking volume is possible. The low variance due to specific combining ability effects for most quality traits points toward an additive gene action requires quality selection within both heterotic groups. Consequently, hybrid wheat can combine high grain yield with high bread making quality. However, the future use of wheat hybrids strongly depends on the establishment of a cost-efficient and reliable seed production system.

Comparative compositions of metabolites and dietary fibre components in doughs and breads produced from bread wheat, emmer and spelt and using yeast and sourdough processes.

Wholemeal flours from blends of bread wheat, emmer and spelt were processed into bread using yeast-based and sourdough fermentation. The bread wheat flour contained significantly higher concentrations of total dietary fibre and fructans than the spelt and emmer flours, the latter having the lowest contents. Breadmaking using sourdough and yeast systems resulted in changes in composition from flour to dough to bread including increases in organic acids and mannitol in the sourdough system and increases in amino acids and sugars (released by hydrolysis of proteins and starch, respectively) in both processing systems. The concentrations of fructans and raffinose (the major endogenous FODMAPs) were reduced by yeast and sourdough fermentation, with yeast having the greater effect. Both systems resulted in greater increases in sugars and glycerol in emmer than in bread wheat and spelt, but the significance of these differences for human health has not been established.

Reciprocal Recurrent Genomic Selection Is Impacted by Genotype-by-Environment Interactions.

Reciprocal recurrent genomic selection is a breeding strategy aimed at improving the hybrid performance of two base populations. It promises to significantly advance hybrid breeding in wheat. Against this backdrop, the main objective of this study was to empirically investigate the potential and limitations of reciprocal recurrent genomic selection. Genome-wide predictive equations were developed using genomic and phenotypic data from a comprehensive population of 1,604 single crosses between 120 female and 15 male wheat lines. Twenty superior female lines were selected for initiation of the reciprocal recurrent genomic selection program. Focusing on the female pool, one cycle was performed with genomic selection steps at the F2 (60 out of 629 plants) and the F5 stage (49 out of 382 plants). Selection gain for grain yield was evaluated at six locations. Analyses of the phenotypic data showed pronounced genotype-by-environment interactions with two environments that formed an outgroup compared to the environments used for the genome-wide prediction equations. Removing these two environments for further analysis resulted in a selection gain of 1.0 dt ha-1 compared to the hybrids of the original 20 parental lines. This underscores the potential of reciprocal recurrent genomic selection to promote hybrid wheat breeding, but also highlights the need to develop robust genome-wide predictive equations.

Optimum breeding strategies using genomic and phenotypic selection for the simultaneous improvement of two traits.

KEY MESSAGE: A breeding strategy combining genomic with one-stage phenotypic selection maximizes annual selection gain for net merit. Choice of the selection index strongly affects the selection gain expected in individual traits. 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.

Comprehensive proteome analysis of bread deciphering the allergenic potential of bread wheat, spelt and rye.

BACKGROUND/OBJECTIVES: Cereal products like flour and bread are known to trigger diseases such as wheat allergy, celiac disease and non-celiac wheat sensitivity (NCWS). Some of these diseases are caused by allergenic proteins, the expression of which might vary depending on the grain type and manufacturing processes. Therefore, we examined the protein composition and abundance of potentially allergenic proteins in flours from bread wheat, spelt and rye, and corresponding breads. MATERIALS AND METHODS: Using Nano-LC-ESI-MS/MS and label free quantification (LFQ) we analyzed the proteome of six different bread flours (wholegrain and superfine flours from rye, spelt and bread wheat) and 14 bread types (yeast and sourdough fermented breads from all flours and wheat breads plus/minus bread improver). Potentially allergenic proteins in flours and breads were functionally categorized using the Pfam database and relatively quantified by LFQ. RESULTS: We could show that almost equal numbers of proteins can be identified in rye- and spelt samples compared to wheat samples using the Uniprot bread wheat protein database, indicating high sequence conservation between cereals. In total, 4424 proteins were identified in the 20 flour and bread samples. The average number of identified proteins in flour (2719 ± 243) was slightly higher than in bread (2283 ± 232; P < 0.001). In wheat- and spelt wholegrain flour higher protein numbers (wheat: 2891 ± 90; spelt: 2743 ± 140) were identified on average than in superfine flour (wheat: 2562 ± 79; P = 0.009; spelt: 2431 ± 140; P = 0.004). Neither the absolute number nor the abundance distribution of potentially allergenic proteins were dependent on the flour type or the fermentation process, but known allergenic proteins like gliadins showed higher relative abundance in spelt- and wheat samples, compared to rye samples. CONCLUSION: We provide comprehensive proteome data for six flour types and related breads showing that the grain species have greater influence on proteome composition than milling and fermentation processes. Our data indicate that allergenic proteins are not selectively degraded during bread production and are more abundant in bread wheat and spelt compared to rye. SIGNIFICANCE: Our proteomics study revealed that bread contains a number of potentially and proven allergenic proteins. Most likely allergenicity is not dependent on milling or conventional fermentation processes, but on the grain type. Relative abundance of allergenic proteins was higher in spelt- and wheat samples than in rye samples. Considering rye bread as better suited to atopic individuals predisposed to react to cereal allergens, clinical trials are warranted to verify this assumption.

Genetic architecture underlying the expression of eight α-amylase trypsin inhibitors.

KEY MESSAGE: Wheat cultivars largely differ in the content and composition of ATI proteins, but heritability was quite low for six out of eight ATIs. The genetic architecture of ATI proteins is built up of few major and numerous small effect QTL. 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.

Unlocking big data doubled the accuracy in predicting the grain yield in hybrid wheat.

The potential of big data to support businesses has been demonstrated in financial services, manufacturing, and telecommunications. Here, we report on efforts to enter a new data era in plant breeding by collecting genomic and phenotypic information from 12,858 wheat genotypes representing 6575 single-cross hybrids and 6283 inbred lines that were evaluated in six experimental series for yield in field trials encompassing ~125,000 plots. Integrating data resulted in twofold higher prediction ability compared with cases in which hybrid performance was predicted across individual experimental series. Our results suggest that combining data across breeding programs is a particularly appropriate strategy to exploit the potential of big data for predictive plant breeding. This paradigm shift can contribute to increasing yield and resilience, which is needed to feed the growing world population.

Characterization of 150 Wheat Cultivars by LC-MS-Based Label-Free Quantitative Proteomics Unravels Possibilities to Design Wheat Better for Baking Quality and Human Health.

Wheat (Triticum aestivum ssp. aestivum) contributes to 20% of the human protein supply, delivers essential amino acids and is of fundamental importance for bread and pasta quality. Wheat proteins are also involved in adverse human reactions like celiac disease (CD), wheat allergy (WA) and non-celiac wheat sensitivity (NCWS). Using liquid chromatography-mass spectrometry (LC-MS)-based label-free quantitative (LFQ) proteomics of aqueous flour extracts, we determined 756 proteins across 150 wheat cultivars grown in three environments. However, only 303 proteins were stably expressed across all environments in at least one cultivar and only 89 proteins thereof across all 150 cultivars. This underlines the large influence of environmental conditions on the expression of many proteins. Wheat cultivars varied largely in their protein profile, shown by high coefficients of variation across different cultivars. Heritability (h2) ranged from 0-1, with 114 proteins having h² > 0.6, including important proteins for baking quality and human health. The expression of these 114 proteins should be amenable to targeted manipulation across the wheat supply chain by varietal choice and breeding for designing healthier wheat with better quality. Further technical development is urgently required to assign functions to identifiable proteins labeled yet uncharacterized in databases and speeding up detection methods to routinely use proteomics in wheat supply chains.

Hybrid QconCAT-Based Targeted Absolute and Data-Independent Acquisition-Based Label-Free Quantification Enables In-Depth Proteomic Characterization of Wheat Amylase/Trypsin Inhibitor Extracts.

Wheat amylase/trypsin inhibitors (ATIs) have gained significant relevance as inducers of intestinal and extra-intestinal inflammation. In this study, we present a novel hybrid data-independent acquisition (DIA) liquid chromatography-mass spectrometry (LC-MS) approach, combining QconCAT technology with short microflow LC gradients and DIA and apply the method toward the quantitative proteome analysis of ATI extracts. The presented method is fast, robust, and reproducible and provides precise QconCAT-based absolute quantification of major ATI proteins while simultaneously quantifying the proteome by label-free quantification (LFQ). We analyzed extracts of 60 varieties of common wheat grown in replication and evaluated the reproducibility and precision of the workflow for the quantification of ATIs. Applying the method to analyze different wheat species (i.e., common wheat, spelt, durum wheat, emmer, and einkorn) and comparing the results to published data, we validated inter-laboratory and cross-methodology reproducibility of ATI quantification, which is essential in the context of large-scale breeding projects. Additionally, we applied our workflow to assess environmental effects on ATI expression, analyzing ATI content and proteome of same varieties grown at different locations. Finally, we explored the potential of combining QconCAT-based absolute quantification with DIA-based LFQ proteome analysis for the generation of new hypotheses or assay development.

Comparing the Potential of Marker-Assisted Selection and Genomic Prediction for Improving Rust Resistance in Hybrid Wheat.

Improving leaf rust and stripe rust resistance is a central goal in wheat breeding. The objectives of this study were to (1) elucidate the genetic basis of leaf rust and stripe rust resistance in a hybrid wheat population, (2) compare the findings using a previously published hybrid wheat data set, and (3) contrast the prediction accuracy with those of genome-wide prediction. The hybrid wheat population included 1,744 single crosses from 236 parental lines. The genotypes were fingerprinted using a 15k SNP array and evaluated for leaf rust and stripe rust resistance in multi-location field trials. We observed a high congruency of putative quantitative trait loci (QTL) for leaf rust resistance between both populations. This was not the case for stripe rust resistance. Accordingly, prediction accuracy of the detected QTL was moderate for leaf rust but low for stripe rust resistance. Genome-wide selection increased the prediction accuracy slightly for stripe rust albeit at a low level but not for leaf rust. Thus, our findings suggest that marker-assisted selection seems to be a robust and efficient tool to improve leaf rust resistance in European wheat hybrids.

High-resolution proteomics reveals differences in the proteome of spelt and bread wheat flour representing targets for research on wheat sensitivities.

Wheat consumption can trigger celiac disease, allergic reactions and non-celiac wheat sensitivity (NCWS) in humans. Some people with NCWS symptoms claim a better tolerability of spelt compared to bread wheat products. We therefore investigated potential differences in the proteomes of spelt and bread wheat flour using nano LC-ESI-MS/MS on a set of 15 representative varieties for each of the two species. Based on the bread wheat reference, we detected 3,050 proteins in total and for most of them the expression was mainly affected by the environment. By contrast, 274 and 409 proteins in spelt and bread wheat, respectively, had a heritability ≥ 0.4 highlighting the potential to influence their expression level by varietal choice. We found 84 and 193 unique proteins for spelt and bread wheat, respectively, and 396 joint proteins, which expression differed significantly (p ≤ 0.05) when comparing both species. Thus, about one third of proteins differed significantly between spelt and bread wheat. Of them, we identified 81 proteins with high heritability, which therefore might be interesting candidates for future research on wheat hypersensitivities.

Comparative quantitative LC-MS/MS analysis of 13 amylase/trypsin inhibitors in ancient and modern Triticum species.

Amylase/trypsin inhibitors (ATIs) are major wheat allergens and they are also implicated in causing non-celiac gluten sensitivity and worsening other inflammatory conditions. With only few studies on ATI contents in different Triticum species available so far, we developed a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) method based on stable isotope dilution assays to quantitate the 13 most important ATIs in a well-defined sample set of eight cultivars of common wheat and durum wheat (modern species), as well as spelt, emmer and einkorn (ancient species) grown at three locations in Germany, respectively. Only few ATIs with low contents were detected in einkorn. In contrast, spelt had the highest total ATI contents. Emmer and common wheat had similar total ATI contents, with durum wheat having lower contents than common wheat. Due to the lack of correlation, it was not possible to estimate ATI contents based on crude protein contents. The wheat species had a higher influence on ATI contents than the growing location and the heritability of this trait was high. Despite comparatively low intra-species variability, some cultivars were identified that may be promising candidates for breeding for naturally low ATI contents.

Negative dominance and dominance-by-dominance epistatic effects reduce grain-yield heterosis in wide crosses in wheat.

The genetics underlying heterosis, the difference in performance of crosses compared with midparents, is hypothesized to vary with relatedness between parents. We established a unique germplasm comprising three hybrid wheat sets differing in the degree of divergence between parents and devised a genetic distance measure giving weight to heterotic loci. Heterosis increased steadily with heterotic genetic distance for all 1903 hybrids. Midparent heterosis, however, was significantly lower in the hybrids including crosses between elite and exotic lines than in crosses among elite lines. The analysis of the genetic architecture of heterosis revealed this to be caused by a higher portion of negative dominance and dominance-by-dominance epistatic effects. Collectively, these results expand our understanding of heterosis in crops, an important pillar toward global food security.