Structural and genetical studies on the high-molecular-weight subunits of wheat glutenin : Part 1: Allelic variation in subunits amongst varieties of wheat (Triticum aestivum)

Comparative Label-Free Proteomics Study on Celiac Disease-Active Epitopes in Common Wheat, Spelt, Durum Wheat, Emmer, and Einkorn

Wheat species with various ploidy levels may be different regarding their immunoreactive potential in celiac disease (CD), but a comprehensive comparison of peptide sequences with known epitopes is missing. Thus, we used an untargeted liquid chromatography tandem mass spectrometry method to analyze the content of peptides with CD-active epitope in the five wheat species common wheat, spelt, durum wheat, emmer, and einkorn. In total, 494 peptides with CD-active epitope were identified. Considering the average of the eight cultivars of each species, spelt contained the highest number of different peptides with CD-active epitope (193 ± 12, mean ± SD). Einkorn showed the smallest variability of peptides (63 ± 4) but higher amounts of certain peptides compared to the other species. The wheat species differ in the presence and distribution of CD-active epitopes; hence, the entirety of peptides with CD-active epitope is crucial for the assessment of their immunoreactive potential.

Assessment of intra- and inter-genetic diversity in tetraploid and hexaploid wheat genotypes based on omega, gamma and alpha-gliadin profiles

Durum and bread wheat are well adapted to the Mediterranean Basin. Twenty-three genotypes of each species were grown to evaluate the intra- and inter-genetic diversity based on omega (ω), gamma (γ) and alpha (α)-gliadin profiles. To achieve this purpose, the endosperm storage proteins (both gliadins and glutenins) were extracted from wheat grains and electrophoresed on sodium dodecyl sulfate (SDS)-polyacrylamide gels. The results of SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) revealed nine polymorphic loci out of 16 loci with durum wheat genotypes and nine polymorphic loci out of 18 loci with bead wheat genotypes. The polymorphisms revealed by the SDS-PAGE were 56% and 50% in durum and bread wheat genotypes, respectively. Using the cluster analysis, the durum wheat genotypes were clustered into five groups, while the bread wheat genotypes were grouped into six clusters using un-weighed pair group mean analyses based on ω, γ, and α-gliadins profiles. The 46 durum and bread wheat genotypes were grouped into seven clusters based on the combined ω, γ, and α-gliadins profiles revealed by the SDS-PAGE. The in silico analysis determined the intra-genetic diversity between bread and durum wheat based on the sequences of ω, γ, and α-gliadins. The alignment of ω-gliadin revealed the highest polymorphism (52.1%) between bread and durum wheat, meanwhile, the alignment of γ and α-gliadins revealed very low polymorphism 6.6% and 15.4%, respectively. According to computational studies, all gliadins contain a lot of glutamine and proline residues. The analysis revealed that the bread wheat possessed ω and γ -gliadins with a lower content of proline and a higher content of glutamine than durum wheat. In contrast, durum wheat possessed α-gliadin with a lower content of proline and a higher content of glutamine than bread wheat. In conclusion, the SDS-PAGE, in silico and computational analyses are effective tools to determine the intra- and inter-genetic diversity in tetraploid and hexaploid wheat genotypes based on ω, γ, and α-gliadins profiles.

Molecular Characterization and Marker Development of the HMW-GS Gene from Thinopyrum elongatum for Improving Wheat Quality

The quality of wheat primarily depends on its storage protein quality, especially in regards to gluten content and high-molecular-weight glutenin subunits (HMW-GS). The number of HMW-GS alleles is limited in bread wheat (Triticum aestivum L.), whereas it is abundant in wheat relatives. Therefore, HMW-GS alleles from wheat relatives could provide a potential for improving quality in wheat breeding. Thinopyrum elongatum (EE) is one of the relatives of wheat. The E genome is closely related to the ABD genome in wheat; therefore, Th. elongatum is often used as an excellent exogenous gene donor for wheat genetic improvement. In this study, the high-molecular glutenin subunit gene was cloned and sequenced from Th. elongatum. A specific molecular marker for identifying the Glu-1Ey subunit gene was developed and applied to detected wheat-Th. elongatum alien introgression lines. Quality analysis indicated that the substitution and addition lines containing Th. elongatum alleles significantly (p < 0.05) increased grain protein content by 3.76% to 5.11%, wet-gluten content by 6.55% to 8.73%, flour 8-MW by 0.25% to 6.35%, and bread volume value by 33.77 mL to 246.50 mL, in comparing it with Chinese Spring. The GMP content and lactic acid SRC showed significant positive correlations with flour processing quality and might be used as indicators for wheat quality. The results were expected to provide a novel route for improving processing quality in wheat quality breeding.

Wheat end-use quality: State of art, genetics, genomics-assisted improvement, future challenges, and opportunities

Wheat is the most important source of food, feed, and nutrition for humans and livestock around the world. The expanding population has increasing demands for various wheat products with different quality attributes requiring the development of wheat cultivars that fulfills specific demands of end-users including millers and bakers in the international market. Therefore, wheat breeding programs continually strive to meet these quality standards by screening their improved breeding lines every year. However, the direct measurement of various end-use quality traits such as milling and baking qualities requires a large quantity of grain, traits-specific expensive instruments, time, and an expert workforce which limits the screening process. With the advancement of sequencing technologies, the study of the entire plant genome is possible, and genetic mapping techniques such as quantitative trait locus mapping and genome-wide association studies have enabled researchers to identify loci/genes associated with various end-use quality traits in wheat. Modern breeding techniques such as marker-assisted selection and genomic selection allow the utilization of these genomic resources for the prediction of quality attributes with high accuracy and efficiency which speeds up crop improvement and cultivar development endeavors. In addition, the candidate gene approach through functional as well as comparative genomics has facilitated the translation of the genomic information from several crop species including wild relatives to wheat. This review discusses the various end-use quality traits of wheat, their genetic control mechanisms, the use of genetics and genomics approaches for their improvement, and future challenges and opportunities for wheat breeding.

Molecular Characterization and SNP-Based Molecular Marker Development of Two Novel High Molecular Weight Glutenin Genes from Triticum spelta L

Spelt wheat (Triticum spelta L., 2n=6x=42, AABBDD) is a valuable source of new gene resources for wheat genetic improvement. In the present study, two novel high molecular weight glutenin subunits (HMW-GS) 1Ax2.1* at Glu-A1 and 1By19* at Glu-B1 from German spelt wheat were identified. The encoding genes of both subunits were amplified and cloned by allele-specific PCR (AS-PCR), and the complete sequences of open reading frames (ORF) were obtained. 1Ax2.1* with 2478 bp and 1By19* with 2163 bp encoded 824 and 720 amino acid residues, respectively. Molecular characterization showed that both subunits had a longer repetitive region, and high percentage of α-helices at the N- and C-termini, which are beneficial for forming superior gluten macropolymers. Protein modelling by AlphaFold2 revealed similar three-diamensional (3D) structure features of 1Ax2.1* with two x-type superior quality subunits (1Ax1 and 1Ax2*) and 1By19* with four y-type superior quality subunits (1By16, 1By9, 1By8 and 1By18). Four cysteine residues in the three x-type subunits (1Ax2.1*, 1Ax1 and 1Ax2*) and the cysteine in intermediate repeat region of y-type subunits were not expected to participate in intramolecular disulfide bond formation, but these cysteines might form intermolecular disulfide bonds with other glutenins and gliadins to enhance gluten macropolymer formation. The SNP-based molecular markers for 1Ax2.1* and 1By19* genes were developed, which were verified in different F2 populations and recombination inbred lines (RILs) derived from crossing between spelt wheat and bread wheat cultivars. This study provides data on new glutenin genes and molecular markers for wheat quality improvement.

Challenges and opportunities for proteomics and the improvement of bread wheat quality

Wheat remains a critical global food source, pressured by climate change and the need to maximize yield, improve processing and nutritional quality and ensure safety. An enormous amount of research has been conducted to understand gluten protein composition and structure in relation to end-use quality, yet progress has become stagnant. This is mainly due to the need and inability to biochemically characterize the intact functional glutenin polymer in order to correlate to quality, necessitating reduction to monomeric subunits and a loss of contextual information. While some individual gluten proteins might have a positive or negative influence on gluten quality, it is the sum total of these proteins, their relative and absolute expression, their sub-cellular trafficking, the amount and size of glutenin polymers, and ratios between gluten protein classes that define viscoelasticity of gluten. The sub-cellular trafficking of gluten proteins during seed maturation is still not completely clear and there is evidence of dual pathways and therefore different destinations for proteins, either constitutively or temporally. The trafficking of proteins is also unclear in endosperm cells as they undergo programmed cell death; Golgi disappear around 12 DPA but protein filling continues at least to 25 DPA. Modulation of the timing of cellular events will invariably affect protein deposition and therefore gluten strength and function. Existing and emerging proteomics technologies such as proteoform profiling and top-down proteomics offer new tools to study gluten protein composition as a whole system and identify compositional patterns that can modify gluten structure with improved functionality.

Comparison of effect of using hard and soft wheat on the high molecular weight-glutenin subunits profile and the quality of produced cookie

Twelve wheat genotypes with variable grain hardness were evaluated for grain, flour, pasting, dough rheological properties, high molecular weight glutenin subunits (HMW-GS) and their relationship with cookie quality characteristics. The degree of hardness played an important role in the expression of characters under study. Genotypes with higher grain hardness index (GHI) showed higher dough development time and dough stability. GHI and solvent retention capacity were positively related to each other and negatively to spread factor. GluD1 locus of majority of hard wheat genotypes showed 5 + 10 subunit while soft wheat (SW) genotypes with 2 + 12 subunit related to gluten quality and dough properties. Overall, variation in subunits at GluD1 locus led to greater variation amongst studied genotypes followed by GluB1 and GluA1. Subunits Null at GluA1, 20, 7 + 8 and 7 + 9 at GluB1, and 2 + 12 and 5 + 10 at GluD1 showed a profound effect on flour, dough and cookie quality. Distribution of different HMW-GS, gluten characteristics and GHI, thus emerged as major parameters for selection of wheat genotypes for development of cookies. SW (QBP 13-11) with the lowest GHI and HMW-GS profile (2*, 7 and 2 + 12 subunit) showed the highest cookie SF and the lowest BS, thereby, turning out to be the best suitable genotype for producing cookies.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13197-021-05272-5.

Premature Termination Codon of 1Dy12 Gene Improves Cookie Quality in Ningmai9 Wheat

The area between middle and lower reaches of the Yangtze River is the largest region for soft wheat production in China. In soft wheat breeding, the lack of germplasm with desirable quality for end-use products is a barrier. Ningmai9 is the main variety of soft wheat planted in this area. To create germplasm with better quality and yield potential than Ningmai9, mutants of HMW-GSs in Ningmai9 induced by ethylmethanesulfonate (EMS) were obtained. SDS-PAGE showed that two mutants, md10 and md11, were HMW-GS 1Dy deletions. DNA sequencing confirmed that one mutation was caused by a C/T substitution, resulting in the change of CAA encoding glutamine into the termination codon TAA, and another mutation was due to a G/A substitution in the central repetitive domain of the coding region, causing TGG encoding tryptophan to become the termination codon TGA. The premature termination codon of the 1Dy12 gene affected the expression of 1Dy12 and kept the mRNA at a lower transcription level during the kernel development stage in comparison with the wild type. HMW-GS 1Dy12 deletion mutants decreased the content of HMW-GSs and glutenin macropolymers, mixograph envelope peak time and TIMEX width, water solvent retention capacity (WSRC), and lactic acid solvent retention capacity (LASRC). In the HMW-GS 1Dy12 deletion lines, the sugar-snap cookie diameter was 8.70-8.74 cm, which was significantly larger than that in the wild type of 8.0 cm. There were no significant differences in spike number, kernel number, thousand kernel weight, and yield between the deletion lines and wild type. Overall, the study indicated that the knockout of the HMW-GS gene induced by EMS is an effective way to improve wheat quality, and deletion mutants of HMW-GS 1Dy12 decrease gluten strength and increase sugar snap cookie diameter without yield penalty in Ningmai9 wheat.

Wheat Quality Formation and Its Regulatory Mechanism

Elucidation of the composition, functional characteristics, and formation mechanism of wheat quality is critical for the sustainable development of wheat industry. It is well documented that wheat processing quality is largely determined by its seed storage proteins including glutenins and gliadins, which confer wheat dough with unique rheological properties, making it possible to produce a series of foods for human consumption. The proportion of different gluten components has become an important target for wheat quality improvement. In many cases, the processing quality of wheat is closely associated with the nutritional value and healthy effect of the end-products. The components of wheat seed storage proteins can greatly influence wheat quality and some can even cause intestinal inflammatory diseases or allergy in humans. Genetic and environmental factors have great impacts on seed storage protein synthesis and accumulation, and fertilization and irrigation strategies also greatly affect the seed storage protein content and composition, which together determine the final end-use quality of wheat. This review summarizes the recent progress in research on the composition, function, biosynthesis, and regulatory mechanism of wheat storage proteins and their impacts on wheat end-product quality.

High molecular weight glutenin gene diversity in Aegilops tauschii demonstrates unique origin of superior wheat quality

Central to the diversity of wheat products was the origin of hexaploid bread wheat, which added the D-genome of Aegilops tauschii to tetraploid wheat giving rise to superior dough properties in leavened breads. The polyploidization, however, imposed a genetic bottleneck, with only limited diversity introduced in the wheat D-subgenome. To understand genetic variants for quality, we sequenced 273 accessions spanning the known diversity of Ae. tauschii. We discovered 45 haplotypes in Glu-D1, a major determinant of quality, relative to the two predominant haplotypes in wheat. The wheat allele 2 + 12 was found in Ae. tauschii Lineage 2, the donor of the wheat D-subgenome. Conversely, the superior quality wheat allele 5 + 10 allele originated in Lineage 3, a recently characterized lineage of Ae. tauschii, showing a unique origin of this important allele. These two wheat alleles were also quite similar relative to the total observed molecular diversity in Ae. tauschii at Glu-D1. Ae. tauschii is thus a reservoir for unique Glu-D1 alleles and provides the genomic resource to begin utilizing new alleles for end-use quality improvement in wheat breeding programs.

Molecular Characterization of Novel x-Type HMW Glutenin Subunit 1B × 6.5 in Wheat

A novel high molecular weight glutenin subunit encoded by the Glu-1B locus was identified in the French genotype Bagou, which we named 1B × 6.5. This subunit differed in SDS-PAGE from well-known 1B × 6 and 1B × 7 subunits, which are also encoded at this locus. Subunit 1B × 6.5 has a theoretical molecular weight of 88,322.83 Da, which is more mobile than 1B × 6 subunit, and isoelectric point (pI) of about 8.7, which is lower than that for 1B × 6 subunit. The specific primers were designed to amplify and sequence 2476 bp of the Glu-1B locus from genotype Bagou. A high level of similarity was found between the sequence encoding 1B × 6.5 and other x-type encoding alleles of this locus.

Post-translational cleavage of HMW-GS Dy10 allele improves the cookie-making quality in common wheat (Triticum aestivum)

Wheat is a major staple food crop worldwide because of the unique properties of wheat flour. High molecular weight glutenin subunits (HMW-GSs), which are among the most critical determinants of wheat flour quality, are responsible for the formation of glutenin polymeric structures via interchain disulfide bonds. We herein describe the identification of a new HMW-GS Dy10 allele (Dy10-m619SN). The amino acid substitution (serine-to-asparagine) encoded in this allele resulted in a partial post-translational cleavage that produced two new peptides. These new peptides disrupted the interactions among gluten proteins because of the associated changes to the number of available cysteine residues for interchain disulfide bonds. Consequently, Dy10-m619SN expression decreased the size of glutenin polymers and weakened glutens, which resulted in wheat dough with improved cookie-making quality, without changes to the glutenin-to-gliadin ratio. In this study, we clarified the post-translational processing of HMW-GSs and revealed a new genetic resource useful for wheat breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01238-9.

A novel NAC family transcription factor SPR suppresses seed storage protein synthesis in wheat

The synthesis of seed storage protein (SSP) is mainly regulated at the transcriptional level. However, few transcriptional regulators of SSP synthesis have been characterized in common wheat (Triticum aestivum) owing to the complex genome. As the A genome donor of common wheat, Triticum urartu could be an elite model in wheat research considering its simple genome. Here, a novel NAC family transcription factor TuSPR from T. urartu was found preferentially expressed in developing endosperm during grain-filling stages. In common wheat transgenically overexpressing TuSPR, the content of total SSPs was reduced by c. 15.97% attributed to the transcription declines of SSP genes. Both in vitro and in vivo assays showed that TuSPR bound to the cis-element 5'-CANNTG-3' distributed in SSP gene promoters and suppressed the transcription. The homolog in common wheat TaSPR shared a conserved function with TuSPR on SSP synthesis suppression. The knock-down of TaSPR in common wheat resulted in 7.07%-20.34% increases in the total SSPs. Both TuSPR and TaSPR could be superior targets in genetic engineering to manipulate SSP content in wheat, and this work undoubtedly expands our knowledge of SSP gene regulation.

Exploring the End-Use Quality Potential of a Collection of Spanish Bread Wheat Landraces

Modern plant-breeding practices have narrowed the genetic base of wheat, such that there is a need to introduce new germplasms with underexploited diversity into breeding programs. Wheat landraces are a very valuable resource when searching for genetic variation, which not only possess increased adaptability, but also quality-related traits. Several studies have shown a wide genetic diversity in Spanish wheat landraces compared to other germplasm collections; therefore, the main objective of this study is to analyze the variability in a collection of 189 landraces from the Spanish National Plant Genetic Resources Centre (Centro de Recursos Fitogenéticos, CRF-INIA, Alcalá de Henares), in relation to end-use quality traits. We characterized the whole collection for high-molecular-weight glutenin and puroindoline allelic composition, and for gluten strength. In addition, grain protein content, grains per spike, and thousand kernel weight were evaluated in samples from four-year field trials. The relationship between glutenin composition and quality was evaluated, and some alleles strongly associated with high quality were identified in the collection, some of them specific for Iberian landraces. The results also show the presence of novel variability within high-molecular-weight glutenin and puroindolines, which needs to be characterized further in order to assess its influence on wheat quality. In addition, a set of landraces showing outstanding values for gluten quality and a good agronomic performance was selected for testing in field trials in order to evaluate the suitability of their direct use in cropping systems.

High-throughput analysis of high-molecular weight glutenin subunits in 665 wheat genotypes using an optimized MALDI-TOF-MS method

Gluten protein composition determines the rheological characteristics of wheat dough and is influenced by variable alleles with distinct effects on processing properties. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), we determined the high-molecular weight glutenin subunit (HMW-GS) composition of 665 wheat genotypes employed in breeding programs in South Korea. We identified 22 HMW-GS alleles, including 3 corresponding to the Glu-A1 locus, 14 to Glu-B1, and 5 to Glu-D1. The Glu-1 quality score, which is an important criterion for high-quality wheat development, was found to be 10 for 105/665 (15.79%) of the studied genotypes, and included the following combinations of HMW-GS: 2*, 7 + 8, 5 + 10; 2*, 17 + 18, 5 + 10; 1, 7 + 8, 5 + 10; and 1, 17 + 18, 5 + 10. To select wheat lines with the 1Bx7 overexpression (1Bx7OE) subunit, which is known to have a positive effect on wheat quality, we used a combination of MALDI-TOF-MS and published genotyping markers and identified 6 lines carrying 1Bx7OE out of the 217 showing a molecular weight of 83,400 Da, consistent with 1Bx7G2 and 1Bx7OE. This study demonstrates that the MALDI-TOF-MS method is fast, accurate, reliable, and effective in analyzing large numbers of wheat germplasms or breeding lines in a high-throughput manner.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02637-z.

Contribution to Breadmaking Performance of Two Different HMW Glutenin 1Ay Alleles Expressed in Hexaploid Wheat

Two expressed alleles of the 1Ay high-molecular-weight glutenin subunit (HMW-GS), 1Ay21* and 1AyT1, previously introduced in durum and bread wheat, were separately introgressed into the Australian bread wheat (Triticum aestivum L.) cv. Livingston. The developed lines had different allelic compositions compared to that of the parental cultivar (1Ax1), having either 1Ax21+1Ay21* or 1Ax1+1AyT1 at the Glu-A1 locus. Since 1Ax21 and 1Ax1 are known to have the same effects on quality, differences observed between the two sets of the developed lines are attributed to the two introgressed Ay genes. Yield and agronomic performance of the lines were evaluated in the field, and the protein, dough, and baking quality attributes were evaluated by large-scale quality testing. Results demonstrated that the subunit 1Ay21* increased unextractable polymeric protein by up to 14.3% and improved bread loaf volume by up to 9.2%. On the other hand, subunit 1AyT1 increased total grain protein by up to 9% along with dough elasticity. Furthermore, milling extraction was higher, and flour ash was lower in the 1Ay21* lines compared to the lines integrating 1AyT1. Both sets of the 1Ay introgression lines reduced dough-mixing time compared to the recurrent parent Livingston. The results also showed that 1Ay21* had a higher potential to improve the baking quality than 1AyT1 under the Livingston genetic background. Both alleles showed the potential to be utilized in breeding programs to improve the breadmaking quality.

Development of an Optimized MALDI-TOF-MS Method for High-Throughput Identification of High-Molecular-Weight Glutenin Subunits in Wheat

Because high-molecular-weight glutenin subunits (HMW-GS) are important contributors to wheat end-use quality, there is a need for high-throughput identification of HMW-GS in wheat genetic resources and breeding lines. We developed an optimized method using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to distinguish individual HMW-GS by considering the effects of the alkylating reagent in protein extraction, solvent components, dissolving volume, and matrix II components. Using the optimized method, 18 of 22 HMW-GS were successfully identified in standard wheat cultivars by differences in molecular weights or by their associations with other tightly linked subunits. Interestingly, 1Bx7 subunits were divided into 1Bx7 group 1 and 1Bx7 group 2 proteins with molecular weights of about 82,400 and 83,000 Da, respectively. Cultivars containing the 1Bx7 group 2 proteins were distinguished from those containing 1Bx7OE using well-known DNA markers. HMW-GS 1Ax2* and 1Bx6 and 1By8 and 1By8*, which are difficult to distinguish due to very similar molecular weights, were easily identified using RP-HPLC. To validate the method, HMW-GS from 38 Korean wheat varieties previously evaluated by SDS-PAGE combined with RP-HPLC were analyzed by MALDI-TOF-MS. The optimized MALDI-TOF-MS method will be a rapid, high-throughput tool for selecting lines containing desirable HMW-GS for breeding efforts.

Effects of 1Dy12 subunit silencing on seed storage protein accumulation and flour-processing quality in a common wheat somatic variation line

Dissecting the functions of high molecular weight glutenin subunits (HMW-GSs) is helpful for improving wheat quality via breeding. In this study, we used a wheat mutant AS273 in which HMW-GS 1Dy12 was silenced to investigate the silencing mechanism of 1Dy12 and its effects on gluten accumulation and flour-processing quality. Results suggested that the expression of 1Dy12 in AS273 was decreased by one fifth during grain development; a stop codon produced by a base mutation (C/T) led to truncated translation; the absence of 1Dy12 stimulated the accumulation of low molecular weight glutenin subunits (LMW-GSs), gliadins, and glutenin macropolymers, and was resulted in larger protein bodies; AS273 had an inferior flour-processing performance. Based on the outputs achieved in this study it is concluded that 1Dy12 makes important contributions to bread, sponge cake and biscuit-processing quality.

Mass spectrometry of in-gel digests reveals differences in amino acid sequences of high-molecular-weight glutenin subunits in spelt and emmer compared to common wheat

High-molecular-weight glutenin subunits (HMW-GS) play an important role for the baking quality of wheat. The ancient wheats emmer and spelt differ in their HMW-GS pattern compared to modern common wheat and this might be one reason for their comparatively poor baking quality. The aim of this study was to elucidate similarities and differences in the amino acid sequences of two 1Bx HMW-GS of common wheat, spelt and emmer. First, the sodium dodecyl polyacrylamide gel electrophoresis (SDS-PAGE) system was optimized to separate common wheat, spelt and emmer Bx6 and Bx7 from other HMW-GS (e.g., 1Ax and 1By) in high concentrations. The in-gel digests of the Bx6 and Bx7 bands were analyzed by untargeted LC-MS/MS experiments revealing different UniProtKB accessions in spelt and emmer compared to common wheat. The HMW-GS Bx6 and Bx7, respectively, of emmer and spelt showed differences in the amino acid sequences compared to those of common wheat. The identities of the peptide variations were confirmed by targeted LC-MS/MS. These peptides can be used to differentiate between Bx6 and Bx7 of spelt and emmer and Bx6 and Bx7 of common wheat. The findings should help to increase the reliability and curation status of wheat protein databases and to understand the effects of protein structure on the functional properties. Graphical abstract.

Determination of HMW - GS in wheat using SDS - PAGE and Lab-on-chip methods

SDS-PAGE is widely used to determine the amounts of the different gluten protein types. However, this method is time-consuming, especially at early stages of wheat breeding, when large number of samples needs to be analyzed. On the other hand, LoC (Lab-on-Chip) technique has the potential for a fast, reliable, and automatable analysis of proteins. Benefits and limitations of Lab-on-Chip method over SDS-PAGE method in gluten proteins evaluation were explored in order to determine in which way LoC method should be improved in order to make its results more compliant with the results of SDS-PAGE. Chip electrophoresis provides a very good reproducibility of HMW-GS patterns. Moreover this approach is much faster than the conventional SDS-PAGE methods requiring several hours for an analysis. Another advantage over traditional gel electrophoresis is lower sample and reagent volume requirements, as well as specialized protein standards for accurate reproducibility and quantification. In the present study, we identified novel complex allele located at the locus Glu-1B.

Deciphering the Genetics of Major End-Use Quality Traits in Wheat

Improving the end-use quality traits is one of the primary objectives in wheat breeding programs. In the current study, a population of 127 recombinant inbred lines (RILs) derived from a cross between Glenn (PI-639273) and Traverse (PI-642780) was developed and used to identify quantitative trait loci (QTL) for 16 end-use quality traits in wheat. The phenotyping of these 16 traits was performed in nine environments in North Dakota, USA. The genotyping for the RIL population was conducted using the wheat Illumina iSelect 90K SNP assay. A high-density genetic linkage map consisting of 7,963 SNP markers identified a total of 76 additive QTL (A-QTL) and 73 digenic epistatic QTL (DE-QTL) associated with these traits. Overall, 12 stable major A-QTL and three stable DE-QTL were identified for these traits, suggesting that both A-QTL and DE-QTL played an important role in controlling end-use quality traits in wheat. The most significant A-QTL (AQ.MMLPT.ndsu.1B) was detected on chromosome 1B for mixograph middle line peak time. The AQ.MMLPT.ndsu.1B A-QTL was located very close to the position of the Glu-B1 gene encoding for a subunit of high molecular weight glutenin and explained up to 24.43% of phenotypic variation for mixograph MID line peak time. A total of 23 co-localized QTL loci were detected, suggesting the possibility of the simultaneous improvement of the end-use quality traits through selection procedures in wheat breeding programs. Overall, the information provided in this study could be used in marker-assisted selection to increase selection efficiency and to improve the end-use quality in wheat.

Variable Immunogenic Potential of Wheat: Prospective for Selection of Innocuous Varieties for Celiac Disease Patients via in vitro Approach

Celiac Disease (CD) is a multifactorial, autoimmune enteropathy activated by cereal proteins in genetically predisposed individuals carrying HLA DQ2/8 genes. A heterogenous gene combination of the cereal prolamins is documented in different wheat genotypes, which is suggestive of their variable immunogenic potential. In the current study, four wheat varieties (C591, C273, 9D, and K78) identified via in silico analysis were analyzed for immunogenicity by measuring T-cell proliferation rate and levels of inflammatory cytokines (Interferon-γ and Tumor Necrosis Factor-α). Peripheral Blood Mononuclear Cells and biopsy derived T-cell lines isolated from four CD patients in complete remission and two controls were stimulated and cultured in the presence of tissue transglutaminase activated pepsin-trypsin (PT) digest of total gliadin extract from test varieties. The immunogenicity was compared with PBW 621, one of the widely cultivated wheat varieties. Phytohaemagglutinin-p was taken as positive control, along with unstimulated cells as negative control. Rate of cell proliferation (0.318, 0.482; 0.369, 0.337), concentration of IFN- γ (107.4, 99.2; 117.9, 99.7 pg/ml), and TNF- α (453.8, 514.2; 463.8, 514.2 pg/ml) was minimum in cultures supplemented with wheat antigen from C273, when compared with other test varieties and unstimulated cells. Significant difference in toxicity levels among different wheat genotypes to stimulate celiac mucosal T-cells and PBMC's was observed; where C273 manifested least immunogenic response amongst the test varieties analyzed.

In Vitro Screening of Bioactive Compounds in some Gluten-Free Plants

Electrophoretic, antioxidant, and FTIR profiles of some varieties of amaranth, quinoa, and buckwheat seeds and their by products were compared. Water extracts of these products were evaluated by the Folin-Ciocalteau method in order to determine total phenolic content. The antioxidant activities were determined by 2,2'-azobis-2-methyl-propanimidamide, ferric-reducing/antioxidant power, and cupric reducing antioxidant capacity radical scavenging assays. FTIR spectra showed the secondary structure of pseudocereals in the ranges of amides I, II, and III shifts. Results of evaluated methods could be used to control several products (seeds, flours, extracts, flakes, roasting) with high phenolic content and antioxidant activity suitable for supplementation in food applications. Graphical Abstract ᅟ.

Mechanisms, origin and heredity of Glu-1Ay silencing in wheat evolution and domestication

KEY MESSAGE

Allotetraploidization drives Glu-1Ay silencing in polyploid wheat. The high-molecular-weight glutenin subunit gene, Glu-1Ay, is always silenced in common wheat via elusive mechanisms. To investigate its silencing and heredity during wheat polyploidization and domestication, the Glu-1Ay gene was characterized in 1246 accessions containing diploid and polyploid wheat worldwide. Eight expressed Glu-1Ay alleles (in 71.81% accessions) and five silenced alleles with a premature termination codon (PTC) were identified in Triticum urartu; 4 expressed alleles (in 41.21% accessions), 13 alleles with PTCs and 1 allele with a WIS 2-1A retrotransposon were present in wild tetraploid wheat; and only silenced alleles with PTC or WIS 2-1A were in cultivated tetra- and hexaploid wheat. Both the PTC number and position in T. urartu Glu-1Ay alleles (one in the N-terminal region) differed from its progeny wild tetraploid wheat (1-5 PTCs mainly in the repetitive domain). The WIS 2-1A insertion occurred ~ 0.13 million years ago in wild tetraploid wheat, much later than the allotetraploidization event. The Glu-1Ay alleles with PTCs or WIS 2-1A that arose in wild tetraploid wheat were fully succeeded to cultivated tetraploid and hexaploid wheat. In addition, the Glu-1Ay gene in wild einkorn inherited to cultivated einkorn. Our data demonstrated that the silencing of Glu-1Ay in tetraploid and hexaploid wheat was attributed to the new PTCs and WIS 2-1A insertion in wild tetraploid wheat, and most silenced alleles were delivered to the cultivated tetraploid and hexaploid wheat, providing a clear evolutionary history of the Glu-1Ay gene in the wheat polyploidization and domestication processes.

Quantitative trait loci associated with soft wheat quality in a cross of good by moderate quality parents

Information on the genetic control of the quality traits of soft wheat (Triticum aestivum) is essential for breeding. Our objective was to identify QTL associated with end-use quality. We developed 150 F4-derived lines from a cross of Pioneer 26R46 × SS550 and tested them in four environments. We measured flour yield (FY), softness equivalent (SE), test weight (TW), flour protein content (FP), alkaline water retention capacity (AWRC), and solvent retention capacity (SRC) of water (WA), lactic acid (LA), sucrose (SU), sodium carbonate (SO). Parents differed for nine traits, transgressive segregants were noted, and heritability was high (0.67 to 0.90) for all traits. We detected QTL distributed on eight genomic regions. The QTL with the greatest effects were located on chromosome 1A, 1B, and 6B with each affecting at least five of ten quality traits. Pioneer 26R46 is one of the best quality soft wheats. The large-effect QTL on 1A novel and accounted for much of the variation for AWRC (r² = 0.26), SO (0.26) and SE (0.25), and FY (0.15) and may explain why Pioneer 26R46 has such superior quality. All alleles that increased a trait came from the parent with the highest trait value. This suggests that in any population that marker-assisted selection for these quality traits could be conducted by simply selecting for the alleles at key loci from the parent with the best phenotype without prior mapping.

A novel compensating wheat-Thinopyrum elongatum Robertsonian translocation line with a positive effect on flour quality

Wheat flours are used to produce bread, pasta, breakfast cereals, and biscuits; the various properties of these end-products are attributed to the gluten content, produced as seed storage proteins in the wheat endosperm. Thus, genes encoding gluten protein are major targets of wheat breeders aiming to improve the various properties of wheat flour. Here, we describe a novel compensating wheat-Thinopyrum elongatum Robertsonian translocation (T1AS.1EL) line involving the short arm of wheat chromosome 1A (1AS) and the long arm of Th. elongatum chromosome 1E (1EL); we developed this line through centric breakage-fusion. Compared to the common wheat cultivars Chinese Spring and Norin 61, we detected two additional 1EL-derived high-molecular-weight glutenin subunits (HMW-GSs) in the T1AS.1EL plants. Based on the results of an SDS-sedimentation volume to estimate the gluten strength of T1AS.1EL-derived flour, we predict that T1AS.1EL-derived flour is better suited to bread-making than Chinese Spring- and Norin 61-derived flour and that this is because of its greater gluten diversity. Also, we were able to assign 33 of 121 wheat PCR-based Landmark Unique Gene markers to chromosome 1E of Th. elongatum. These markers can now be used for further chromosome engineering of the Th. elongatum segment of T1AS.1EL.

Development of a new set of molecular markers for examining Glu-A1 variants in common wheat and ancestral species

In common wheat (Triticum aestivum L.), allelic variations of Glu-A1 locus have important influences on grain end-use quality. Among the three Glu-A1 alleles, Glu-A1a and -A1b encode the high-molecular-weight glutenin subunits (HMW-GSs) 1Ax1 and 1Ax2*, respectively, whereas Glu-A1c does not specify any subunit. Here, we detected a total of 11 Glu-A1 locus haplotypes (H1 to H11) in three wheat species, by developing and using a new set of DNA markers (Xrj5, Xid3, Xrj6, Xid4 and Xrj7). The main haplotypes found in the diploid wheat T. urartu were H1, H4, H5 and H6, with H1 and H4 expressing both 1Ax and 1Ay subunits. The major haplotypes revealed for tetraploid wheat (T. turgidum) were H1, H8 and H9, with the lines expressing both 1Ax and 1Ay belonging to H1, H4 or H7. Four major haplotypes (H1, H9, H10 and H11) were discovered in common wheat, with Glu-A1a associated with H1 and H8, Glu-A1b with H10 or H11, and Glu-A1c with H9. The Glu-A1 locus haplotypes and the new set of DNA markers have potential to be used for more effectively studying and utilizing the molecular variations of Glu-A1 to improve the end-use quality of common wheat are discussed.

New insight into the function of wheat glutenin proteins as investigated with two series of genetic mutants

Among the three major food crops (rice, wheat and maize), wheat is unique in accumulating gluten proteins in its grains. Of these proteins, the high and low molecular weight glutenin subunits (HMW-GSs and LMW-GSs) form glutenin macropolymers that are vital for the diverse end-uses of wheat grains. In this work, we developed a new series of deletion mutants lacking one or two of the three Glu-1 loci (Glu-A1, -B1 and -D1) specifying HMW-GSs. Comparative analysis of single and double deletion mutants reinforced the suggestion that Glu-D1 (encoding the HMW-GSs 1Dx2 and 1Dy12) has the largest effects on the parameters related to gluten and dough functionalities and breadmaking quality. Consistent with this suggestion, the deletion mutants lacking Glu-D1 or its combination with Glu-A1 or Glu-B1 generally exhibited strong decreases in functional glutenin macropolymers (FGMPs) and in the incorporation of HMW-GSs and LMW-GSs into FGMPs. Further examination of two knockout mutants missing 1Dx2 or 1Dy12 showed that 1Dx2 was clearly more effective than 1Dy12 in promoting FGMPs by enabling the incorporation of more HMW-GSs and LMW-GSs into FGMPs. The new insight obtained and the mutants developed by us may aid further research on the control of wheat end-use quality by glutenin proteins.

Transfer of HMW glutenin subunits from Aegilops kotschyi to wheat through radiation hybridization

High molecular weight glutenin subunits (HMWGS) are responsible for dough elasticity and bread making quality of bread wheat. Related wild non-progenitor species, Aegilops kotschyi possesses higher molecular weight x and y glutenin subunits than the bread wheat cultivars. A wheat-Aegilops substitution line with 1U chromosome was used for the transfer of (HMWGS) of 1U to wheat by using pollen radiation hybridization approach. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiling showed different patterns of allelic variations with either the presence or absence of HMWGS, Glu-1A (1, null), Glu-1B (7, 7 + 8, 17 + 18) and Glu-1D (5 + 10, 2 + 12, null). The pollen irradiated wheat-Aegilops derivatives, B-56-1-4-2, B-56-1-4-3, B-14-1 and B-14-2 with Glu1Ux and 1Uy and absence or presence of some Glu-1A and Glu-1B HMWGS showed high micro SDS sedimentation test (MST) values while B-16-1 and B-16-2 had moderate MST values and high protein content. However, B-58-3 with transfer of Glu-1Ux + 1Uy for Glu-1D showed very low MST values indicating that Glu-1Ux + 1Uy enhance MST value only in the presence of Glu1D HMWGS. The transfer/substitution of alien HMW-GS for Glu-1A and or Glu-1B loci only can lead to improved bread making quality of wheat.

Multiple elements controlling the expression of wheat high molecular weight glutenin paralogs

Analysis of gene expression data generated by high-throughput microarray transcript profiling experiments coupled with cis-regulatory elements enrichment study and cluster analysis can be used to define modular gene programs and regulatory networks. Unfortunately, the high molecular weight glutenin subunits of wheat (Triticum aestivum) are more similar than microarray data alone would allow to distinguish between the three homoeologous gene pairs. However, combining complementary DNA (cDNA) expression libraries with microarray data, a co-expressional network was built that highlighted the hidden differences between these highly similar genes. Duplex clusters of cis-regulatory elements were used to focus the co-expressional network of transcription factors to the putative regulatory network of Glu-1 genes. The focused network helped to identify several transcriptional gene programs in the endosperm. Many of these programs demonstrated a conserved temporal pattern across the studied genotypes; however, few others showed variance. Based on this network, transient gene expression assays were performed with mutated promoters to inspect the control of tissue specificity. Results indicated that the interactions of the ABRE│CBF cluster with distal promoter regions may have a dual role in regulation by both recruiting the transcription complex as well as suppressing it in non-endosperm tissue. A putative model of regulation is discussed.

Effect of Allelic Variation at the Glu-3/Gli-1 Loci on Breadmaking Quality Parameters in Hexaploid Wheat (Triticum aestivum L.)

Low molecular weight glutenin subunits (LMW-GS) encoded by the Glu-3 loci are known to contribute to wheat breadmaking quality. However, the specific effect of individual Glu-3 alleles is not well understood due to their complex protein banding patterns in SDS-PAGE and tight linkage with gliadins at the Gli-1 locus. Using DNA markers and a backcross program we developed a set of nine near isogenic lines (NILs) including different Glu-A3/GliA-1 or Glu-B3/Gli-B1 alleles in the genetic background of the Argentine variety ProINTA Imperial. The nine NILs and the control were evaluated in three different field trials in Argentina. Significant genotype-by-environment interactions were detected for most quality parameters indicating that the effects of the Glu-3/Gli-1 alleles are modulated by environmental differences. None of the NILs showed differences in total flour protein content, but relative changes in the abundance of particular classes of proteins cannot be ruled out. On average, the Glu-A3f, Glu-B3b, Glu-B3g and Glu-B3i_Man alleles were associated with the highest values in gluten strength-related parameters, while Glu-A3e, Glu-B3a and Glu-B3i_Chu were consistently associated with weak gluten and low quality values. The value of different Glu3/Gli-1 allele combinations to improve breadmaking quality is discussed.

Quality of synthetic hexaploid wheat containing null alleles at Glu-A1 and Glu-B1 loci

Triticum turgidum ssp. dicoccon PI94668 and PI349045 were identified as containing null alleles at Glu-A1 and Glu-B1 loci in previous investigation. Sequencing of the respective HMW-GS genes Ax, Bx, Ay and By in both accessions indicated equal DNA lengths with gene silencing caused by 1 to 4 in-frame stop codon(s) in the open reading frames. Six synthetic hexaploid wheat lines were produced by crossing PI94668 or PI349045 with six Aegilops tauschii by spontaneous chromosome doubling of unreduced gametes. As expected, these amphiploids had three different HMW-GS: Dx 3.1(t) + Dy11(*t), Dx2.1(t) +10(t) and Dx2(t) +Dy12(t) in Glu-D1 but double nulls in Glu-A1 and Glu-B1. Quality tests showed that most quality parameters in two T. turgidum ssp. dicoccon parents were very low due to the lack of HMW-GSs. However, incorporation of HMW-GS from Ae. tauschii in six synthetic hexaploid wheat lines significantly increased most quality related parameters. The potential values of these wheat lines in improving the quality of wheat are discussed.

Genome evolution due to allopolyploidization in wheat

The wheat group has evolved through allopolyploidization, namely, through hybridization among species from the plant genera Aegilops and Triticum followed by genome doubling. This speciation process has been associated with ecogeographical expansion and with domestication. In the past few decades, we have searched for explanations for this impressive success. Our studies attempted to probe the bases for the wide genetic variation characterizing these species, which accounts for their great adaptability and colonizing ability. Central to our work was the investigation of how allopolyploidization alters genome structure and expression. We found in wheat that allopolyploidy accelerated genome evolution in two ways: (1) it triggered rapid genome alterations through the instantaneous generation of a variety of cardinal genetic and epigenetic changes (which we termed "revolutionary" changes), and (2) it facilitated sporadic genomic changes throughout the species' evolution (i.e., evolutionary changes), which are not attainable at the diploid level. Our major findings in natural and synthetic allopolyploid wheat indicate that these alterations have led to the cytological and genetic diploidization of the allopolyploids. These genetic and epigenetic changes reflect the dynamic structural and functional plasticity of the allopolyploid wheat genome. The significance of this plasticity for the successful establishment of wheat allopolyploids, in nature and under domestication, is discussed.

Proteogenomic Characterization of Novel x-Type High Molecular Weight Glutenin Subunit 1Ax1.1

Analysis of Portuguese wheat (Triticum aestivum L.) landrace 'Barbela' revealed the existence of a new x-type high molecular weight-glutenin subunit (HMW-GS) encoded at the Glu-A1 locus, which we named 1Ax1.1. Using one-dimensional and two-dimensional electrophoresis and mass spectrometry, we compared subunit 1Ax1.1 with other subunits encoded at the Glu-A1 locus. Subunit 1Ax1.1 has a theoretical molecular weight of 93,648 Da (or 91,508 Da for the mature protein) and an isoelectric point (pI) of about 5.7, making it the largest and most acidic HMW-GS known to be encoded at Glu-A1. Specific primers were designed to amplify and sequence 2601 bp of the Glu-A1 locus from the 'Barbela 28' wheat genome. A very high level of identity was found between the sequence encoding 1Ax1.1 and those encoding other alleles of the locus. The major difference found was an insertion of 36 amino acids in the central repetitive domain.