Genomic and functional genomics analyses of gluten proteins and prospect for simultaneous improvement of end-use and health-related traits in wheat

Deciphering the Transcriptional Regulatory Network Governing Starch and Storage Protein Biosynthesis in Wheat for Breeding Improvement

Starch and seed storage protein (SSP) composition profoundly impact wheat grain yield and quality. To unveil regulatory mechanisms governing their biosynthesis, transcriptome, and epigenome profiling is conducted across key endosperm developmental stages, revealing that chromatin accessibility, H3K27ac, and H3K27me3 collectively regulate SSP and starch genes with varying impact. Population transcriptome and phenotype analyses highlight accessible promoter regions' crucial role as a genetic variation resource, influencing grain yield and quality in a core collection of wheat accessions. Integration of time-serial RNA-seq and ATAC-seq enables the construction of a hierarchical transcriptional regulatory network governing starch and SSP biosynthesis, identifying 42 high-confidence novel candidates. These candidates exhibit overlap with genetic regions associated with grain size and quality traits, and their functional significance is validated through expression-phenotype association analysis among wheat accessions and loss-of-function mutants. Functional analysis of wheat abscisic acid insensitive 3-A1 (TaABI3-A1) with genome editing knock-out lines demonstrates its role in promoting SSP accumulation while repressing starch biosynthesis through transcriptional regulation. Excellent TaABI3-A1Hap1 with enhanced grain weight is selected during the breeding process in China, linked to altered expression levels. This study unveils key regulators, advancing understanding of SSP and starch biosynthesis regulation and contributing to breeding enhancement.

Physico-Chemical and Rheological Trait-Based Identification of Indian Wheat Varieties Suitable for Different End-Uses

India has increased its wheat production phenomenally in the last two decades and it now has a buffer stock of 9.7 million tonnes. However, despite the release of several wheat cultivars, the end-use quality traits of Indian wheat varieties have not been explored in-depth to determine the increasing demand of the domestic processing industry as well as export. In this study, 55 wheat genotypes including 47 released varieties, and 8 genetic stocks were grown along with 10 Australian varieties grown during cropping seasons: 2019-2020 and 2020-2021 and diversity in different physiochemical and rheological traits was evaluated. They showed considerable diversity in all the quality traits studied. However, very few genotypes could be found suitable for any one end-use. Five genotypes were found to possess four to five traits for superior bread-making quality. Two varieties and three advanced breeding lines had up to four good chapati quality traits. None of the released varieties investigated had suitable traits for biscuit making; however, two breeding lines possessed requisite quality traits suitable for biscuit making. It is, therefore, concluded that systematic breeding efforts are required to develop genotypes that bring together the most important quality traits in a single genotype to be suitable for domestic industry as well as for export.

Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement

Despite recent progress in crop genomics studies, the genomic changes brought about by modern breeding selection are still poorly understood, thus hampering genomics-assisted breeding, especially in polyploid crops with compound genomes such as common wheat (Triticum aestivum). In this work, we constructed genome resources for the modern elite common wheat variety Aikang 58 (AK58). Comparative genomics between AK58 and the landrace cultivar Chinese Spring (CS) shed light on genomic changes that occurred through recent varietal improvement. We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study (HGWAS) approach, which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci. A total of 123 major HGWAS loci were detected using a genetic population derived from AK58 and CS. Elite homoeologous haplotypes (HHs), formed by combinations of subgenomic homoeologs of the associated loci, were found in both parents and progeny, and many could substantially improve wheat yield and related traits. We built a website where users can download genome assembly sequence and annotation data for AK58, perform blast analysis, and run JBrowse. Our work enriches genome resources for wheat, provides new insights into genomic changes during modern wheat improvement, and suggests that efficient mining of elite HHs can make a substantial contribution to genomics-assisted breeding in common wheat and other polyploid crops.

Gliadin and glutenin genomes and their effects on the technological aspect of wheat-based products

Wheat is the most important crops worldwide, providing about one-fifth of the daily protein and calories for human consumption. The quality of cereal-based products is principally governed by the genetic basis of gluten (glutenin and gliadin proteins), which exists in a wide range of variable alleles and is controlled by clusters of genes. There are certain limitations associated with gluten characteristics, which can be genetically manipulated. The present review aimed to investigate the correlation between the genetic characteristics of gluten protein components and wheat-based product's quality. According to various references, Glu-B1d (6 + 8), Glu-B1h (14 + 15) and Glu-B1b (7 + 8) are related to higher gluten strength and pasta quality, while, subunits Dx2 + Dy12 and Dx5 + Dy10, are usually present at the Glu-D1 locus in bread wheat, resulted in lower cooked firmness in pasta. Moreover, introducing Gli-D1/Glu-D3 and Glu-D1 loci into durum wheat genomes, causing to provide the maximum values of gluten index in pasta products. 1Dx5 + 1Dy10 alleles determine the level of increase in dough's consistency, elasticity, viscosity, and extensibility quality of baking and appropriate bread loaf volume, while 1Dx2 + 1Dy12 as the alleles associated with poor baking quality, being more suitable for soft wheat/pastry end uses. Bx7, Bx7OE, 1Bx17 + 1By18, 1Bx13 + 1By16, Bx7 + By9 and 1Bx7 + 1By8 at Glu-B1alleles and 1Ax2* found on Glu-A1, augmented dough strength and has positive effects on consistency, extensibility, viscosity, and elasticity of bread dough. Breeding programs by genome editing have made gluten a promoting component for improving cereal-based products.

Novel Genetic Loci from Triticum timopheevii Associated with Gluten Content Revealed by GWAS in Wheat Breeding Lines

The content and quality of gluten in wheat grain is a distinctive characteristic that determines the final properties of wheat flour. In this study, a genome-wide association study (GWAS) was performed on a wheat panel consisting of bread wheat varieties and the introgression lines (ILs) obtained via hybridization with tetraploid wheat relatives. A total of 17 stable quantitative trait nucleotides (QTNs) located on chromosomes 1D, 2A, 2B, 3D, 5A, 6A, 7B, and 7D that explained up to 21% of the phenotypic variation were identified. Among them, the QTLs on chromosomes 2A and 7B were found to contain three and six linked SNP markers, respectively. Comparative analysis of wheat genotypes according to the composition of haplotypes for the three closely linked SNPs of chromosome 2A indicated that haplotype TT/AA/GG was characteristic of ten ILs containing introgressions from T. timopheevii. The gluten content in the plants with TT/AA/GG haplotype was significantly higher than in the varieties with haplotype GG/GG/AA. Having compared the newly obtained data with the previously reported quantitative trait loci (QTLs) we inferred that the locus on chromosome 2A inherited from T. timopheevii is potentially novel. The introgression lines containing the new locus can be used as sources of genetic factors to improve the quality traits of bread wheat.

Fusing the 3'UTR of seed storage protein genes leads to massive recombinant protein accumulation in seeds

The demand for recombinant proteins is rising dramatically, and effective production systems are currently being developed. The production of recombinant proteins in plants is a promising approach due to its low cost and low risk of contamination of the proteins with endotoxins or infectious agents from the culture serum. Plant seeds primarily accumulate seed storage proteins (SSPs), which are transcribed and translated from a few genes; therefore, the mechanism underlying SSP accumulation has been studied to help devise ways to increase recombinant protein production. We found that the 3'UTR of SSP genes are essential for SSP accumulation and can be used in the production of recombinant proteins in Arabidopsis. Fusion of the 3'UTR of SSP genes to the 3' ends of DNA sequences encoding recombinant proteins enables massive accumulation of recombinant proteins with enzymatic activity in Arabidopsis seeds. This method is also applicable to the production of human Interferon Lambda-3 (IFN-lambda 3), a candidate biopharmaceutical compound against hepatitis C infection. Considering the low cost and ease of protein production in Arabidopsis, as well as the rapid growth of this plant, our method is useful for large-scale preparation of recombinant proteins for both academic research and biopharmaceutical production.

An elite γ-gliadin allele improves end-use quality in wheat

Gluten is composed of glutenins and gliadins and determines the viscoelastic properties of dough and end-use quality in wheat (Triticum aestivum L.). Gliadins are important for wheat end-use traits, but the contribution of individual gliadin genes is unclear, since gliadins are encoded by a complex, multigenic family, including many pseudogenes. We used CRISPR/Cas9-mediated gene editing and map-based cloning to investigate the contribution of the γ-gliadin genes annotated in the wheat cultivar 'Fielder', showing that Gli-γ1-1D and Gli-γ2-1B account for most of the γ-gliadin accumulation. The impaired activity of only two γ-gliadin genes in knockout mutants improved end-use quality and reduced gluten epitopes associated with celiac disease (CD). Furthermore, we identified an elite haplotype of Gli-γ1-1D linked to higher end-use quality in a wheat germplasm collection and developed a molecular marker for this allele for marker-assisted selection. Our findings provide information and tools for biotechnology-based and classical breeding programs aimed at improving wheat end-use quality.

The additive interactions between high-molecular-weight glutenin subunits and tannic acid improve the wheat quality

Wheat gluten proteins, especially high-molecular-weight glutenin subunits (HMW-GS), are the main contributor to flour processing quality. Tannic acid (TA) consisting of a central glucose unit and ten gallic acid molecules is a phenolic acid that improves the processing quality. However, the underlying mechanism of TA's improvement remains largely unknown. Here, we showed that TA's improving effects on gluten aggregation, dough-mixing and bread-making properties were directly associated with the kinds of HMW-GS expressed in wheat seeds in HMW-GS near-isogenic lines (NILs). We established a biochemical framework, elucidated the additive effects of HMW-GS-TA interaction and discovered that TA cross-linked specifically with wheat glutenins but not gliadins, and reduced gluten surface hydrophobicity and SH content depending on the kinds of expressed HMW-GS in the wheat seeds. We also demonstrated that hydrogen bonds play an essential role in TA-HMW-GS interactions and improvement of wheat processing quality. Additionally, the effects of TA on the antioxidant capacity and on nutrient (protein and starch) digestibility were also investigated in the NILs of HMW-GS. TA increased antioxidant capacity but did not affect the digestion of starches and proteins. Our results revealed that TA more effectively strengthened wheat gluten in the presence of more HMW-GS kinds, highlighting TA's potential as an improver toward healthy and quality bread and demonstrating that manipulating hydrogen bonds was a previously overlooked approach to improve wheat quality.

A multi-omic resource of wheat seed tissues for nutrient deposition and improvement for human health

As a globally important staple crop, wheat seeds provide us with nutrients and proteins. The trend of healthy dietary has become popular recently, emphasizing the consumption of whole-grain wheat products and the dietary benefits. However, the dynamic changes in nutritional profiles of different wheat seed regions (i.e., the embryo, endosperm and outer layers) during developmental stages and the molecular regulation have not been well studied. Here, we provide this multi-omic resource of wheat seeds and describe the generation, technical assessment and preliminary analyses. This resource includes a time-series RNA-seq dataset of the embryo, endosperm and outer layers of wheat seeds and their corresponding metabolomic dataset, covering the middle and late stages of seed development. Our RNA-seq experiments profile the expression of 63,708 genes, while the metabolomic data includes the abundance of 984 metabolites. We believe that this was the first reported transcriptome and metabolome dataset of wheat seeds that helps understand the molecular regulation of the deposition of beneficial nutrients and hence improvements for nutritional and processing quality traits.

Tailoring crops with superior product quality through genome editing: an update

In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.

Transcriptome and Proteome Analysis Revealed the Influence of High-Molecular-Weight Glutenin Subunits (HMW-GSs) Deficiency on Expression of Storage Substances and the Potential Regulatory Mechanism of HMW-GSs

The processing quality of wheat is affected by seed storage substances, such as protein and starch. High-molecular-weight glutenin subunits (HMW-GSs) are the major components of wheat seed storage proteins (SSPs); they are also key determinators of wheat end-use quality. However, the effects of HMW-GSs absence on the expression of other storage substances and the regulation mechanism of HMW-GSs are still limited. Previously, a wheat transgenic line LH-11 with complete deletions of HMW-GSs was obtained through introducing an exogenous gene Glu-1E^bx to the wild-type cultivar Bobwhite by transgenic approach. In this study, comparative seed transcriptomics and proteomics of transgenic and non-transgenic lines at different seed developmental stages were carried out to explore the changes in genes and proteins and the underlying regulatory mechanism. Results revealed that a number of genes, including genes related to SSPs, carbohydrates metabolism, amino acids metabolism, transcription, translation, and protein process were differentially enriched. Seed storage proteins displayed differential expression patterns between the transgenic and non-transgenic line, a major rise in the expression levels of gliadins were observed at 21 and 28 days post anthesis (DPA) in the transgenic line. Changes in expressions of low-molecular-weight glutenins (LMW-GSs), avenin-like proteins (ALPs), lipid transfer proteins (LTPs), and protease inhibitors (PIs) were also observed. In addition, genes related to carbohydrate metabolism were differentially expressed, which probably leads to a difference in starch component and deposition. A list of gene categories participating in the accumulation of SSPs was proposed according to the transcriptome and proteome data. Six genes from the MYB and eight genes from the NAC transcription families are likely important regulators of HMW-GSs accumulation. This study will provide data support for understanding the regulatory network of wheat storage substances. The screened candidate genes can lay a foundation for further research on the regulation mechanism of HMW-GSs.

Transcriptome Analysis Reveals Potential Mechanism in Storage Protein Trafficking within Developing Grains of Common Wheat

Gluten proteins are the major storage protein fraction in the mature wheat grain. They are restricted to the starchy endosperm, which defines the viscoelastic properties of wheat dough. The synthesis of these storage proteins is controlled by the endoplasmic reticulum (ER) and is directed into the vacuole via the Golgi apparatus. In the present study, transcriptome analysis was used to explore the potential mechanism within critical stages of grain development of wheat cultivar "Shaannong 33" and its sister line used as the control (CK). Samples were collected at 10 DPA (days after anthesis), 14 DPA, 20 DPA, and 30 DPA for transcriptomic analysis. The comparative transcriptome analysis identified that a total of 18,875 genes were differentially expressed genes (DEGs) between grains of four groups "T10 vs. CK10, T14 vs. CK14, T20 vs. CK20, and T30 vs. CK30", including 2824 up-regulated and 5423 down-regulated genes in T30 vs. CK30. Further, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment highlighted the maximum number of genes regulating protein processing in the endoplasmic reticulum (ER) during grain enlargement stages (10-20 DPA). In addition, KEGG database analysis reported 1362 and 788 DEGs involved in translation, ribosomal structure, biogenesis, flavonoid biosynthesis pathway and intracellular trafficking, secretion, and vesicular transport through protein processing within ER pathway (ko04141). Notably, consistent with the higher expression of intercellular storage protein trafficking genes at the initial 10 DPA, there was relatively low expression at later stages. Expression levels of nine randomly selected genes were verified by qRT-PCR, which were consistent with the transcriptome data. These data suggested that the initial stages of "cell division" played a significant role in protein quality control within the ER, thus maintaining the protein quality characteristics at grain maturity. Furthermore, our data suggested that the protein synthesis, folding, and trafficking pathways directed by a different number of genes during the grain enlargement stage contributed to the observed high-quality characteristics of gluten protein in Shaannong 33 (Triticum aestivum L.).

Unprocessed wheat γ-gliadin reduces gluten accumulation associated with the endoplasmic reticulum stress and elevated cell death

Along with increasing demands for high yield, elite processing quality and improved nutrient value in wheat, concerns have emerged around the effects of gluten in wheat-based foods on human health. However, knowledge of the mechanisms regulating gluten accumulation remains largely unexplored. Here we report the identification and characterization of a wheat low gluten protein 1 (lgp1) mutant that shows extremely low levels of gliadins and glutenins. The lgp1 mutation in a single γ-gliadin gene causes defective signal peptide cleavage, resulting in the accumulation of an excessive amount of unprocessed γ-gliadin and a reduced level of gluten, which alters the endoplasmic reticulum (ER) structure, forms the autophagosome-like structures, leads to the delivery of seed storage proteins to the extracellular space and causes a reduction in starch biosynthesis. Physiologically, these effects trigger ER stress and cell death. This study unravels a unique mechanism that unprocessed γ-gliadin reduces gluten accumulation associated with ER stress and elevated cell death in wheat. Moreover, the reduced gluten level in the lgp1 mutant makes it a good candidate for specific diets for patients with diabetes or kidney diease.

Marker-assisted introgression of genes into rye translocation leads to the improvement in bread making quality of wheat (Triticum aestivum L.)

Introgression of genes from related species can be a powerful way to genetically improve crop yields, but selection for one trait can come at the cost to others. Wheat varieties with translocation of the short arm of chromosome 1 from the B genome of wheat (1BS) with the short arm of chromosome 1 from rye (1RS) are popular globally for their positive effect on yield and stress resistance. Unfortunately, this translocation (1BL.1RS) is also associated with poor bread making quality, mainly due to the presence of Sec-1 on its proximal end, encoding secalin proteins, and the absence of Glu-B3/Gli-B1-linked loci on its distal end, encoding low molecular weight glutenin subunits (LMW-GS). The present study aims to replace these two important loci on the 1RS arm with the wheat 1BS loci, in two popular Indian wheat varieties, PBW550 and DBW17, to improve their bread-making quality. Two donor lines in the cultivar Pavon background with absence of the Sec-1 locus and presence of the Glu-B3/Gli-B1 locus, respectively, were crossed and backcrossed with these two selected wheat varieties. In the advancing generations, marker assisted foreground selection was done for Sec-1^- and Glu-B3/Gli-B1⁺ loci while recurrent parent recovery was done with the help of SSR markers. BC₂F₅ and BC₂F₆ near isosgenic lines (NILs) with absence of Sec-1 and presence of Glu-B3/Gli-B1 loci were evaluated for two years in replicated yield trials. As a result of this selection, thirty promising lines were generated that demonstrated improved bread making quality but also balanced with improved yield-related traits compared to the parental strains. The study demonstrates the benefits of using marker-assisted selection to replace a few loci with negative effects within larger alien translocations for crop improvement.

Dissection of the Genetic Architecture for Quantities of Gliadins Fractions in Wheat (Triticum aestivum L.)

Gliadin is a group of grain storage proteins that confers extensibility/viscosity to the dough and are vital to end-use quality in wheat. Moreover, gliadins are one of the important components for nutritional quality because they contain the nutritional unprofitable epitopes that cause chronic immune-mediated intestinal disorder in genetically susceptible individuals designated celiac disease (CD). The main genetic loci encoding the gliadins were revealed by previous studies; however, the genes related to the content of gliadins and their fractions were less elucidated. To illustrate the genetic basis of the content of gliadins and their fractions comprehensively, a recombinant inbred line (RIL) population that consisted of 196 lines was constructed from the two parents, Luozhen No.1 and Zhengyumai 9987. Quantitative trait loci (QTL) controlling the content of total gliadins and their fractions (ω-, α-, and γ-gliadin) were screened genome-widely under four environments across 2 years. Totally, thirty QTL which explained 1.97-12.83% of the phenotypic variation were detected to be distributed on 17 chromosomes and they were gathered into 12 clusters. One hundred and one pairs of epistatic QTL (E-QTL) were revealed, among which five were involved with the total gliadins and its fractions content QTL located on chromosome 1AS, 1DS, 4DS, 1DL, and 6AS. Three Kompetitive Allele-Specific PCR (KASP) markers were developed from three major QTL clusters located on chromosomes 6A, 6D, and 7D, respectively. The present research not only dissects the genetic loci for improving the content of gliadins and their three fractions, but may also contribute to marker-assisted selection of varieties with appropriate gliadin fractions content for end-use quality and health benefit at the early developmental stages and early breeding generations.

Targeting Induced Local Lesions in the Wheat DEMETER and DRE2 Genes, Responsible for Transcriptional Derepression of Wheat Gluten Proteins in the Developing Endosperm

Wheat is a major source of energy and nutrition worldwide, but it is also a primary cause of frequent diet-induced health issues, specifically celiac disease, for which the only effective therapy so far is strict dietary abstinence from gluten-containing grains. Wheat gluten proteins are grouped into two major categories: high-molecular-weight glutenin subunits (HMWgs), vital for mixing and baking properties, and gliadins plus low-molecular-weight glutenin subunits (LMWgs) that contain the overwhelming majority of celiac-causing epitopes. We put forth a hypothesis that eliminating gliadins and LMWgs while retaining HMWgs might allow the development of reduced-immunogenicity wheat genotypes relevant to most gluten-sensitive individuals. This hypothesis stems from the knowledge that the molecular structures and regulatory mechanisms of the genes encoding the two groups of gluten proteins are quite different, and blocking one group's transcription, without affecting the other's, is possible. The genes for gliadins and LMWgs have to be de-methylated by 5-methylcytosine DNA glycosylase/lyase (DEMETER) and an iron-sulfur (Fe-S) cluster biogenesis enzyme (DRE2) early during endosperm development to permit their transcription. In this study, a TILLING (Targeting Induced Local Lesions IN Genomes) approach was undertaken to identify mutations in the homoeologous DEMETER (DME) and DRE2 genes in common and durum wheat. Lines with mutations in these genes were obtained that displayed reduced content of immunogenic gluten proteins while retaining essential baking properties. Although our data at first glance suggest new possibilities for treating celiac disease and are therefore of medical and agronomical interest, it also shows that inducing mutations in the DME and DRE2 genes analyzed here affected pollen viability and germination. Hence there is a need to develop other approaches in the future to overcome this undesired effect.

Promoter DNA hypermethylation of TaGli-γ-2.1 positively regulates gluten strength in bread wheat

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TaGli-γ-2.1 belonged to a subgroup of γ-gliadin multigene family.

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TaGli-γ-2.1 was a negative regulatory factor in gluten strength.

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Methylation of pTaGli-γ-2.1 played a key role in regulating TaGli-γ-2.1 expression.

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Lower γ-gliadin content followed with hypermethylation of pTaGli-γ-2.1.

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Decreasing TaGli-γ-2.1 expression could be used to improve gluten strength in wheat breeding.

Introduction

Gliadins are the major components of gluten proteins with vital roles on properties of end-use wheat product and health-relate quality of wheat. However, the function and regulation mechanisms of γ-gliadin genes remain unclear.

Objectives

Dissect the effect of DNA methylation in the promoter of γ-gliadin gene on its expression level and gluten strength of wheat.

Methods

The prokaryotic expression and reduction–oxidation reactions were performed to identify the effect of TaGli-γ-2.1 on dough strength. Bisulfite analysis and 5-Aza-2′-deoxycytidine treatment were used to verify the regulation of TaGli-γ-2.1 expression by pTaGli-γ-2.1 methylation. The content of gluten proteins composition was measured by RP-HPLC, and the gluten strength was measured by Gluten Index and Farinograph.

Results

TaGli-γ-2.1 was classified into a subgroup of γ-gliadin multigene family and was preferentially expressed in the later period of grain filling. Addition of TaGli-γ-2.1 protein fragment into strong gluten wheat flour significantly decreased the stability time. Hypermethylation of three CG loci of pTaGli-γ-2.1 conferred to lower TaGli-γ-2.1 expression. Treatment with 5-Aza-2′-deoxycytidine in seeds of strong gluten wheat varieties increased the expression levels of TaGli-γ-2.1. Furthermore, the accumulations of gliadin and γ-gliadin were significantly decreased in hypermethylated wheat varieties, corresponding with the increasing of gluten index and dough stability time.

Conclusion

Epigenetic modification of pTaGli-γ-2.1 affected gluten strength by modulating the proportion of gluten proteins. Hypermethylation of pTaGli-γ-2.1 is a novel genetic resource for enhancing gluten strength in wheat quality breeding.

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.

The Effect of Abiotic Stresses on the Protein Composition of Four Hungarian Wheat Varieties

Global climate change in recent years has resulted in extreme heat and drought events that significantly influence crop production and endanger food security. Such abiotic stress during the growing season has a negative effect on yield as well as on the functional properties of wheat grain protein content and composition. This reduces the value of grain, as these factors significantly reduce end-use quality. In this study, four Hungarian bread wheat cultivars (Triticum aestivum ssp. aestivum) with different drought and heat tolerance were examined. Changes in the size- and hydrophobicity-based distribution of the total proteins of the samples have been monitored by SE- and RP-HPLC, respectively, together with parallel investigations of changes in the amounts of the R5 and G12 antibodies related to celiac disease immunoreactive peptides. Significant difference in yield, protein content and composition have been observed in each cultivar, altering the amounts of CD-related gliadin, as well as the protein parameters directly related to techno-functional properties (Glu/Gli ratio, UPP%). The extent of changes largely depended on the timing of the abiotic stress. The severity of the negative effect depended on the growth stage in which abiotic stress occurred.

Characterization of novel LMW-i genes with nine cysteine residues from Chinese wheat landraces (Triticum aestivum L.) and analysis of their functional properties on dough mixing

The low-molecular-weight glutenin subunits (LMW-GS) with extra cysteine numbers have attracted great research interest for their potential quality value. In this study, 14 LMW-i type genes (YD1-YD14) were isolated from three types of Chinese wheat landraces; and nine of 14 genes (YD1-YD9) had nine cysteines, and the other five genes contained eight cysteines. Phylogenic analysis suggested that all 14 LMW-i genes were related to Glu-A3-1 variants Glu-A3-17/FJ 549934 and Glu-A3-15/FJ 549932. Six randomly selected genes, five genes including YD 1 with nine cysteines and the remaining one with eight cysteines, were successfully expressed in bacteria as mature proteins with a molecular mass of ~ 46 kDa. These proteins were traced to corresponding seed storage proteins for having similar elution times in reverse phase high-performance liquid chromatography (RP-HPLC) profiles. Mass spectrometry verified that bacterial expressed protein pET-30a-YD1 was LMW-i. Dough mixing experiments for incorporation of 50 mg pET-30a-YD1 proteins into the base flour of weak gluten wheat cv. "Chuannong 16" indicated that the dough strength of mixing flours was noticeably weaker than that of the control, which was reflected by mixing parameters in 8-min curve width, peak width, peak height, mixing time, and right of peak slope. The results suggested that the LMW-i genes with nine cysteine residues in the present study contributed to inferior quality properties for wheat flour.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03044-8.

Genome-Wide Identification, Characterization and Expression Pattern Analysis of the γ-Gliadin Gene Family in the Durum Wheat (Triticum durum Desf.) Cultivar Svevo

Very recently, the genome of the modern durum wheat cv. Svevo was fully sequenced, and its assembly is publicly available. So, we exploited the opportunity to carry out an in-depth study for the systematic characterization of the γ-gliadin gene family in the cv. Svevo by combining a bioinformatic approach with transcript and protein analysis. We found that the γ-gliadin family consists of nine genes that include seven functional genes and two pseudogenes. Three genes, Gli-γ1a, Gli-γ3a and Gli-γ4a, and the pseudogene Gli-γ2a* mapped on the A genome, whereas the remaining four genes, Gli-γ1b, Gli-γ2b, Gli-γ3b and Gli-γ5b, and the pseudogene Gli-γ4b* mapped on the B genome. The functional γ-gliadins presented all six domains and eight-cysteine residues typical of γ-gliadins. The Gli-γ1b also presented an additional cysteine that could possibly have a role in the formation of the gluten network through binding to HMW glutenins. The γ-gliadins from the A and B genome differed in their celiac disease (CD) epitope content and composition, with the γ-gliadins from the B genome showing the highest frequency of CD epitopes. In all the cases, almost all the CD epitopes clustered in the central region of the γ-gliadin proteins. Transcript analysis during seed development revealed that all the functional γ-gliadin genes were expressed with a similar pattern, although significant differences in the transcript levels were observed among individual genes that were sometimes more than 60-fold. A progressive accumulation of the γ-gliadin fraction was observed in the ripening seeds that reached 34% of the total gliadin fraction at harvest maturity. We believe that the insights generated in the present study could aid further studies on gliadin protein functions and future breeding programs aimed at the selection of new healthier durum wheat genotypes.

Genetic identification and characterization of chromosomal regions for kernel length and width increase from tetraploid wheat

BACKGROUND

Improvement of wheat gercTriticum aestivum L.) yield could relieve global food shortages. Kernel size, as an important component of 1000-kernel weight (TKW), is always a significant consideration to improve yield for wheat breeders. Wheat related species possesses numerous elite genes that can be introduced into wheat breeding. It is thus vital to explore, identify, and introduce new genetic resources for kernel size from wheat wild relatives to increase wheat yield.

RESULTS

In the present study, quantitative trait loci (QTL) for kernel length (KL) and width (KW) were detected in a recombinant inbred line (RIL) population derived from a cross between a wild emmer accession 'LM001' and a Sichuan endemic tetraploid wheat 'Ailanmai' using the Wheat 55 K single nucleotide polymorphism (SNP) array-based constructed linkage map and phenotype from six different environments. We identified eleven QTL for KL and KW including two major ones QKL.sicau-AM-3B and QKW.sicau-AM-4B, the positive alleles of which were from LM001 and Ailanmai, respectively. They explained 17.57 to 44.28% and 13.91 to 39.01% of the phenotypic variance, respectively. For these two major QTL, Kompetitive allele-specific PCR (KASP) markers were developed and used to successfully validate their effects in three F3 populations and two natural populations containing a panel of 272 Chinese wheat landraces and that of 300 Chinese wheat cultivars, respectively. QKL.sicau-AM-3B was located at 675.6-695.4 Mb on chromosome arm 3BL. QKW.sicau-AM-4B was located at 444.2-474.0 Mb on chromosome arm 4BL. Comparison with previous studies suggested that these two major QTL were likely new loci. Further analysis indicated that the positive alleles of QKL.sicau-AM-3B and QKW.sicau-AM-4B had a great additive effect increasing TKW by 6.01%. Correlation analysis between KL and other agronomic traits showed that KL was significantly correlated to spike length, length of uppermost internode, TKW, and flag leaf length. KW was also significantly correlated with TKW. Four genes, TRIDC3BG062390, TRIDC3BG062400, TRIDC4BG037810, and TRIDC4BG037830, associated with kernel development were predicted in physical intervals harboring these two major QTL on wild emmer and Chinese Spring reference genomes.

CONCLUSIONS

Two stable and major QTL for KL and KW across six environments were detected and verified in three biparental populations and two natural populations. Significant relationships between kernel size and yield-related traits were identified. KASP markers tightly linked the two major QTL could contribute greatly to subsequent fine mapping. These results suggested the application potential of wheat related species in wheat genetic improvement.

A Case Study of the Response of Immunogenic Gluten Peptides to Sourdough Proteolysis

Celiac disease is activated by digestion-resistant gluten peptides that contain immunogenic epitopes. Sourdough fermentation is a potential strategy to reduce the concentration of these peptides within food. However, we currently know little about the effect of partial sourdough fermentation on immunogenic gluten. This study examined the effect of a single sourdough culture (representative of those that the public may consume) on the digestion of immunogenic gluten peptides. Sourdough bread was digested via the INFOGEST protocol. Throughout digestion, quantitative and discovery mass spectrometry were used to model the kinetic release profile of key immunogenic peptides and profile novel peptides, while ELISA probed the gluten's allergenicity. Macrostructural studies were also undertaken. Sourdough fermentation altered the protein structure, in vitro digestibility, and immunogenic peptide release profile. Interestingly, sourdough fermentation did not decrease the total immunogenic peptide concentration but altered the in vitro digestion profile of select immunogenic peptides. This work demonstrates that partial sourdough fermentation can alter immunogenic gluten digestion, and is the first study to examine the in vitro kinetic profile of immunogenic gluten peptides from sourdough bread.

Proteome and transcriptome analyses of wheat near isogenic lines identifies key proteins and genes of wheat bread quality

The regulation of wheat protein quality is a highly complex biological process involving multiple metabolic pathways. To reveal new insights into the regulatory pathways of wheat glutenin synthesis, we used the grain-filling period wheat grains of the near-isogenic lines NIL-723 and NIL-1010, which have large differences in quality, to perform a combined transcriptome and proteome analysis. Compared with NIL-1010, NIL-723 had 1287 transcripts and 355 proteins with significantly different abundances. Certain key significantly enriched pathway were identified, and wheat quality was associated with alanine, aspartate and glutamate metabolism, nitrogen metabolism and alpha-linolenic acid metabolism. Differentially expressed proteins (DEPs) or Differentially expressed genes (DEGs) in amino acid synthesis pathways were upregulated primarily in the glycine (Gly), methionine (Met), threonine (Thr), glutamic acid (Glu), proline (proC), cysteine (Cys), and arginine (Arg) synthesis and downregulated in the tryptophan (trpE), leucine (leuC), citrulline (argE), and ornithine (argE) synthesis. Furthermore, to elucidate changes in glutenin in the grain synthesis pathway, we plotted a regulatory pathway map and found that DEGs and DEPs in ribosomes (RPL5) and the ER (HSPA5, HYOU1, PDIA3, PDIA1, Sec24, and Sec31) may play key roles in regulating glutenin synthesis. The transcriptional validation of some of the differentially expressed proteins through real-time quantitative PCR analysis further validated the transcriptome and proteomic results.

Posttranslational Modification of Waxy to Genetically Improve Starch Quality in Rice Grain

The waxy (Wx) gene, encoding the granule-bound starch synthase (GBSS), is responsible for amylose biosynthesis and plays a crucial role in defining eating and cooking quality. The waxy locus controls both the non-waxy and waxy rice phenotypes. Rice starch can be altered into various forms by either reducing or increasing the amylose content, depending on consumer preference and region. Low-amylose rice is preferred by consumers because of its softness and sticky appearance. A better way of improving crops other than downregulation and overexpression of a gene or genes may be achieved through the posttranslational modification of sites or regulatory enzymes that regulate them because of their significance. The impact of posttranslational GBSSI modifications on extra-long unit chains (ELCs) remains largely unknown. Numerous studies have been reported on different crops, such as wheat, maize, and barley, but the rice starch granule proteome remains largely unknown. There is a need to improve the yield of low-amylose rice by employing posttranslational modification of Wx, since the market demand is increasing every day in order to meet the market demand for low-amylose rice in the regional area that prefers low-amylose rice, particularly in China. In this review, we have conducted an in-depth review of waxy rice, starch properties, starch biosynthesis, and posttranslational modification of waxy protein to genetically improve starch quality in rice grains.

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.

A rapid and sensitive lateral flow immunoassay (LFIA) for the detection of gluten in foods

The gluten protein found in a variety of cereal grains is a food allergen that can elicit a spectrum of immuno-inflammatory responses in people. Consumer awareness has prompted changes in food labeling requirements, expanded gluten-free food product availability and increased demand for effective gluten testing methodologies. To meet the challenges associated with gluten testing from diverse and complex foods we developed a lateral flow immunoassay (LFIA) using a pair of novel gliadin monoclonal antibodies (MAbs). Using a visual gold reporter, we show sensitive gluten detection (150 ng/mL) from complex food substrates using a fast (<5 min) and easy testing methodology. In this report we characterize the binding properties of a cohort of newly generated gliadin monoclonal antibodies suitable for gluten detection using multiple assay formats and introduce a novel plug-n-play test strip platform with integrated test components in a single-use format.

The Gluten Gene: Unlocking the Understanding of Gluten Sensitivity and Intolerance

Wheat flour is one of the most important food ingredients containing several essential nutrients including proteins. Gluten is one of the major protein components of wheat consisted of glutenin (encoded on chromosome 1) and gliadin (encoded on chromosome 1 and 6) and there are around hundred genes encoding it in wheat. Gluten proteins have the ability of eliciting the pathogenic immune responses and hypersensitivity reactions in susceptible individuals called “gluten-related disorders (GRDs)”, which include celiac disease (CD), wheat allergy (WA), and non-celiac gluten sensitivity (NCGS). Currently removing gluten from the diet is the only effective treatment for mentioned GRDs and studies for the appropriate and alternative therapeutic approaches are ongoing. Accordingly, several genetic studies have focused on breeding wheat with low immunological properties through gene editing methods. The present review considers genetic characteristics of gluten protein components, focusing on their role in the incidence of gluten-related diseases, and genetic modifications conducted to produce wheat with less immunological properties.

Could Global Intensification of Nitrogen Fertilisation Increase Immunogenic Proteins and Favour the Spread of Coeliac Pathology?

Fertilisation of cereal crops with nitrogen (N) has increased in the last five decades. In particular, the fertilisation of wheat crops increased by nearly one order of magnitude from 1961 to 2010, from 9.84 to 93.8 kg N ha-1 y-1. We hypothesized that this intensification of N fertilisation would increase the content of allergenic proteins in wheat which could likely be associated with the increased pathology of coeliac disease in human populations. An increase in the per capita intake of gliadin proteins, the group of gluten proteins principally responsible for the development of coeliac disease, would be the responsible factor. We conducted a global meta-analysis of available reports that supported our hypothesis: wheat plants growing in soils receiving higher doses of N fertilizer have higher total gluten, total gliadin, α/β-gliadin, γ-gliadin and ω-gliadin contents and higher gliadin transcription in their grain. We thereafter calculated the per capita annual average intake of gliadins from wheat and derived foods and found that it increased from 1961 to 2010 from approximately 2.4 to 3.8 kg y-1 per capita (+1.4 ± 0.18 kg y-1 per capita, mean ± SE), i.e., increased by 58 ± 7.5%. Finally, we found that this increase was positively correlated with the increase in the rates of coeliac disease in all the available studies with temporal series of coeliac disease. The impacts and damage of over-fertilisation have been observed at an environmental scale (e.g., eutrophication and acid rain), but a potential direct effect of over-fertilisation is thus also possible on human health (coeliac disease).

QTL analysis of farinograph and mixograph related traits in spring wheat under heat stress conditions

Farinograph and mixograph-related parameters are key elements in wheat end-products quality. Understanding the genetic control of these traits and the influence of environmental factors such as heat stress, and their interaction are critical for developing cultivars with improved for those traits. To identify QTL for six farinograph and three mixograph traits, two double haploid (DH) populations (Yecora Rojo × Ksu106 and Klasic × Ksu105) were used in experiments conducted at Riyadh and Al Qassim locations under heat stress. Single nucleotide polymorphism (SNP) markers were used to determine the number of QTLs controlling these parameters. The genetic analysis of farinograph and mixograph-related traits showed considerable variation with transgressive segregation regardless of heat stress conditions in both locations. A total of 108 additive QTLs were detected for the six farinograph and three mixograph traits in the Yecora Rojo × Ksu106 population in both locations under heat treatments. These QTLs were distributed over all 21 wheat chromosomes except 3A. Similarly, in Klassic × Ksu105 population, there were an additional 68 QTLs identified over the two locations and were allocated on all chromosomes except 1D, 2A, 6A, and 6D. In population (Yecora Rojo × Ksu106), the QTL on chromosome 7A (Excalibur_c62415_288) showed significant effects for farinograph and mixograph traits (FDDT, FDST, FBD, M × h8, and M × t) under normal and heat stress condition at both locations. Interestingly, several QTLs that are related to farinograph and mixograph traits, which showed stable expression under both locations, were detected on chromosome 7A in population (Klassic × Ksu105). Results from this study show the quantitative nature of the genetic control of the studied traits and constitute a step toward identifying major QTLs that can be sued molecular-marker assisted breeding to develop new improved quality wheat cultivars.

The genetic diversity of group-1 homoeologs and characterization of novel LMW-GS genes from Chinese Xinjiang winter wheat landraces (Triticum aestivum L.)

Group-1 homoelog genes in wheat genomes encode storage proteins and are the major determinants of wheat product properties. Consequently, understanding the genetic diversity of group-1 homoelogs and genes encoding storage proteins, especially the low-molecular-weight glutenins (LMW-GSs), within wheat landrace genomes is necessary to further improve the quality of modern wheat crops. The genetic diversity of group-1 homoelogs in 75 Xinjiang winter wheat landraces was evaluated by Diversity Arrays Technology (DArT) markers. These data were used to select 15 landraces for additional LMW-GS gene isolation. The genetic similarity coefficients among landraces were highly similar regardless if considering the diversity markers on 1A, 1B, and 1D chromosomes individually or using all of the markers together. These similarities were evinced by the generation of four similar cluster dendrograms that comprised 11-15 landrace groups, regardless of the dataset used to generate the dendrograms. A total of 105 LMW-GS sequences corresponding to 79 unique genes were identified overall by using primers designed to target Glu-A3 and Glu-B3 loci, and 54 mature proteins were predicted from the unique LMW-GS genes. Nine novel chimeric LMW-GS genes were also identified, of which, one was recombinant for -i/-m, one for -s/-m, and seven for -m/-m parent genes, respectively. Phylogenetic analysis separated all of the LMW-GSs into three clades that were supported by moderate bootstrap values (> 70%). The clades corresponded to LMW-GS genes primarily harboring different N-terminals. These results provide useful information for better understanding the evolutionary genetics of the important Glu-3 locus of wheat, and they also provide new novel gene targets that can potentially be exploited to improve wheat quality.

Over-Expressing TaSPA-B Reduces Prolamin and Starch Accumulation in Wheat (Triticum aestivum L.) Grains

Starch and prolamin composition and content are important indexes for determining the processing and nutritional quality of wheat (Triticum aestivum L.) grains. Several transcription factors (TFs) regulate gene expression during starch and protein biosynthesis in wheat. Storage protein activator (TaSPA), a member of the basic leucine zipper (bZIP) family, has been reported to activate glutenin genes and is correlated to starch synthesis related genes. In this study, we generated TaSPA-B overexpressing (OE) transgenic wheat lines. Compared with wild-type (WT) plants, the starch content was slightly reduced and starch granules exhibited a more polarized distribution in the TaSPA-B OE lines. Moreover, glutenin and ω- gliadin contents were significantly reduced, with lower expression levels of related genes (e.g., By15, Dx2, and ω-1,2 gliadin gene). RNA-seq analysis identified 2023 differentially expressed genes (DEGs). The low expression of some DEGs (e.g., SUSase, ADPase, Pho1, Waxy, SBE, SSI, and SS II a) might explain the reduction of starch contents. Some TFs involved in glutenin and starch synthesis might be regulated by TaSPA-B, for example, TaPBF was reduced in TaSPA-B OE-3 lines. In addition, dual-luciferase reporter assay indicated that both TaSPA-B and TaPBF could transactivate the promoter of ω-1,2 gliadin gene. These results suggest that TaSPA-B regulates a complex gene network and plays an important role in starch and protein biosynthesis in wheat.