Dissecting conserved cis-regulatory modules of Glu-1 promoters which confer the highly active endosperm-specific expression via stable wheat transformation

Beyond pathways: Accelerated flavonoids candidate identification and novel exploration of enzymatic properties using combined mapping populations of wheat

Although forward-genetics-metabolomics methods such as mGWAS and mQTL have proven effective in providing myriad loci affecting metabolite contents, they are somehow constrained by their respective constitutional flaws such as the hidden population structure for GWAS and insufficient recombinant rate for QTL. Here, the combination of mGWAS and mQTL was performed, conveying an improved statistical power to investigate the flavonoid pathways in common wheat. A total of 941 and 289 loci were, respectively, generated from mGWAS and mQTL, within which 13 of them were co-mapped using both approaches. Subsequently, the mGWAS or mQTL outputs alone and their combination were, respectively, utilized to delineate the metabolic routes. Using this approach, we identified two MYB transcription factor encoding genes and five structural genes, and the flavonoid pathway in wheat was accordingly updated. Moreover, we have discovered some rare-activity-exhibiting flavonoid glycosyl- and methyl-transferases, which may possess unique biological significance, and harnessing these novel catalytic capabilities provides potentially new breeding directions. Collectively, we propose our survey illustrates that the forward-genetics-metabolomics approaches including multiple populations with high density markers could be more frequently applied for delineating metabolic pathways in common wheat, which will ultimately contribute to metabolomics-assisted wheat crop improvement.

TaTPS11 enhances wheat cold resistance by regulating source-sink factor

The presence of sugar in plant tissue can lead to an increase in the osmotic pressure within cells, a decrease in the freezing point of plants, and protection against ice crystal damage to the tissue. Trehalose is closely related to sucrose, which comprises the largest proportion of sugar and has become a hot topic of research in recent years. Our previous studies have confirmed that a key trehalose synthesis gene, TaTPS11, from the cold-resistant winter wheat DM1, could enhance the cold resistance of plants by increasing sugar content. However, the underlying mechanism behind this phenomenon remains unclear. In this study, we cloned TaTPS11-6D, edited TaTPS11-6D using CRISPR/Cas9 technology and transformed 'Fielder' to obtain T2 generation plants. We screened out OE3-3 and OE8-7 lines with significantly higher cold resistance than that of 'Fielder' and Cri 4-3 edited lines with significantly lower cold resistance than that of 'Fielder'. Low temperature storage limiting factors were measured for OE3-3, OE8-7 and Cri 4-3 treated at different temperatures.The results showed that TaTPS11-6D significantly increased the content of sugar in plants and the transfer of sugar from source to storage organs under cold conditions. The TaTPS11-6D significantly increased the levels of salicylic, jasmonic, and abscisic acids while also significantly decreasing the level of gibberellic acid. Our research improves the model of low temperature storage capacity limiting factor.

Dynamic metabolite QTL analyses provide novel biochemical insights into kernel development and nutritional quality improvement in common wheat

Despite recent advances in crop metabolomics, the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown. Here, we performed widely targeted metabolite profiling of kernels from three developmental stages (grain-filling kernels [FKs], mature kernels [MKs], and germinating kernels [GKs]) using a population of 159 recombinant inbred lines. We detected 625 annotated metabolites and mapped 3173, 3143, and 2644 metabolite quantitative trait loci (mQTLs) in FKs, MKs, and GKs, respectively. Only 52 mQTLs were mapped at all three stages, indicating the high stage specificity of the wheat kernel metabolome. Four candidate genes were functionally validated by in vitro enzymatic reactions and/or transgenic approaches in wheat, three of which mediated the tricin metabolic pathway. Metabolite flux efficiencies within the tricin pathway were evaluated, and superior candidate haplotypes were identified, comprehensively delineating the tricin metabolism pathway in wheat. Finally, additional wheat metabolic pathways were re-constructed by updating them to incorporate the 177 candidate genes identified in this study. Our work provides new information on variations in the wheat kernel metabolome and important molecular resources for improvement of wheat nutritional quality.

Orchestrating seed storage protein and starch accumulation toward overcoming yield-quality trade-off in cereal crops

Achieving high yield and good quality in crops is essential for human food security and health. However, there is usually disharmony between yield and quality. Seed storage protein (SSP) and starch, the predominant components in cereal grains, determine yield and quality, and their coupled synthesis causes a yield-quality trade-off. Therefore, dissection of the underlying regulatory mechanism facilitates simultaneous improvement of yield and quality. Here, we summarize current findings about the synergistic molecular machinery underpinning SSP and starch synthesis in the leading staple cereal crops, including maize, rice and wheat. We further evaluate the functional conservation and differentiation of key regulators and specify feasible research approaches to identify additional regulators and expand insights. We also present major strategies to leverage resultant information for simultaneous improvement of yield and quality by molecular breeding. Finally, future perspectives on major challenges are proposed.

Wheat Pm55 alleles exhibit distinct interactions with an inhibitor to cause different powdery mildew resistance

Powdery mildew poses a significant threat to wheat crops worldwide, emphasizing the need for durable disease control strategies. The wheat-Dasypyrum villosum T5AL·5 V#4 S and T5DL·5 V#4 S translocation lines carrying powdery mildew resistant gene Pm55 shows developmental-stage and tissue-specific resistance, whereas T5DL·5 V#5 S line carrying Pm5V confers resistance at all stages. Here, we clone Pm55 and Pm5V, and reveal that they are allelic and renamed as Pm55a and Pm55b, respectively. The two Pm55 alleles encode coiled-coil, nucleotide-binding site-leucine-rich repeat (CNL) proteins, conferring broad-spectrum resistance to powdery mildew. However, they interact differently with a linked inhibitor gene, SuPm55 to cause different resistance to wheat powdery mildew. Notably, Pm55 and SuPm55 encode unrelated CNL proteins, and the inactivation of SuPm55 significantly reduces plant fitness. Combining SuPm55/Pm55a and Pm55b in wheat does not result in allele suppression or yield penalty. Our results provide not only insights into the suppression of resistance in wheat, but also a strategy for breeding durable resistance.

Identifying cis-Acting Elements Associated with the High Activity and Endosperm Specificity of the Promoters of Genes Encoding Low-Molecular-Weight Glutenin Subunits in Common Wheat (Triticum aestivum)

Low-molecular-weight glutenin subunits (LMW-GSs) associated with bread-baking quality and flour nutrient quality accumulate in endosperms of common wheat and related species. However, the mechanism underlying the expression regulation of genes encoding LMW-GSs has not been fully elucidated. In this study, we identified LMW-D2 and LMW-D7, which are highly and weakly expressed, respectively, via the analysis of RNA-sequencing data of Chinese Spring wheat and wheat transgenic lines transformed with 5' deletion promoter fragments and GUS fusion constructs. The 605-bp fragment upstream of the LMW-D2 start codon could drive high levels of GUS expression in the endosperm. The truncated endosperm box located at the -300 site resulted in the loss of LMW-D2 promoter activity, and a single-nucleotide polymorphism on the GCN4 motif was closely related to the expression of LMW-GSs. TCT and TGACG motifs, as well as the others located on the 5' distal end, might also be involved in the transcription regulation of LMW-GSs. In transgenic lines, fusion proteins of LMW-GS and GUS were deposited into protein bodies. Our findings provide new insights into the mechanism underlying the transcription regulation of LMW-GSs and will contribute to the development of wheat endosperm as a bioreactor for the production of nutraceuticals, antibodies, vaccines, and medicinal proteins.

Efficient proteome-wide identification of transcription factors targeting Glu-1: A case study for functional validation of TaB3-2A1 in wheat

High-molecular-weight glutenin subunits (HMW-GS), a major component of seed storage proteins (SSP) in wheat, largely determine processing quality. HMW-GS encoded by GLU-1 loci are mainly controlled at the transcriptional level by interactions between cis-elements and transcription factors (TFs). We previously identified a conserved cis-regulatory module CCRM1-1 as the most essential cis-element for Glu-1 endosperm-specific high expression. However, the TFs targeting CCRM1-1 remained unknown. Here, we built the first DNA pull-down plus liquid chromatography-mass spectrometry platform in wheat and identified 31 TFs interacting with CCRM1-1. TaB3-2A1 as proof of concept was confirmed to bind to CCRM1-1 by yeast one hybrid and electrophoretic mobility shift assays. Transactivation experiments demonstrated that TaB3-2A1 repressed CCRM1-1-driven transcription activity. TaB3-2A1 overexpression significantly reduced HMW-GS and other SSP, but enhanced starch content. Transcriptome analyses confirmed that enhanced expression of TaB3-2A1 down-regulated SSP genes and up-regulated starch synthesis-related genes, such as TaAGPL3, TaAGPS2, TaGBSSI, TaSUS1 and TaSUS5, suggesting that it is an integrator modulating the balance of carbon and nitrogen metabolism. TaB3-2A1 also had significant effects on agronomic traits, including heading date, plant height and grain weight. We identified two major haplotypes of TaB3-2A1 and found that TaB3-2A1-Hap1 conferred lower seed protein content, but higher starch content, plant height and grain weight than TaB3-2A1-Hap2 and was subjected to positive selection in a panel of elite wheat cultivars. These findings provide a high-efficiency tool to detect TFs binding to targeted promoters, considerable gene resources for dissecting regulatory mechanisms underlying Glu-1 expression, and a useful gene for wheat improvement.

Mapping of quantitative trait loci for leaf rust resistance in the wheat population 'Xinmai 26/Zhoumai 22'

Leaf rust, caused by the fungal pathogen Puccinia triticina (Pt), is one of the major and dangerous diseases of wheat, and has caused serious yield loss of wheat worldwide. Here, we investigated adult-plant resistance (APR) to leaf rust in a recombinant inbred line (RIL) population derived from 'Xinmai 26' and 'Zhoumai 22' over 3 years. Linkage mapping for APR to leaf rust revealed four quantitative trait loci (QTL) in this RIL population. Two QTL, QLr.hnau-2BS and QLr.hnau-3BS were contributed by 'Zhoumai22', whereas QLr.hnau-2DS and QLr.hnau-5AL were contributed by 'Xinmai 26'. The QLr.hnau-2BS covering a race-specific resistance gene Lr13 showed the most stable APR to leaf rust. Overexpression of Lr13 significantly increased APR to leaf rust. Interestingly, we found that a CNL(coiled coil-nucleotide-binding site-leucine-rich repeat)-like gene, TaCN, in QLr.hnau-2BS completely co-segregated with leaf rust resistance. The resistant haplotype TaCN-R possessed half the sequence of the coiled-coil domain of TaCN protein. Lr13 strongly interacted with TaCN-R, but did not interact with the full-length TaCN (TaCN-S). In addition, TaCN-R was significantly induced after Pt inoculation and changed the sub-cellular localization of Lr13 after interaction. Therefore, we hypothesized that TaCN-R mediated leaf rust resistance possibly by interacting with Lr13. This study provides important QTL for APR to leaf rust, and new insights into understanding how a CNL gene modulates disease resistance in common wheat.

CRISPR-mediated iron and folate biofortification in crops: advances and perspectives

Micronutrient deficiency conditions, such as anemia, are the most prevalent global health problem due to inadequate iron and folate in dietary sources. Biofortification advancements can propel the rapid amelioration of nutritionally beneficial components in crops that are required to combat the adverse effects of micronutrient deficiencies on human health. To date, several strategies have been proposed to increase micronutrients in plants to improve food quality, but very few approaches have intrigued `clustered regularly interspaced short palindromic repeats' (CRISPR) modules for the enhancement of iron and folate concentration in the edible parts of plants. In this review, we discuss two important approaches to simultaneously enhance the bioavailability of iron and folate concentrations in rice endosperms by utilizing advanced CRISPR-Cas9-based technology. This includes the 'tuning of cis-elements' and 'enhancer re-shuffling' in the regulatory components of genes that play a vital role in iron and folate biosynthesis/transportation pathways. In particular, base-editing and enhancer re-installation in native promoters of selected genes can lead to enhanced accumulation of iron and folate levels in the rice endosperm. The re-distribution of micronutrients in specific plant organs can be made possible using the above-mentioned contemporary approaches. Overall, the present review discusses the possible approaches for synchronized iron and folate biofortification through modification in regulatory gene circuits employing CRISPR-Cas9 technology.

The pathway of melatonin biosynthesis in common wheat (Triticum aestivum)

Melatonin (Mel) is a multifunctional biomolecule found in both animals and plants. In plants, the biosynthesis of Mel from tryptophan (Trp) has been delineated to comprise of four consecutive reactions. However, while the genes encoding these enzymes in rice are well characterized no systematic evaluation of the overall pathway has, as yet, been published for wheat. In the current study, the relative contents of six Mel-pathway-intermediates including Trp, tryptamine (Trm), serotonin (Ser), 5-methoxy tryptamine (5M-Trm), N-acetyl serotonin (NAS) and Mel, were determined in 24 independent tissues spanning the lifetime of wheat. These studies indicated that Trp was the most abundant among the six metabolites, followed by Trm and Ser. Next, the candidate genes expressing key enzymes involved in the Mel pathway were explored by means of metabolite-based genome-wide association study (mGWAS), wherein two TDC genes, a T5H gene and one SNAT gene were identified as being important for the accumulation of Mel pathway metabolites. Moreover, a 463-bp insertion within the T5H gene was discovered that may be responsible for variation in Ser content. Finally, a ASMT gene was found via sequence alignment against its rice homolog. Validations of these candidate genes were performed by in vitro enzymatic reactions using proteins purified following recombinant expression in Escherichia coli, transient gene expression in tobacco, and transgenic approaches in wheat. Our results thus provide the first comprehensive investigation into the Mel pathway metabolites, and a swift candidate gene identification via forward-genetics strategies, in common wheat.

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.

Wheat genomic study for genetic improvement of traits in China

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.

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.

TaNAC100 acts as an integrator of seed protein and starch synthesis exerting pleiotropic effects on agronomic traits in wheat

High-molecular-weight glutenin subunits (HMW-GS) are major components of seed storage proteins (SSPs) and largely determine the processing properties of wheat (Triticum aestivum) flour. HMW-GS are encoded by the GLU-1 loci and regulated at the transcriptional level by interaction between cis-elements and transcription factors (TFs). We recently validated the function of conserved cis-regulatory modules (CCRMs) in GLU-1 promoters, but their interacting TFs remained uncharacterized. Here we identified a CCRM-binding NAM-ATAF-CUC (NAC) protein, TaNAC100, through yeast one-hybrid (Y1H) library screening. Transactivation assays demonstrated that TaNAC100 could bind to the GLU-1 promoters and repress their transcription activity in tobacco (Nicotiana benthamiana). Overexpression of TaNAC100 in wheat significantly reduced the contents of HMW-GS and other SSPs as well as total seed protein. This was confirmed by transcriptome analyses. Conversely, enhanced expression of TaNAC100 increased seed starch contents and expression of key starch synthesis-related genes, such as TaGBSS1 and TaSUS2. Y1H assays also indicated TaNAC100 binding with the promoters of TaGBSS1 and TaSUS2. These results suggest that TaNAC100 functions as a hub controlling seed protein and starch synthesis. Phenotypic analyses showed that TaNAC100 overexpression repressed plant height, increased heading date, and promoted seed size and thousand kernel weight. We also investigated sequence variations in a panel of cultivars, but did not identify significant association of TaNAC100 haplotypes with agronomic traits. The findings not only uncover a useful gene for wheat breeding but also provide an entry point to reveal the mechanism underlying metabolic balance of seed storage products.

Quantitative traits loci mapping and molecular marker development for total glutenin and glutenin fraction contents in wheat

BACKGROUND

Glutenin contents and compositions are crucial factors influencing the end-use quality of wheat. Although the composition of glutenin fractions is well known, there has been relatively little research on the genetic basis of glutenin fractions in wheat.

RESULTS

To elucidate the genetic basis for the contents of glutenin and its fractions, a population comprising 196 recombinant inbred lines (RILs) was constructed from two parents, Luozhen No.1 and Zhengyumai 9987, which differ regarding their total glutenin and its fraction contents (except for the By fraction). Forty-one additive Quantitative Trait Loci (QTL) were detected in four environments over two years. These QTL explained 1.3% - 53.4% of the phenotypic variation in the examined traits. Forty-three pairs of epistatic QTL (E-QTL) were detected in the RIL population across four environments. The QTL controlling the content of total glutenin and its seven fractions were detected in clusters. Seven clusters enriched with QTL for more than three traits were identified, including a QTL cluster 6AS-3, which was revealed as a novel genetic locus for glutenin and related traits. Kompetitive Allele-Specific PCR (KASP) markers developed from the main QTL cluster 1DL-2 and the previously developed KASP marker for the QTL cluster 6AS-3 were validated as significantly associated with the target traits in the RIL population and in natural varieties.

CONCLUSIONS

This study identified novel genetic loci related to glutenin and its seven fractions. Additionally, the developed KASP markers may be useful for the marker-assisted selection of varieties with high glutenin fraction content and for identifying individuals in the early developmental stages without the need for phenotyping mature plants. On the basis of the results of this study and the KASP markers described herein, breeders will be able to efficiently select wheat lines with favorable glutenin properties and develop elite lines with high glutenin subunit contents.

Comparative sequence analysis across Brassicaceae, regulatory diversity in KCS5 and KCS6 homologs from Arabidopsis thaliana and Brassica juncea, and intronic fragment as a negative transcriptional regulator

Intra- and epicuticular-waxes primarily comprising of very long chain aliphatic lipid (VLCFA), terpenoids and secondary metabolites such as sterol and flavonoids played a major role in successful colonization of terrestrial ecosystem by aquatic plants and are thus considered as a key evolutionary innovation. The key rate limiting step of Fatty Acid (FA) biosynthesis of condensation/elongation are catalyzed by the enzyme, β-ketoacyl coenzyme A synthase (KCS), part of FAE (Fatty Acid Elongase) complex. KCS6 has been shown to be responsible for elongation using C22 fatty acid as substrate and is considered essential for synthesis of VLCFA for cuticular waxes. Earlier studies have established KCS5 as a close paralog of KCS6 in Arabidopsis thaliana, albeit with non-redundant function. We subsequently established segmental duplication responsible for origin of KCS6-KCS5 paralogy which is exclusive to Brassicaceae. In the present study, we aim to understand impact of duplication on regulatory diversification and evolution, through sequence and functional analysis of cis-regulatory element of KCS5 and KCS6. High level of sequence variation leading to conservation of only the proximal end of the promoter corresponding to the core promoter was observed among Brassicaceae members; such high diversity was also revealed when sliding window analysis revealed only two to three phylogenetic footprints. Profiling of transcription factor binding sites (TFBS) across Brassicaceae shows presence of light, hormone and stress responsive motifs; a few motifs involved in tissue specific expression (Skn-1; endosperm) were also detected. Functional characterization using transcriptional fusion constructs revealed regulatory diversification when promoter activity of homologs from A. thaliana and Brassica juncea were compared. When subjected to 5-Azacytidine, altered promoter activity was observed, implying role of DNA methylation in transcriptional regulation. Finally, investigation of the role of an 87 bp fragment from first intron that is retained in a splice variant, revealed it to be a transcriptional repressor. This is a first report on comparative sequence and functional analysis of transcriptional regulation of KCS5 and KCS6; further studies are required before manipulation of cuticular waxes as a strategy for mitigating stress.

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.

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

KEY MESSAGE

Recent genomic and functional genomics analyses have substantially improved the understanding on gluten proteins, which are important determinants of wheat grain quality traits. The new insights obtained and the availability of precise, versatile and high-throughput genome editing technologies will accelerate simultaneous improvement of wheat end-use and health-related traits. Being a major staple food crop in the world, wheat provides an indispensable source of dietary energy and nutrients to the human population. As worldwide population grows and living standards rise in both developed and developing countries, the demand for wheat with high quality attributes increases globally. However, efficient breeding of high-quality wheat depends on critically the knowledge on gluten proteins, which mainly include several families of prolamin proteins specifically accumulated in the endospermic tissues of grains. Although gluten proteins have been studied for many decades, efficient manipulation of these proteins for simultaneous enhancement of end-use and health-related traits has been difficult because of high complexities in their expression, function and genetic variation. However, recent genomic and functional genomics analyses have substantially improved the understanding on gluten proteins. Therefore, the main objective of this review is to summarize the genomic and functional genomics information obtained in the last 10 years on gluten protein chromosome loci and genes and the cis- and trans-factors regulating their expression in the grains, as well as the efforts in elucidating the involvement of gluten proteins in several wheat sensitivities affecting genetically susceptible human individuals. The new insights gathered, plus the availability of precise, versatile and high-throughput genome editing technologies, promise to speed up the concurrent improvement of wheat end-use and health-related traits and the development of high-quality cultivars for different consumption needs.