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Wheat is a staple food for more than 35% of the world's population, with wheat flour used to make hundreds of baked goods. Superior end-use quality is a major breeding target; however, improving it is especially time-consuming and expensive. Furthermore, genes encoding seed-storage proteins (SSPs) form multi-gene families and are repetitive, with gaps commonplace in several genome assemblies. To overcome these barriers and efficiently identify superior wheat SSP alleles, we developed "PanSK" (Pan-SSP k -mer) for genotype-to-phenotype prediction based on an SSP-based pangenome resource. PanSK uses 29-mer sequences that represent each SSP gene at the pangenomic level to reveal untapped diversity across landraces and modern cultivars. Genome-wide association studies with k -mers identified 23 SSP genes associated with end-use quality that represent novel targets for improvement. We evaluated the effect of rye secalin genes on end-use quality and found that removal of ω-secalins from 1BL/1RS wheat translocation lines is associated with enhanced end-use quality. Finally, using machine-learning-based prediction inspired by PanSK, we predicted the quality phenotypes with high accuracy from genotypes alone. This study provides an effective approach for genome design based on SSP genes, enabling the breeding of wheat varieties with superior processing capabilities and improved end-use quality. PanSK is a pangenomic approach based on k -mers that catalogs seed-storage protein (SSP) genes in wheat, enabling prediction and enhancement of end-use quality. Using 29-mer sequences to represent SSP gene diversity at the pangenome level, PanSK facilitates the identification of key genes linked to superior processing qualities. Combined with machine-learning predictions, it significantly advances the breeding of wheat varieties with improved end-use characteristics. [ABSTRACT FROM AUTHOR]

Different grain sources of whiskey have great potential for aroma expression. In this paper, four whiskeys fermented from different raw materials (barley, wheat, highland barley, and sorghum) were compared. Gas chromatography–mass spectrometry (GC-MS) and sensory evaluation were used to determine the composition of the aromatic compounds. A correlation analysis was further conducted between the aromatic compounds and sensory evaluations. Barley whiskey and wheat whiskey had more pronounced fruity, floral, and grain aromas, attributed to esters and terpenes. Barley whiskey had the most compounds (55), followed by highland barley whiskey (54). Highland barley whiskey had the greatest number of unique aroma compounds (seven). It exhibited a unique cocoa aroma related to concentrations of trans-2-nonenal, γ-nonanolactone, 1-nonanol, isoamyl lactate, 2-butanol, and 6-methyl-5-hepten-2-one. Sorghum whiskey had a specific leather and mushroom aroma attributed to 6-methyl-5-hepten-2-one, ethyl lactate, ethyl caprate, phenethyl octanoate, farnesol, α-terpineol, 3-methyl-1-pentanol, and methyleugenol. Alcohols were the main aroma components of grain whiskeys. Isoamyl alcohol (231.59~281.39 mg/L), phenylethyl alcohol (5.755~9.158 mg/L), citronellol (0.224~4.103 mg/L), β-damascenone (0.021~2.431 mg/L), geraniol (0.286~1.416 mg/L), isoamyl acetate (0.157~0.918 mg/L), phenylacetaldehyde (0.162~0.470 mg/L), linalool (0.024~0.148 mg/L), 1-octen-3-ol (0.016~0.145 mg/L), trans-2-nonenal (0.027~0.105 mg/L), and trans-2-octen-1-ol (0.011~0.054 mg/L) were all important aroma compounds in the whiskeys. [ABSTRACT FROM AUTHOR]

Key message: This study precisely mapped and validated a quantitative trait locus (QTL) located on chromosome 4B for flag leaf angle in wheat. Flag leaf angle (FLANG) is closely related to crop architecture and yield. We previously identified the quantitative trait locus (QTL) QFLANG-4B for FLANG on chromosome 4B, located within a 14-cM interval flanked by the markers Xbarc20 and Xzyh357, using a mapping population of recombinant inbred lines (RILs) derived from a cross between Nongda3331 (ND3331) and Zang1817. In this study, we fine-mapped QFLANG-4B and validated its associated genetic effect. We developed a BC3F3 population using ND3331 as the recurrent parent through marker-assisted selection, as well as near-isogenic lines (NILs) by selfing BC3F3 plants carrying different heterozygous segments for the QFLANG-4B region. We obtained eight recombinant types for QFLANG-4B, narrowing its location down to a 5.3-Mb region. This region contained 76 predicted genes, 7 of which we considered to be likely candidate genes for QFLANG-4B. Marker and phenotypic analyses of individual plants from the secondary mapping populations and their progeny revealed that the FLANG of the ND3331 allele is significantly higher than that of the Zang1817 allele in multiple environments. These results not only provide a basis for the map-based cloning of QFLANG-4B, but also indicate that QFLANG-4B has great potential for marker-assisted selection in wheat breeding programs designed to improve plant architecture and yield. [ABSTRACT FROM AUTHOR]

Summary: Grain size is one of the important traits in wheat breeding programs aimed at improving yield, and cytokinins, mainly involved in cell division, have a positive impact on grain size. Here, we identified a novel wheat gene TaMADS‐GS encoding type I MADS‐box transcription factor, which regulates the cytokinins signalling pathway during early stages of grain development to modulate grain size and weight in wheat. TaMADS‐GS is exclusively expressed in grains at early stage of seed development and its knockout leads to delayed endosperm cellularization, smaller grain size and lower grain weight. TaMADS‐GS protein interacts with the Polycomb Repressive Complex 2 (PRC2) and leads to repression of genes encoding cytokinin oxidase/dehydrogenases (CKXs) stimulating cytokinins inactivation by mediating accumulation of the histone H3 trimethylation at lysine 27 (H3K27me3). Through the screening of a large wheat germplasm collection, an elite allele of the TaMADS‐GS exhibits higher ability to repress expression of genes inactivating cytokinins and a positive correlation with grain size and weight, thus representing a novel marker for breeding programs in wheat. Overall, these findings support the relevance of TaMADS‐GS as a key regulator of wheat grain size and weight. [ABSTRACT FROM AUTHOR]

Summary: 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. See also the Commentary on this article by Gao & Liu, 239: 5–6. [ABSTRACT FROM AUTHOR]

Key message: We identified ten QTLs controlling SDS-SV trait in a RIL population derived from ND3331 and Zang1817. Pinb-D1p is an elite allele from Tibetan semi‑wild wheat for good end-use quality. Gluten strength is an important factor for wheat processing and end-product quality and is commonly characterized using the sodium dodecyl sulfate-sedimentation volume (SDS-SV) test. The objective of this study was to identify quantitative trait loci (QTLs) associated with wheat SDS-SV traits using a recombinant inbred line (RIL) population derived from common wheat line NongDa3331 (ND3331) and Tibetan semi-wild wheat accession Zang1817. We detected 10 QTLs controlling SDS-SV on chromosomes 1A, 1B, 3A, 4A, 4B, 5A, 5D, 6B and 7A, with individual QTLs explaining 2.02% to 15.53% of the phenotypic variation. They included four major QTLs, Qsdss-1A, Qsdss-1B.1, Qsdss-1B.2, and Qsdss-5D, whose effects on SDS-SV were due to the Glu-A1 locus encoding the high-molecular-weight glutenin subunit 1Ax1, the 1B/1R translocation, 1Bx7 + 1By8 at the Glu-B1 locus, and the hardness-controlling loci Pina-D1 and Pinb-D1, respectively. We developed KASP markers for the Glu-A1, Glu-B1, and Pinb-D1 loci. Importantly, we showed for the first time that the hardness allele Pinb-D1p positively affects SDS-SV, making it a good candidate for wheat quality improvement. These results broaden our understanding of the genetic characterization of SDS-SV, and the QTLs identified are potential target regions for fine-mapping and marker-assisted selection in wheat breeding programs. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

Differential gene expression between hybrids and their parents is considered to be associated with heterosis. However, the physiological functions and possible contribution to heterosis of these differentially expressed genes are unknown. We have isolated one hybrid upregulated gene encoding putative wheat ADP-ribosylation factor, designated TaARF. In this study, real-time quantitative reverse transcription-polymerase chain reaction analysis indicated that the TaARF transcript was preferentially expressed in root, node and crown, and the accumulation of TaARF mRNA in hybrid was more than 1.5-fold higher than that in two parents. In order to understand possible roles of the putative wheat ARF gene, TaARF was overexpressed in Arabidopsis, and the transgenic plants were characterized. We show that ectopic overexpression of TaARF in Arabidopsis leads to increased leaf area, increased growth rate and earlier transition to flowering, suggesting that TaARF plays significant roles in growth and development. This study provides evidence demonstrating that TaARF plays important roles in growth and development and we speculate that the upregulated expression of this gene might contribute to the heterosis observed in wheat root and leaf growth. [ABSTRACT FROM AUTHOR]

Abstract: Small RNAs related to RNA interference are key molecules in many developmental processes, in which they can both regulate developmental gene expression and maintain the integrity of the genome and epigenome. In plants, short interfering RNAs (siRNAs) of 24nt in length are an abundant type of small RNA associated with transposable elements (TEs), other repetitive sequences, and viral defense. One means by which TE-associated siRNAs affect genome integrity is by altering chromatin structure through a process called RNA-directed DNA methylation (RdDM). In this paper, we describe a comparative survey of siRNAs from wheat seedling leaves, seedling roots, young spikelets, and grains at 8 and 15days after pollination (DAP). We find that the general patterns of siRNA distributions are similar across different TEs and within TEs of the same family regardless of tissue, but the relative abundance of 24-nt siRNAs is highest in developing grains. We also find that TEs that are transcriptionally active in endosperm are associated with the highest siRNA abundance not only in grains, but also in other tissues as well. These results suggest that RdDM is an important feature of developing wheat grain and are consistent with the hypothesis that TE expression in endosperm results in increased TE siRNAs, and that RdDM is a conserved feature of plant seed development. [Copyright &y& Elsevier]

Abstract: Ribosomal proteins (RPs) are major components of ribosomes, and are regulated both developmentally and environmentally in plants. In this study, by using in silico cloning approach 15 putative wheat ribosomal protein (TaRP) genes with complete open reading frame (ORF) were identified. The amino acid sequence analysis indicated that several structural amino acid motifs with high similarity to that of mammalian RPs, such as basic and acid residues, zinc finger motif and nuclear localization signals, existed in these putative wheat RP genes. Genomic sequences in coding region of six TaRP genes were obtained, and 1–4 introns were identified in different TaRP genes, the intron patterns were also determined and compared to that of corresponding genes from rice and Arabidopsis. In silico expression analysis of the 14 putative wheat RP genes indicated that they were abundantly expressed in various tissues, and transcript amounts for most of ribosomal protein genes were highest in rapidly growing tissues, such as crown. The expression patterns of 11 TaRP genes were significantly correlated (r =0.87, P <0.05), suggesting that they were regulated by coordinate gene expression. Seven putative wheat RP genes were mapped in 21 chromosome bins on 11 chromosomes by in silico mapping. Moreover, it was interesting to note that TaRP genes were differentially expressed between hybrid F1 and parents in root and leaf. [Copyright &y& Elsevier]

Seed germination is important for grain yield and quality and rapid, near-simultaneous germination helps in cultivation; however, cultivars that germinate too readily can undergo preharvest sprouting (PHS), which causes substantial losses in areas that tend to get rain around harvest time. Moreover, our knowledge of mechanisms regulating seed germination in wheat (Triticum aestivum) remains limited. In this study, we analyzed function of a wheat-specific microRNA 9678 (miR9678), which is specifically expressed in the scutellum of developing and germinating seeds. Overexpression of miR9678 delayed germination and improved resistance to PHS in wheat through reducing bioactive gibberellin (GA) levels; miR9678 silencing enhanced germination rates. We provide evidence that miR9678 targets a long noncoding RNA (WSGAR) and triggers the generation of phased small interfering RNAs that play a role in the delay of seed germination. Finally, we found that abscisic acid (ABA) signaling proteins bind the promoter of miR9678 precursor and activate its expression, indicating that miR9678 affects germination by modulating the GA/ABA signaling. [ABSTRACT FROM AUTHOR]

• HSP90s were identified to be substrates of TaSAP5 using two independent methods. • TaSAP5 interacts with HSP90C and facilitates their ubiquitination in vivo. • TaSAP5 promotes degradation of HSP90C protein via the 26S proteasome. Protein ubiquitination is a major post-translational modification important for diverse biological processes. In wheat (Triticum aestivum) and Arabidopsis thaliana , STRESS-ASSOCIATED PROTEIN 5 (SAP5) is involved in drought tolerance, acting as an E3 ubiquitin ligase to target DRIP and MBP-1 for degradation. To identify further target proteins of SAP5, we implemented two independent approaches in this work. We used ubiquitylome capture with a di-Gly-Lys antibody-based peptide enrichment and affinity purification with a polyubiquitin antibody coupled with mass spectrometry to elucidate the SAP5-dependent ubiquitylation of its target proteins in response to osmotic stress. Wild type or TaSAP5 -overexpressing Arabidopsis line, which was more tolerant to osmotic stress according to our previous study, were used here. We identified HSP90C (chloroplast heat shock protein 90) as a substrate of TaSAP5. Further biochemical experiments indicated that TaSAP5 interacts with HSP90C and mediates its degradation by the 26S proteasome. Our work also demonstrates that ubiquitylome profiling is an effective approach to search for substrates of the TaSAP5 E3 ubiquitin ligase when heterologously expressed in Arabidopsis. [ABSTRACT FROM AUTHOR]