Community Resource: Large-Scale Proteogenomics to Refine Wheat Genome Annotations.

is an important crop whose reference genome (International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.1) offers a valuable resource for understanding wheat genetic structure, improving agronomic traits, and developing new cultivars. A key aspect of gene model annotation is protein-level evidence of gene expression obtained from proteomics studies, followed up by proteogenomics to physically map proteins to the genome.

Bioaccessibility of Phenolic Compounds, Resistant Starch, and Dietary Fibers from Australian Green Banana during In Vitro Digestion and Colonic Fermentation.

Green bananas contain a substantial amount of resistant starch (RS), dietary fiber (DF), and phytochemicals, which exhibit potent antioxidant capabilities, primarily attributable to the abundance of polyphenols. The objective of this study was to assess the variations in the contents and bioaccessibility of RS, DF, and phenolic compounds in three types of Australian green bananas (Cavendish "", Ladyfinger " L.", and Ducasse ""), along with their antioxidant capacities, and the production of short-chain fatty acids (SCFAs) following in vitro simulated gastrointestinal digestion and colonic fermentation.

Large flour aggregates containing ordered B + V starch crystals significantly improved the digestion resistance of starch in pretreated multigrain flour.

The starch digestibility of flour is influenced by both physicochemical treatment and flour particle size, but the interactive effect of these two factors is still unclear. In this study, the effect of pullulanase debranching, combined with heat-moisture treatment (P-HMT), on starch digestibility of multi-grain flours (including oat, buckwheat and wheat) differing in particle size was investigated. The results showed that the larger-size flour always resulted in a higher resistant starch (RS) content either in natural or treated multi-grain flour (NMF or PHF).

Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased α-linolenic (ω-3) content in S. hispanica seeds.

Salvia hispanica L. (chia) is a source of abundant ω-3 polyunsaturated fatty acids (ω-3-PUFAs) that are highly beneficial to human health. The genomic basis for this accrued ω-3-PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S.

Wheat Water-Soluble Carbohydrate Remobilisation under Water Deficit by .

Fructan 1-exohydrolase (1-FEH) is one of the major enzymes in water-soluble carbohydrate (WSC) remobilisation for grains in wheat. We investigated the functional role of , , and isoforms in WSC remobilisation under post-anthesis water deficit using mutation lines derived from the Australian wheat variety Chara. F1 seeds, developed by backcrossing the , , and mutation lines with Chara, were genotyped using the Infinium 90K SNP iSelect platform to characterise the mutated region.

Centromere repositioning and shifts in wheat evolution.

The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms. Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat. Here, we comprehensively analyzed centromeres from the de novo-assembled common wheat cultivar Aikang58 (AK58), Chinese Spring (CS), and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing, whole-genome bisulfite sequencing, RNA sequencing, assay for transposase-accessible chromatin using sequencing, and comparative genomics.

Evaluating intra-action reviews at points of entry: ongoing learning opportunities during the COVID-19 pandemic.

Background: Long-lasting crises, such as the COVID-19 pandemic, require proper interim evaluation in order to optimize response. The World Health Organization and the European Center for Disease Control have recently promoted the in(tra)-action review (IAR) method for this purpose. We systematically evaluated the added value of two IARs performed in the Dutch point of entry (PoE) setting.

Effects of Composition and Strength of Wheat Gluten on Starch Structure, Digestion Properties and the Underlying Mechanism.

To understand the effect of gluten on starch digestion characteristics, the structural characteristics of protein, starch, and starch digestion attributes were explored by using flours of four wheat near-isogenic lines. Protein and starch fractions from the four flours were used to form so-called recombinant flours where glutenin and gliadin protein fractions, in different ratios, were combined with starch and heated in a water slurry at 80 °C for 5 min. We found that starch digestibility of the recombinant flours could be reproducibly modified by altering the long- and short-range molecular order of starch through varying the attributes of the gluten protein by virtue of the gluten strength as well as the proportions of glutenin and gliadins.

Integrating Wheat Nucleolus Structure and Function: Variation in the Wheat Ribosomal RNA and Protein Genes.

We review the coordinated production and integration of the RNA (ribosomal RNA, rRNA) and protein (ribosomal protein, RP) components of wheat cytoplasmic ribosomes in response to changes in genetic constitution, biotic and abiotic stresses. The components examined are highly conserved and identified with reference to model systems such as human, Arabidopsis, and rice, but have sufficient levels of differences in their DNA and amino acid sequences to form fingerprints or gene haplotypes that provide new markers to associate with phenotype variation. Specifically, it is argued that populations of ribosomes within a cell can comprise distinct complements of rRNA and RPs to form units with unique functionalities.

Multi-year field evaluation of nicotianamine biofortified bread wheat.

Conventional breeding efforts for iron (Fe) and zinc (Zn) biofortification of bread wheat (Triticum aestivum L.) have been hindered by a lack of genetic variation for these traits and a negative correlation between grain Fe and Zn concentrations and yield. We have employed genetic engineering to constitutively express (CE) the rice (Oryza sativa) nicotianamine synthase 2 (OsNAS2) gene and upregulate biosynthesis of two metal chelators - nicotianamine (NA) and 2'-deoxymugineic acid (DMA) - in bread wheat, resulting in increased Fe and Zn concentrations in wholemeal and white flour.

Macromolecular networks interactions in wheat flour dough matrices during sequential thermal-mechanical treatment.

Differences in Mixolab measurements of dough processing were examined using, as a base, flour from pure breeding, isogenic, wheat lines carrying either the high molecular weight glutenin subunits 5 + 10 or 2 + 12. Before dough pasting, subunits 5 + 10 tend to form a stable gluten network relying mainly on disulfide bonds and hydrogen bonds, but 2 + 12 flour was prone to generating fragile protein aggregates dominated by disulfide bonds and hydrophobicity. During dough pasting, a broader protein network rich in un-extractable polymeric proteins, disulfide bonds and β-sheets was formed in the dough with subunits 5 + 10, thus resulting in an extensive and compact protein-starch complex which was characterized by high thermal stability and low starch gelatinization, while in the dough of the 2 + 12 line, a porous protein-starch gel with fragmented protein aggregates was controlled by the combination of disulfide bonds, hydrophobicity and hydrogen bonds that facilitated the formation of antiparallel β-sheets.

Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly.

Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.

Origin and adaptation to high altitude of Tibetan semi-wild wheat.

Tibetan wheat is grown under environmental constraints at high-altitude conditions, but its underlying adaptation mechanism remains unknown. Here, we present a draft genome sequence of a Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao) accession Zang1817 and re-sequence 245 wheat accessions, including world-wide wheat landraces, cultivars as well as Tibetan landraces.

Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China.

Controlled pedigrees and the multi-decade timescale of national crop plant breeding programs offer a unique experimental context for examining how selection affects plant genomes. More than 3000 wheat cultivars have been registered, released, and documented since 1949 in China. In this study, a set of 145 elite cultivars selected from historical points of wheat breeding in China were re-sequenced.

Status and Potential of Single-Cell Transcriptomics for Understanding Plant Development and Functional Biology.

The advent of modern "omics" technologies (genomics, transcriptomics, proteomics, and metabolomics) are attributed to innovative breakthroughs in genome sequencing, bioinformatics, and analytic tools. An organism's biological structure and function is the result of the concerted action of single cells in different tissues. Single cell genomics has emerged as a ground-breaking technology that has greatly enhanced our understanding of the complexity of gene expression at a microscopic resolution and holds the potential to revolutionize the way we characterize complex cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, function, and networking.

Proteomic profiling of developing wheat heads under water-stress.

A replicated iTRAQ (isobaric tags for relative and absolute quantification) study on developing wheat heads from two doubled haploid (DH) lines identified from a cross between cv Westonia x cv Kauz characterized the proteome changes influenced by reproductive stage water-stress. All lines were exposed to 10 days of water-stress from early booting (Zadok 40), with sample sets taken from five head developmental stages. Two sample groups (water-stressed and control) account for 120 samples that required 18 eight-plex iTRAQ runs.

The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms.

In the year 2018, the world witnessed the finale of the race to sequence the genome of the world's most widely grown crop, the common wheat. Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature. A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries, taking a conventional strategy similar to that for sequencing Arabidopsis and rice, became ferocious over time as both sequencing technologies and genome assembling methodologies advanced.

Signatures for torque variation in wheat dough structure are affected by enzymatic treatments and heating.

Molecular interactions in dough are poorly defined but affect final product usage. By monitoring changes in torque as dough is formed, we identified 80-85 °C as a gateway stage determining dough collapse during the mixing/heating process. We propose that this phenomenon is a diagnostic signature linked to integral features of dough complexes formed by some wheat varieties but not others.

Solubility variation of wheat dough proteins: A practical way to track protein behaviors in dough processing.

To understand wheat dough protein behavior under dual mixing and thermal treatment, solubility of Mixolab-dough proteins were investigated using nine extraction buffers of different dissociation capacities. Size exclusion high performance liquid chromatography (SE-HPLC) and two-dimensional gel electrophoresis (2-DGE) demonstrated that overall changes of protein fractions and dynamic responses of specific proteins during dough processing were well reflected by their solubility variations. After starch pasting, the abundance of 0.

The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat.

Wheat is one of the most important staple crops worldwide and also an excellent model species for crop evolution and polyploidization studies. The breakthrough of sequencing the bread wheat genome and progenitor genomes lays the foundation to decipher the complexity of wheat origin and evolutionary process as well as the genetic consequences of polyploidization. In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat cv.

Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat.

Background: Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive.

Results: By investigating the whole-genome resequencing data of 93 accessions from worldwide populations of bread wheat and its diploid and tetraploid progenitors, together with 90 published exome-capture data, we find that the B subgenome has more variations than A and D subgenomes, including SNPs and deletions.

Can community-based signalling behaviour in Saccharomyces cerevisiae be called quorum sensing? A critical review of the literature.

Quorum sensing is a well-described mechanism of intercellular signalling among bacteria, which involves cell-density-dependent chemical signal molecules. The concentration of these quorum-sensing molecules increases in proportion to cell density until a threshold value is exceeded, which triggers a community-wide response. In this review, we propose that intercellular signalling mechanisms can be associated with a corresponding ecological interaction type based on similarities between how the interaction affects the signal receiver and producer.