GrainGenes: Tools and Content to Assist Breeders Improving Oat Quality

Blake, Victoria; Wight, Charlene P.; Yao, Eric; Sen, Taner Z.

doi:10.3390/foods11070914

Cited by 4 publications

(5 citation statements)

References 36 publications

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“…The JBrowse tracks from the two studies can be compared directly (https:// wheat.pw.usda.gov/jb/?data=%2Fggds%2Foat-ot3098v2pepsicotracks 'β-glucan QTL (GrainGenes)' and 'QTL/gene inventory: comparative mapping vs QTL/gene inventory: comparative mapping vs. OT3098 v2'). The regions defined in this work, while much longer, always include the QTL locations determined by Blake et al (2022). β-glucan QTLs from other studies often overlap the ones from the more recent studies but, as in the case of ACCase, not always.…”

Section: Further Validation Of the Comparative Mapping Approach Used ...mentioning

confidence: 83%

“…In newer studies, many single SNP markers have been associated with various traits. Blake et al (2022) aligned the GMI SNP markers linked to B-glucan content in studies by Fogarty et al (2020) and Zimmer et al (2020) to OT3098 v2 chromosomes. The present work has associated the same traits to longer chromosome regions through assigning each cM location a position on the OT3098 v2 sequence, rather than through assigning the individual markers.…”

Section: Further Validation Of the Comparative Mapping Approach Used ...mentioning

confidence: 99%

“…GrainGenes contains data related to molecular mapping from wheat, barley, rye and oat and provides analysis tools such as the CMap comparative mapping tool (Fang et al 2003) and genome browsers. More complete reference maps had been the focus of the database; however, resources became available to allow for the addition of smaller oat maps in 2019 (Blake et al 2019). As part of this exercise, the older 'classical genetics' maps were put into molecular map format and included as well.…”

Section: Introductionmentioning

confidence: 99%

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One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa)

Wight,

Blake,

Jellen

et al. 2024

Crop & Pasture Science

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Context Researchers have been accumulating information concerning the locations of genes and quantitative trait loci (QTLs) in cultivated oat (Avena sativa L.) for more than 100 years. Aims The aim of this work was to create an inventory of genes and QTLs found in cultivated hexaploid oat and produce tools to make this resource more useful. Methods By using the positions of perfectly matched, single nucleotide polymorphism markers, each centimorgan (cM) location along the consensus map was assigned to a location on the OT3098 v2 physical map found on the GrainGenes database website (https://wheat.pw.usda.gov/jb/?data=/ggds/oat-ot3098v2-pepsico). This information was then used to assign physical locations to the genes and QTLs in the inventory, where possible. Key results A table comparing the major genetic maps of hexaploid oats to each other, to the 2018 oat consensus map, and to physical chromosomes was produced. Genome browser tracks aligning the consensus map regions and the locations of the genes and QTLs to OT3098 v2 were added to GrainGenes. Conclusions Many oat genes and QTLs identified using genetic mapping could be assigned positions on physical oat chromosomes. However, many of these assigned regions are quite long, owing to the presence of large areas of reduced recombination. Specific examples of identified patterns of recombination between the genetic and physical maps and validated gene and QTL locations are discussed. Implications These resources will assist researchers performing comparative genetic and physical mapping in oat.

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Section: Further Validation Of the Comparative Mapping Approach Used ...mentioning

confidence: 83%

Section: Further Validation Of the Comparative Mapping Approach Used ...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa)

Wight,

Blake,

Jellen

et al. 2024

Crop & Pasture Science

Self Cite

View full text Add to dashboard Cite

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“…usda. gov/ ggpag es/ awn/; Blake et al 2019), the latter also providing ongoing curation. In time, these guidelines may also be adopted by the barley, rye, triticale, and oat research communities, for which similar advances are being made in deciphering their genome sequences; a common set of guidelines would help transfer knowledge between these cereals, which share close phylogenetic relationships and share common breeding targets.…”

Section: Discussionmentioning

confidence: 99%

Updated guidelines for gene nomenclature in wheat

et al. 2023

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Key message Here, we provide an updated set of guidelines for naming genes in wheat that has been endorsed by the wheat research community. Abstract The last decade has seen a proliferation in genomic resources for wheat, including reference- and pan-genome assemblies with gene annotations, which provide new opportunities to detect, characterise, and describe genes that influence traits of interest. The expansion of genetic information has supported growth of the wheat research community and catalysed strong interest in the genes that control agronomically important traits, such as yield, pathogen resistance, grain quality, and abiotic stress tolerance. To accommodate these developments, we present an updated set of guidelines for gene nomenclature in wheat. These guidelines can be used to describe loci identified based on morphological or phenotypic features or to name genes based on sequence information, such as similarity to genes characterised in other species or the biochemical properties of the encoded protein. The updated guidelines provide a flexible system that is not overly prescriptive but provides structure and a common framework for naming genes in wheat, which may be extended to related cereal species. We propose these guidelines be used henceforth by the wheat research community to facilitate integration of data from independent studies and allow broader and more efficient use of text and data mining approaches, which will ultimately help further accelerate wheat research and breeding.

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“…To identify effective hub proteins in the PPI network, we employed various methods within the Cytoscape software through the cytoHubba plugin. 28 Local methods rank hubs based on their relationships with neighboring nodes, while global methods consider node relationships within the entire network. For the identification of unique hub genes, we utilized five different methods of Cytoscape, including maximum neighborhood component (MNC), Degree, and MCC (maximum clique centrality) in the local network, while Closeness, and Bottleneck algorithms in the global network.…”

Section: Protein-protein Interaction Analysis and Detection Of Hub Pr...mentioning

confidence: 99%

Transcriptomic analysis revealed potential regulatory biomarkers and repurposable drugs for breast cancer treatment

Shornale Akter,

Uddin,

Atikur Rahman

et al. 2024

Cancer Reports

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Breast cancer (BC) is the most widespread cancer worldwide. Over 2 million new cases of BC were identified in 2020 alone. Despite previous studies, the lack of specific biomarkers and signaling pathways implicated in BC impedes the development of potential therapeutic strategies. We employed several RNAseq datasets to extract differentially expressed genes (DEGs) based on the intersection of all datasets, followed by protein–protein interaction network construction. Using the shared DEGs, we also identified significant gene ontology (GO) and KEGG pathways to understand the signaling pathways involved in BC development. A molecular docking simulation was performed to explore potential interactions between proteins and drugs. The intersection of the four datasets resulted in 146 DEGs common, including AURKB, PLK1, TTK, UBE2C, CDCA8, KIF15, and CDC45 that are significant hub‐proteins associated with breastcancer development. These genes are crucial in complement activation, mitotic cytokinesis, aging, and cancer development. We identified key microRNAs (i.e., hsa‐miR‐16‐5p, hsa‐miR‐1‐3p, hsa‐miR‐147a, hsa‐miR‐195‐5p, and hsa‐miR‐155‐5p) that are associated with aggressive tumor behavior and poor clinical outcomes in BC. Notable transcription factors (TFs) were FOXC1, GATA2, FOXL1, ZNF24 and NR2F6. These biomarkers are involved in regulating cancer cell proliferation, invasion, and migration. Finally, molecular docking suggested Hesperidin, 2‐amino‐isoxazolopyridines, and NMS‐P715 as potential lead compounds against BC progression. We believe that these findings will provide important insight into the BC progression as well as potential biomarkers and drug candidates for therapeutic development.

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GrainGenes: Tools and Content to Assist Breeders Improving Oat Quality

Cited by 4 publications

References 36 publications

One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa)

One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa)

Updated guidelines for gene nomenclature in wheat

Transcriptomic analysis revealed potential regulatory biomarkers and repurposable drugs for breast cancer treatment

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