Defining the locations of cM regions from the Oat-Consensus-2018 (2018 Mrg) map on the OT3098 v2 sequence
This genome browser track accompanies the article “One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa L.)”, by Wight, et al. (2023) (under review).
Three new tracks have been added to the IWGSC Chinese Spring v1 genome browser aligning QTL and significant markers for salinity, pathology, and agronomic traits.
181 agronomic QTL were created from 354 marker-trait associations (MTAs) in Semagn et al. (2022) Genome-wide association mapping of agronomic traits and grain characteristics in spring wheat under conventional and organic management systems. Crop Science 62:1069 doi.org/10.1002/csc2.20739. MTAs within ~20MB of each other were combined into one 'QTL' for this curation.
GrainGenes has published a tutorial video describing three new BLAST interface features:
1) Selected Databass Box
2) Database Filters
3) Tooltip improvements
Graingenes genome browsers enhance grain research. It provides crosslinks from genes, transcripts, and other features to a variaty of useful external databases.
We have added a new video tutorial describing how to access the external cross-links, which we often refer to as link-outs.
Records in the Intl' Database contain a wealth of inheritance and mutation information, photos and descriptions of mutants, and comprehensive reference lists.
Example of GrainGenes records with new links are below:
Forty-seven independent QTL were mapped on the IWGSC v1 assembly with DArT markers, 14 of which overlapped with previously described genes. These will be added to the Strip Rust track for the IWGSC v1 browser in progress.
2022 Uniform Regional Hard Red Spring Wheat Nursery and Uniform Regional Scab Nursery for Spring Wheat Parents reports are available at https://wheat.pw.usda.gov/GG3/germplasm.
Note that 2013 Uniform Regional Scab Nursery for Spring Wheat Parents report is also updated.
GWAS QTL results in the publications below will soon be aligned on the 2018 IWGSC Chinese Spring v1 wheat genome browser. In preparation for that track these QTL were curated as QTL records in the GrainGenes database with links to significant markers, associated traits, Gene Ontology links, etc. As always in GrainGenes, all significant data is linked from the reference record. See below for the upcoming browser track in progress and please do not hesitate to recommend additions to this track,
Updated: Release Wheat cultivar Attraktion BLAST database and genome browser.
Related publication (Kale et al., 2022): Plant Biotechnology Journal "A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat"
The abstract book for the International Barley Genetics Symposium (IBGS) 2022 that took place in Riga, Latvia is available on the "Barley Boulevard" page under the "Abstracts/Short Talks/Posters from Barley Conferences" section.
Diagnostic marker data were contributed to GrainGenes by Naveenkumar Athiyannan via the GrainGenes Data Template forms. The papers below were curated for new diagnostic PCR primers for Yr27, Yr28, Sr46, and Rg-B1.
Thanks Naveen for this contribution to small grains research.
