GrainGenes Updates

September 2022: Released T3 Markers Track in IWGSC v1, Morex v3, and PepsiCo v2

Relased marker tracks for Wheat Chinese Spring (IWGSC v1), Barley Morex v3, and PepsiCo OT3098 v2

Markers from genotyping protocols loaded in The Triticeae Toolbox (2022 update).

Blake, V., Birkett, C.L., Matthews, D.E., Hane, D., Bradbury, P., Jannink, J. 2016. The Triticeae Toolbox: Combining Phenotype and Genotype Data to Advance Small-Grains Breeding. The Plant Genome. doi: 10.3835/PlantGenome2014.12.0099.

May 2022: The release of A. sativa  (cv Sang), A. longiglumis, and A. insularis genome browsers, BLAST, and Data Download

A high-quality reference genome of A. sativa  (cv Sang) and close relatives of its diploid (Avena longiglumis, AA, 2n = 14) and tetraploid (Avena insularis, CCDD, 2n = 4x = 28) progenitors were published today in Nature: Kamal et al., Nature, 2022.

An accompanying QTL paper was published in Communications Biology: Tinker et al., Comm. Biol., 2022.

GrainGenes created genome browsers and BLAST for these 3 genomes:

May 2022: Protein BLAST

Protein BLAST is now available on our BLAST tool.

In addition to the nucleotide BLAST interface, we created a new tab on our BLAST page for proteins. The databases were arranged chronologically (newer databases go to the top) and by crops. So far, we created eight protein sequence databases that were generated by the sequencing and annotation groups for wheat (Chinese Spring, Kariega, Fielder, Zavitan, and durum), barley (Morex), rye (Weining), and oat (OT3098).

May 2022: BLAST from GrainGenes Genome Browsers

BLAST can now be directly initiated from GrainGenes genome browsers. Feature and sub-feature sequences can be submitted to BLAST from Feature Details dialog. Arbitrary regions can be submitted to BLAST by highlighting the region and selecting the BLAST highlighted region from the BLAST menu within the browsers.

BLAST video tutorials are available that illustrate how to use this feature.

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