May 2022: Curated GWAS Tracks on Barley and Oat Browsers

GrainGenes GWAS to .gff3 Project

A .gff3 (general feature format) file is a common file type that is readable by genome browser software (ex. JBrowse) and conveys multiple types of information: the DNA sequence, tracks aligning molecular markers, annotated genes, quantitative trait loci (QTL), graphical information about gene expression along the chromosome, and more. GrainGenes uses the JBrowse genome browser, allowing the addition of tracks to be simple and straightforward. To respond to the mandate to steer the project to a more genome-centered approach, GrainGenes is curating tracks for GWAS results for the most current RefSeq browsers of the species represented, i.e. wheat, barley, oats, and rye.

Curated GWAS Tracks are Now Available for Oat and Barley!

The list below contains the papers with curated GWAS results on the Barley cv. MorexV3 (2021) browser and the PepsiCo OT3098 v2 Hexaploid Oat (2021) browser. Reciprocal links from the browser to the GrainGenes SQL database exist via the QTL and probe records for significant markers (loci). To assign track positions, sequences for significant markers were BLASTed against the MorexV3 and OT3098v2 browsers for proper alignment.

Oat GWAS QTL on PepsiCo OT3098 v2 Hexaploid Oat (2021) 83 QTL in May 2022.
B-glucan Content

  • 56 QTL from Fogarty et al. (2019) Identification of mixed linkage β-glucan quantitative trait loci and evaluation of AsCslF6 homoeologs in hexaploid oat. Crop Sci 60, 914 DOI 10.1002/csc2.20015 and GrainGenes Link
  • 27 QTL from Zimmer et al. (2020) Genome-wide association for β-glucan content, population structure, and linkage disequilibrium in elite oat germplasm adapted to subtropical environments. Mol Breed 40, 103 DOI 10.1007/s11032-020-01182-0 and GrainGenes Link

Barley GWAS QTL on Barley cv. MorexV3 (2021) 576 QTL in May 2022.
Net Blotch QTL

  • 43 QTL from Tamang et al. (2015) Association Mapping of Seedling Resistance to Spot Form Net Blotch in a Worldwide Collection of Barley. Phytopathology 105, 500 DOI 10.1094/PHYTO-04-14-0106-R and GrainGenes Link
  • 29 QTL from Burlakoti et al. (2016) Genome-wide association study of spot form of net blotch resistance in the Upper Midwest barley breeding programs. Phytopathology 107, 100 DOI 10.1094/PHYTO-03-16-0136-R and GrainGenes Link
  • 29 QTL from Richards et al. (2017) Association mapping utilizing diverse barley lines reveals net form net blotch seedling resistance/susceptibility loci. Theor Appl Genet 130, 915 DOI 10.1007/s00122-017-2860-1 and GrainGenes Link
  • 25 QTL from Vetter et al. (2017) A nested association mapping population identifies multiple small effect QTL conferring resistance against net blotch (Pyrenophora teres f. teres) in wild barley. PLoS ONE 12, e0186803 DOI 10.1371/journal.pone.0186803 and GrainGenes Link
  • 16 QTL from Adhikari et al. (2019) Genome-wide association mapping of seedling net form net blotch resistance in an Ethiopian and Eritrean barley collection. Crop Sci 59, 1625 DOI 10.2135/cropsci2019.01.0003 and GrainGenes Link
  • 32 QTL from Novakazi et al. (2019) Genetic analysis of a worldwide barley collection for resistance to net form of net blotch disease (Pyrenophora teres f. teres). Theor Appl Genet 132, 2633DOI 10.1007/s00122-019-03378-1 and GrainGenes Link
  • 31 QTL from Adhikari et al. (2020) Identification of quantitative trait loci for net form net blotch resistance in contemporary barley breeding germplasm from the USA using genome-wide association mapping. Theor Appl Genet 133, 1019 DOI 10.1007/s00122-019-03528-5 and GrainGenes Link

Other Disease QTL

  • 20 QTL from Steffenson and Mamo (2015) Genome-wide association mapping of Fusarium head blight resistance and agromorphological traits in barley landraces from Ethiopia and Eritrea. Phytopathology 105, 500 DOI doi.org/10.2135/cropsci2014.06.0428 and GrainGenes Link
  • 7 QTL from Case et al. (2017) Genome-wide association study of stem rust resistance in a world collection of cultivated barley. Phytopathology 107, 100 DOI 10.1007/s00122-017-2989-y and GrainGenes Link
  • 9 QTL from Gyawali et al. (2018) Genome wide association studies (GWAS) of spot blotch resistance at the seedling and the adult plant stages in a collection of spring barley. Mol Breed 38, 62 DOI 10.1007/s11032-018-0815-0 and GrainGenes Link
  • 45 QTL from Daba et al. (2019) Genome-wide association studies and candidate gene identification for leaf scald and net blotch in barley (Hordeum vulgare L.). Plant Disease 103, 880 DOI 10.1094/PDIS-07-18-1190-RE and GrainGenes Link
  • 7 QTL from Hernandez et al. (2020) A Genome-Wide Association Study of Resistance to Puccinia striiformis f. sp. hordei and P. graminis f. sp. tritici in Barley and Development of Resistant Germplasm. Phytopathology 110, 1012 DOI 10.1094/PHYTO-11-19-0415-R and GrainGenes Link
  • 74 QTL from Gyawali et al. (2021) Genome-wide association studies revealed novel stripe rust resistance QTL in barley at seedling and adult-plant stages. Euphytica 217, 3 DOI 10.1007/s10681-020-02728-1 and GrainGenes Link

Agronomic Trait QTL

  • 76 QTL from Gyawali et al. (2017) Genome wide association studies (GWAS) of element contents in grain with a special focus on zinc and iron in a world collection of barley (Hordeum vulgare L.) J Cereal Sci 77, 266 DOI 10.1016/j.jcs.2017.08.019 and GrainGenes Link. This was pre-curated as part of a graduate course in ‘Structural and Functional Genomics’ at Montana State University.
  • 11 QTL from Steffenson and Mamo (2015) Genome-wide association mapping of Fusarium head blight resistance and agromorphological traits in barley landraces from Ethiopia and Eritrea. Crop Sci 55, 1494 DOI doi.org/10.2135/cropsci2014.06.0428 and GrainGenes Link
  • 73 QTL from Borrego-Benjumea et al. (2021) Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions. Front Plant Sci 12, 711654 DOI 10.3389/fpls.2021.711654 and GrainGenes Link

Malt Quality QTL