Two Barley Oligo Pool Assay chips (BOPA 1 and 2) were genotyped from the Wild Barley Diversity Collection. Due to its broad geographic distribution and ecological adaptation, this collection is a valuable source of potentially useful genes.
The 318 sampled wild barley accensions, known as the Wild Barley Diversity Collection (WBDC), were genotyped using the Illumina Golden Gate Genotyping Assay with two Barley Oligo Pool assay chips (BOPA1 and BOPA2). The genotype calls were based on machine-scored data using the program ALCHEMY and the SNPs were annotated using the program SNPMeta. The BOPA1 & 2 files contains the output of the ALCHEMY program.
Finally the original individual SSR for barley are publicly available at the website called GrainGenes and the sample used in this dataset are included as a txt file. All three files (tsv and txt) can be opened by text editors.
Sponsorship: USDA NIFA 2011-68002-30029; University of Minnesota Doctoral Dissertation Fellowship; Lieberman-Okinow Endowment at the University of Minnesota; USAID-funded Cereals Comparative Genomics Initiative
Dataset InfoThese fields are compatible with DCAT, an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.
University of Minnesota
Morrell, Peter L.
|Public Access Level|
|Preferred Dataset Citation|
Fang, Zhou; Gonzales, Ana M; Clegg, Michael T; Smith, Kevin P; Muehlbauer, Gary J; Steffenson, Brian J; Morrell, Peter L. (2016). SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley". Retrieved from the Data Repository for the University of Minnesota, http://doi.org/10.13020/D6B59N.
Fang, Z., Gonzales, A., Clegg, M., Smith, K., Muehlbauer, G., Steffenson, B., & Morrell, P. (2014). Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley. G3: Genes|Genomes|Genetics, 4(7), 1193-1203.
Wright, M., Tung, C., Zhao, K., Reynolds, A., McCouch, S., & Bustamante, C. (2010). ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics, 26(23), 2952-2960.
Kono, T., Seth, K., Poland, J., & Morrell, P. (2013). SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Molecular Ecology Resources, 14(2), 419-425.
Close, T., Bhat, P., Lonardi, S., Wu, Y., Rostoks, N., & Ramsay, L. et al. (2009). Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics, 10(1), 582.
|Cites Other Datasets|
National Institute of Food and Agriculture
University of Minnesota
|Dataset DOI (digital object identifier)|
- Genomics & Genetics