SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley"
2016-07-19
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2012
2013
2013
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2014
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Source information
Wild Barley Diversity Collection (WBDC)
GrainGenes
GrainGenes
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Title
SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley"
Published Date
2016-07-19
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Author Contact
Morrell, Peter L
pmorrell@umn.edu
pmorrell@umn.edu
Type
Dataset
Genomics Data
Genomics Data
Abstract
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.
Description
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.
Referenced by
Fang, Z., Gonzales, A. M., Clegg, M. T., Smith, K. P., Muehlbauer, G. J., Steffenson, B. J., & Morrell, P. L. (2014). Two genomic regions contribute disproportionately to geographic differentiation in wild barley. G3: Genes| Genomes| Genetics, 4(7), 1193-1203.
http://dx.doi.org/10.1534/g3.114.010561
http://dx.doi.org/10.1534/g3.114.010561
Related to
Program for SNP genotype calling: Wright, M. H., Tung, C. W., Zhao, K., Reynolds, A., McCouch, S. R., & Bustamante, C. D. (2010). ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics, 26(23), 2952-2960.
http://dx.doi.org/10.1093/bioinformatics/btq533
Program for SNP annotation: Kono, T. J. Y., Seth, K., Poland, J. A. and Morrell, P. L. (2014), SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Molecular Ecology Resources, 14: 419–425.
http://dx.doi.org/10.1111/1755-0998.12183
Source for original barley SSR: GrainGenes
http://wheat.pw.usda.gov/GG3/
The Germplasm used in the study (Wild Barley Diversity Collection): Steffenson BJ, Olivera P, Roy JK, Jin Y, Smith KP, Muehlbauer GJ (2007) A walk on the wild side: mining wild wheat and barley collections for rust resistance genes. Australian Journal of Agricultural Research 58, 532–544.
http://dx.doi.org/10.1071/AR07123
Genotyping assays used in the study: Close, T. J., Bhat, P. R., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., ... & Bozdag, S. (2009). Development and implementation of high-throughput SNP genotyping in barley. BMC genomics, 10(1), 1.
http://dx.doi.org/10.1186/1471-2164-10-582
http://dx.doi.org/10.1093/bioinformatics/btq533
Program for SNP annotation: Kono, T. J. Y., Seth, K., Poland, J. A. and Morrell, P. L. (2014), SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Molecular Ecology Resources, 14: 419–425.
http://dx.doi.org/10.1111/1755-0998.12183
Source for original barley SSR: GrainGenes
http://wheat.pw.usda.gov/GG3/
The Germplasm used in the study (Wild Barley Diversity Collection): Steffenson BJ, Olivera P, Roy JK, Jin Y, Smith KP, Muehlbauer GJ (2007) A walk on the wild side: mining wild wheat and barley collections for rust resistance genes. Australian Journal of Agricultural Research 58, 532–544.
http://dx.doi.org/10.1071/AR07123
Genotyping assays used in the study: Close, T. J., Bhat, P. R., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., ... & Bozdag, S. (2009). Development and implementation of high-throughput SNP genotyping in barley. BMC genomics, 10(1), 1.
http://dx.doi.org/10.1186/1471-2164-10-582
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Funding information
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
University of Minnesota Doctoral Dissertation Fellowship
Lieberman-Okinow Endowment at the University of Minnesota
USAID-funded Cereals Comparative Genomics Initiative
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Previously Published Citation
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Suggested 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 (DRUM), http://doi.org/10.13020/D6B59N.
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