SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley"

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Persistent link to this item

http://doi.org/10.13020/D6B59N
https://hdl.handle.net/11299/181368

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Keywords

environmental association

local adaptation

population structure

chromosome structural variation

wild barley

Collection period

2012
2013

Date completed

2014

Date updated

Time period coverage

Geographic coverage

Source information

Wild Barley Diversity Collection (WBDC)
GrainGenes

Journal Title

Journal ISSN

Volume Title

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

Authors

Fang, Zhou

Gonzales, Ana M

Clegg, Michael T

Smith, Kevin P

Muehlbauer, Gary J

Steffenson, Brian J

Morrell, Peter L

Group

Author Contact

Morrell, Peter L
pmorrell@umn.edu

Type

Dataset
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

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

Replaces

License

Attribution 3.0 United States
https://creativecommons.org/licenses/by/3.0/us/

Publisher

Collections

Data Repository for U of M (DRUM)

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

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Previously Published Citation

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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