Illinois Data Bank

RAD-seq genotypes for a Miscanthus sacchariflorus diversity panel

Cite this dataset:
Clark, Lindsay; Njuguna, Joyce; Jin, Xiaoli; Petersen, Karen; Anzoua, Kossanou G.; Bagmet, Larissa; Chebukin, Pavel; Deuter, Martin; Dzyubenko, Elena; Dzyubenko, Nicolay; Heo, Kweon; Johnson, Douglas A.; Jørgensen, Uffe; Kjeldsen, Jens B.; Nagano, Hironori; Peng, Junhua; Sabitov, Andrey; Yamada, Toshihiko; Yoo, Ji Hye; Yu, Chang Yeon; Long, Stephen P.; Sacks, Erik (2020): RAD-seq genotypes for a Miscanthus sacchariflorus diversity panel. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8170405_V1

Dataset Description

Restriction site-associated DNA sequencing (RAD-seq) data from 643 Miscanthus accessions from a diversity panel, including 613 Miscanthus sacchariflorus, three M. sinensis, and 27 M. xgiganteus. DNA was digested with PstI and MspI, and single-end Illumina sequencing was performed adjacent to the PstI site. Variant and genotype calling was performed with TASSEL-GBSv2, using the Miscanthus sinensis v7.1 reference genome from Phytozome 12 (https://phytozome.jgi.doe.gov). Additional ploidy-aware genotype calling was performed by polyRAD v1.1.

Subject

Life Sciences

Keywords

 variant call format (VCF); genotyping-by-sequencing (GBS); single nucleotide polymorphism (SNP); grass; genetic diversity; biomass

License

 CC BY

Funder

 U.S. Department of Energy (DOE)-Grant:DE-SC0012379

Funder

 U.S. Department of Energy (DOE)-Grant:DE-SC0006634

Funder

 U.S. Department of Agriculture (USDA)-Grant:Cooperative Agreement #59-1275-1-338

Funder

 Energy Biosciences Institute

Funder

 U.S. National Science Foundation (NSF)-Grant:1161490

Corresponding Creator

 Erik Sacks

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Version DOI Comment Publication Date
1 10.13012/B2IDB-8170405_V1 2020-09-18

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