RAD-seq genotypes for a Miscanthus sacchariflorus diversity panel
Citation:
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
Persistent link for this dataset:
Related Dataset Clark, Lindsay V.; Jin, Xiaoli; Petersen, Karen K.; 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 J. (2018): Population genetic structure of Miscanthus sacchariflorus. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0170190_V3
Related Article Lindsay V. Clark, Wittney Mays, Alexander E. Lipka, and Erik J. Sacks (2020) “A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes.” Preprint on bioRxiv. doi:10.1101/2020.01.11.902890
Related Dataset "Genetic diversity of Miscanthus sinensis." Raw DNA sequencing data on NCBI Sequence Read Archive.
Related Dataset "Genetic diversity of Miscanthus sacchariflorus." Raw DNA sequencing data on NCBI Sequence Read Archive.
Related Dataset "Genetic diversity and hybridization of Japanese Miscanthus sinensis and Miscanthus sacchariflorus." Raw DNA sequencing data on NCBI Sequence Read Archive.
Related Dataset "Genetic diversity of Miscanthus in eastern Russia." Raw DNA sequencing data on NCBI Sequence Read Archive.
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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update: {"version_comment"=>[nil, ""], "subject"=>[nil, "Life Sciences"]} 2020-09-21T19:15:28Z