Datasets from: Genetic variation in Miscanthus × giganteus and the importance of estimating genetic distance thresholds for differentiating clones

Głowacka, Katarzyna; Clark, Lindsay V.; Adhikari, Shivani; Peng, Junhua; Stewart, J. Ryan; Nishiwaki, Aya; Yamada, Toshihiko; Jorgensen, Uffe; Hodkinson, Trevor R.; Gifford, Justin; Juvik, John A.; Sacks, Erik J.

Content Files

130618readdepth.R

130621sstacks_analysis.R

batch_9.catalog.alleles.tsv

batch_9.catalog.snps.tsv

batch_9.catalog.tags.tsv

README.txt

SSR Markers on Mxg, Msa, Msi from Glowacka et al Mxg paper - data table.csv

SSR Markers on Mxg, Msa, Msi from Glowacka et al Mxg paper - description.csv

SSR Markers on Mxg, Msa, Msi from Glowacka et al Mxg paper with description.xlsx

sstacks_mxgtxpt.zip

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https://hdl.handle.net/2142/79059 Copy

Description

Title

Datasets from: Genetic variation in Miscanthus × giganteus and the importance of estimating genetic distance thresholds for differentiating clones

Author(s)

• Głowacka, Katarzyna
• Clark, Lindsay V.
• Adhikari, Shivani
• Peng, Junhua
• Stewart, J. Ryan
• Nishiwaki, Aya
• Yamada, Toshihiko
• Jorgensen, Uffe
• Hodkinson, Trevor R.
• Gifford, Justin
• Juvik, John A.
• Sacks, Erik J.

Issue Date

2015

Keyword(s)

• genetic diversity
• genotyping error
• interspecific hybrids
• Miscanthus sacchariflorus
• Miscanthus sinensis
• RAD-seq
• SSR

Date of Ingest

2015-08-26T15:44:18Z

Abstract

Miscanthus × giganteus (Mxg) is an important bioenergy feedstock crop, however, genetic diversity among legacy cultivars may be severely constrained. Only one introduction from Japan to Denmark of this sterile, triploid, vegetatively propagated crop was recorded in the 1930s. We sought to determine if the Mxg cultivars in North America were all synonyms, and if they were derived from the European introduction. We used 64 nuclear and five chloroplast simple sequence repeat (SSR) markers to estimate genetic similarity for 27 Mxg accessions from North America, and compared them with six accessions from Europe, including the species’ type-specimen. A subset of accessions was also evaluated by restriction-site associated DNA sequencing (RAD-seq). In addition, we assessed the potential of new crosses to increase Mxg genetic diversity by comparing eight new triploid Mxg progeny grown from seed, along with samples of the parental species M. sacchariflorus and M. sinensis. Estimates of genotyping error rates were essential for distinguishing between experimental error and true genotypic differences among accessions. Given differences in estimated error rates and costs per marker for SSRs and RAD-seq, the former is currently more cost-effective for determining if two accessions are genetically identical. We concluded that all of the Mxg legacy cultivars were derived via vegetative propagation from a single genet. In contrast with the Mxg legacy cultivars, genetic similarity to the type-specimen of eight new triploid Mxg progeny ranged from 0.46 to 0.56. Though genetic diversity among the Mxg legacy cultivars is critically low, new crosses can provide much-needed variation to growers.

Publisher

Wiley

Type of Resource

dataset / spreadsheet

Genre of Resource

Data

Language

eng

Permalink

http://hdl.handle.net/2142/79059

DOI

https://doi.org/10.1111/gcbb.12166

Sponsor(s)/Grant Number(s)

Energy Biosciences Institute

Copyright and License Information

This dataset is released under a Creative Commons 4.0 Attribution-ShareAlike license.

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