Data from: Candidate variants for additive and interactive effects on bioenergy traits in switchgrass (Panicum virgatum L.) identified by genome-wide association analyses

Ramstein, Guillaume P.; Evans, Joseph; Nandety, Aruna; Saha, Malay C.; Brummer, E. Charles; Kaeppler, Shawn M.; Buell, C. Robin; Casler, Michael D.

doi:10.5061/dryad.km22nh0

Title: Data from: Candidate variants for additive and interactive effects on bioenergy traits in switchgrass (Panicum virgatum L.) identified by genome-wide association analyses

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Abstract

Switchgrass is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving not only simple additive marker effects but also interactions with genetic backgrounds, e.g., ecotypes, or synergies with other markers. We analyzed plant height, carbon content, nitrogen content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotype. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, but also 83,290 markers for marker-by-ecotype interactions and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected based on marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for carbon content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected based on pairwise marker correlations. Furthermore, one marker-by-ecotype interaction and one pairwise interaction were confirmedmore »« less

Authors:

Ramstein, Guillaume P.; Evans, Joseph; Nandety, Aruna; Saha, Malay C.; Brummer, E. Charles; Kaeppler, Shawn M.; Buell, C. Robin; Casler, Michael D.

Univ. of Wisconsin, Madison, WI (United States); Cornell Univ., Ithaca, NY (United States); OSTI
Michigan State Univ., East Lansing, MI (United States)
Samuel Roberts Noble Foundation, Ardmore, OK (United States)
Univ. of Wisconsin, Madison, WI (United States)
Univ. of California, Davis, CA (United States)
Univ. of Wisconsin, Madison, WI (United States); Cornell Univ., Ithaca, NY (United States)

Publication Date:: Thu Jun 06 00:00:00 EDT 2019

DOE Contract Number:: FC02-07ER64494; AC02-05CH11231

Research Org.:: Great Lakes Bioenergy Research Center, Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Subject:: 09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES

OSTI Identifier:: 1873864

DOI:: https://doi.org/10.5061/dryad.km22nh0

Citation Formats


                    Ramstein, Guillaume P., Evans, Joseph, Nandety, Aruna, Saha, Malay C., Brummer, E. Charles, Kaeppler, Shawn M., Buell, C. Robin, and Casler, Michael D. Data from: Candidate variants for additive and interactive effects on bioenergy traits in switchgrass (Panicum virgatum L.) identified by genome-wide association analyses.  United States: N. p., 2019. 
        Web.  doi:10.5061/dryad.km22nh0.

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                    Ramstein, Guillaume P., Evans, Joseph, Nandety, Aruna, Saha, Malay C., Brummer, E. Charles, Kaeppler, Shawn M., Buell, C. Robin, & Casler, Michael D. Data from: Candidate variants for additive and interactive effects on bioenergy traits in switchgrass (Panicum virgatum L.) identified by genome-wide association analyses.  United States.  doi:https://doi.org/10.5061/dryad.km22nh0

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                    Ramstein, Guillaume P., Evans, Joseph, Nandety, Aruna, Saha, Malay C., Brummer, E. Charles, Kaeppler, Shawn M., Buell, C. Robin, and Casler, Michael D. 2019.  
"Data from: Candidate variants for additive and interactive effects on bioenergy traits in switchgrass (Panicum virgatum L.) identified by genome-wide association analyses".  United States.  doi:https://doi.org/10.5061/dryad.km22nh0.  https://www.osti.gov/servlets/purl/1873864. Pub date:Thu Jun 06 00:00:00 EDT 2019

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@article{osti_1873864,

  title        = {Data from: Candidate variants for additive and interactive effects on bioenergy traits in switchgrass (Panicum virgatum L.) identified by genome-wide association analyses},

  author       = {Ramstein, Guillaume P. and Evans, Joseph and Nandety, Aruna and Saha, Malay C. and Brummer, E. Charles and Kaeppler, Shawn M. and Buell, C. Robin and Casler, Michael D.},

  abstractNote = {Switchgrass is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving not only simple additive marker effects but also interactions with genetic backgrounds, e.g., ecotypes, or synergies with other markers. We analyzed plant height, carbon content, nitrogen content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotype. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, but also 83,290 markers for marker-by-ecotype interactions and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected based on marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for carbon content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected based on pairwise marker correlations. Furthermore, one marker-by-ecotype interaction and one pairwise interaction were confirmed in an independent switchgrass panel. Our analyses identified reliable candidate variants for important bioenergy traits in switchgrass. Moreover, they exemplified the importance of interactive effects for the depiction of genetic bases, and illustrated the usefulness of preselection of marker pairs for identifying pairwise marker interactions in association testing.},

  doi          = {10.5061/dryad.km22nh0},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Thu Jun 06 00:00:00 EDT 2019},

  month        = {Thu Jun 06 00:00:00 EDT 2019}

}

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DOI: https://doi.org/10.5061/dryad.km22nh0

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