Expanded genetic variation (SNP) and phenomics (image based) dataset for Populus trichocarpa

Nagle, Michael F; Yuan, Jialin; Kaur, Damanpreet; Ma, Cathleen; Peremyslova, Ekaterina; Jiang, Yuan; Nino de Rivera, Alexo; Jowdy, Sara; Chen, Jin-Gui; Feng, Kai; Yates, Timothy; Yates, Timothy B; Tuskan, Gerald A; Muchero, Wellington; Li, Fuxin; Strauss, Steven H

doi:10.25983/2263365

Title: Expanded genetic variation (SNP) and phenomics (image based) dataset for Populus trichocarpa

Dataset
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Abstract

The image dataset consists of 11,791 images representing 1,219 genotypes of Populus trichocarpa undergoing in planta regeneration. Genotypes were imaged with a median of four weekly timepoints and a median of two replicates each. A representative and diverse subset of 249 images was annotated using the IDEAS annotation interface (ideas.eecs.oregonstate.edu) and these annotated images were used to train a deep semantic segmentation model (PSPNet), which was deployed for inference over the entire dataset. Annotated classes include specific stages of regeneration (callus and shoot) in addition to unregenerated plant material and background. Statistics of relative tissue area were extracted and used for downstream genetic association mapping in a genome-wide association study. The SNP dataset consists of over 40 million single-nucleotide polymorphisms across 1,323 wild accessions of Populus trichocarpa

Authors:

Nagle, Michael F; Yuan, Jialin; Kaur, Damanpreet; Ma, Cathleen; Peremyslova, Ekaterina; Jiang, Yuan; Nino de Rivera, Alexo; Jowdy, Sara; Chen, Jin-Gui; Feng, Kai; Yates, Timothy; Yates, Timothy B; Tuskan, Gerald A; Muchero, Wellington; Li, Fuxin; Strauss, Steven H

Oregon State Univ., Corvallis, OR (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Center for Bioenergy Innovation (CBI)

Publication Date:: Wed Dec 27 04:00:00 UTC 2023

DOE Contract Number:: AC05-00OR22725

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

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

Subject:: 09 BIOMASS FUELS; Populus Trichocarpa, GWAS, phenotyping

OSTI Identifier:: 2263365

DOI:: https://doi.org/10.25983/2263365

Citation Formats


                    Nagle, Michael F, Yuan, Jialin, Kaur, Damanpreet, Ma, Cathleen, Peremyslova, Ekaterina, Jiang, Yuan, Nino de Rivera, Alexo, Jowdy, Sara, Chen, Jin-Gui, Feng, Kai, Yates, Timothy, Yates, Timothy B, Tuskan, Gerald A, Muchero, Wellington, Li, Fuxin, and Strauss, Steven H. Expanded genetic variation (SNP) and phenomics (image based) dataset for Populus trichocarpa.  United States: N. p., 2023. 
        Web.  doi:10.25983/2263365.

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                    Nagle, Michael F, Yuan, Jialin, Kaur, Damanpreet, Ma, Cathleen, Peremyslova, Ekaterina, Jiang, Yuan, Nino de Rivera, Alexo, Jowdy, Sara, Chen, Jin-Gui, Feng, Kai, Yates, Timothy, Yates, Timothy B, Tuskan, Gerald A, Muchero, Wellington, Li, Fuxin, & Strauss, Steven H. Expanded genetic variation (SNP) and phenomics (image based) dataset for Populus trichocarpa.  United States.  doi:https://doi.org/10.25983/2263365

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                    Nagle, Michael F, Yuan, Jialin, Kaur, Damanpreet, Ma, Cathleen, Peremyslova, Ekaterina, Jiang, Yuan, Nino de Rivera, Alexo, Jowdy, Sara, Chen, Jin-Gui, Feng, Kai, Yates, Timothy, Yates, Timothy B, Tuskan, Gerald A, Muchero, Wellington, Li, Fuxin, and Strauss, Steven H. 2023.  
"Expanded genetic variation (SNP) and phenomics (image based) dataset for Populus trichocarpa".  United States.  doi:https://doi.org/10.25983/2263365.  https://www.osti.gov/servlets/purl/2263365. Pub date:Wed Dec 27 04:00:00 UTC 2023

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@article{osti_2263365,

  title        = {Expanded genetic variation (SNP) and phenomics (image based) dataset for Populus trichocarpa},

  author       = {Nagle, Michael F and Yuan, Jialin and Kaur, Damanpreet and Ma, Cathleen and Peremyslova, Ekaterina and Jiang, Yuan and Nino de Rivera, Alexo and Jowdy, Sara and Chen, Jin-Gui and Feng, Kai and Yates, Timothy and Yates, Timothy B and Tuskan, Gerald A and Muchero, Wellington and Li, Fuxin and Strauss, Steven H},

  abstractNote = {The image dataset consists of 11,791 images representing 1,219 genotypes of Populus trichocarpa undergoing in planta regeneration. Genotypes were imaged with a median of four weekly timepoints and a median of two replicates each. A representative and diverse subset of 249 images was annotated using the IDEAS annotation interface (ideas.eecs.oregonstate.edu) and these annotated images were used to train a deep semantic segmentation model (PSPNet), which was deployed for inference over the entire dataset. Annotated classes include specific stages of regeneration (callus and shoot) in addition to unregenerated plant material and background. Statistics of relative tissue area were extracted and used for downstream genetic association mapping in a genome-wide association study. The SNP dataset consists of over 40 million single-nucleotide polymorphisms across 1,323 wild accessions of Populus trichocarpa},

  doi          = {10.25983/2263365},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Wed Dec 27 04:00:00 UTC 2023},

  month        = {Wed Dec 27 04:00:00 UTC 2023}

}

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DOI: https://doi.org/10.25983/2263365

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