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

Dataset · Tue Dec 26 23:00:00 EST 2023

DOI:https://doi.org/10.25983/2263365· OSTI ID:2263365

Nagle, Michael F ^[1]; Yuan, Jialin ^[1]; Kaur, Damanpreet ^[1]; Ma, Cathleen ^[1]; Peremyslova, Ekaterina ^[1]; Jiang, Yuan ^[1]; Nino de Rivera, Alexo ^[1]; Jowdy, Sara ^[2]; Chen, Jin-Gui ^[2]; Feng, Kai ^[2]; Yates, Timothy ^[2]; Yates, Timothy B ^[2]; Tuskan, Gerald A ^[2]; Muchero, Wellington ^[2]; Li, Fuxin ^[2]; Strauss, Steven H ^[1]

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

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

• Research Organization: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 2263365
• Country of Publication: United States
• Language: English

Related Subjects

09 BIOMASS FUELS
Populus Trichocarpa
GWAS
phenotyping