Comprehensive SNP Data for 1,323 GWAS Population in Populus trichocarpa and Combined Annotation Files for P. trichocarpa v3.0 and v3.1

Shu, Meng Jun; Yates, Timothy; Cai, John; Jawdy, Sara; Tuskan, Gerald; Chen, Jin-Gui; Muchero, Wellington

doi:10.25983/2352478

Title: Comprehensive SNP Data for 1,323 GWAS Population in Populus trichocarpa and Combined Annotation Files for P. trichocarpa v3.0 and v3.1

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Abstract

The VCF dataset includes genetic variations found in 1,323 Populus trichocarpa genotypes, providing valuable information for scientists studying plant genetics. Researchers have generated this dataset using whole-genome DNA short-read sequencing on the Illumina Genome Analyzer, HiSeq 2000, and HiSeq 2500 platforms. This sequencing effort ensured a minimum expected sequencing depth of 15×. The dataset comprises more than 9.7 million single nucleotide polymorphisms (SNPs) and indel variants. The combined annotation files are derived from P. trichocarpa v3.0 and v3.1. We merged these files to create a comprehensive annotation file used for GWAS analysis. In total, 38,830 genes overlapped between the two versions. For overlapping genes, we defined the start as the smaller and the end as the larger among the two versions to increase the likelihood of locating candidate genetic loci. Additionally, we included 2,505 unique genes from v3.0 and 4,120 unique genes from v3.1, resulting in a total of 45,455 genes in the updated annotation file.

Authors:

Shu, Meng Jun; Yates, Timothy; Cai, John; Jawdy, Sara; Tuskan, Gerald; Chen, Jin-Gui; Muchero, Wellington

Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
University of Tennessee, Knoxville
Oak Ridge National Laboratory

Publication Date:: Tue May 21 04:00:00 UTC 2024

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 SNPS GWAS

OSTI Identifier:: 2352478

DOI:: https://doi.org/10.25983/2352478

Citation Formats


                    Shu, Meng Jun, Yates, Timothy, Cai, John, Jawdy, Sara, Tuskan, Gerald, Chen, Jin-Gui, and Muchero, Wellington. Comprehensive SNP Data for 1,323 GWAS Population in Populus trichocarpa and Combined Annotation Files for P. trichocarpa v3.0 and v3.1.  United States: N. p., 2024. 
        Web.  doi:10.25983/2352478.

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                    Shu, Meng Jun, Yates, Timothy, Cai, John, Jawdy, Sara, Tuskan, Gerald, Chen, Jin-Gui, & Muchero, Wellington. Comprehensive SNP Data for 1,323 GWAS Population in Populus trichocarpa and Combined Annotation Files for P. trichocarpa v3.0 and v3.1.  United States.  doi:https://doi.org/10.25983/2352478

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                    Shu, Meng Jun, Yates, Timothy, Cai, John, Jawdy, Sara, Tuskan, Gerald, Chen, Jin-Gui, and Muchero, Wellington. 2024.  
"Comprehensive SNP Data for 1,323 GWAS Population in Populus trichocarpa and Combined Annotation Files for P. trichocarpa v3.0 and v3.1".  United States.  doi:https://doi.org/10.25983/2352478.  https://www.osti.gov/servlets/purl/2352478. Pub date:Tue May 21 04:00:00 UTC 2024

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@article{osti_2352478,

  title        = {Comprehensive SNP Data for 1,323 GWAS Population in Populus trichocarpa and Combined Annotation Files for P. trichocarpa v3.0 and v3.1},

  author       = {Shu, Meng Jun and Yates, Timothy and Cai, John and Jawdy, Sara and Tuskan, Gerald and Chen, Jin-Gui and Muchero, Wellington},

  abstractNote = {The VCF dataset includes genetic variations found in 1,323 Populus trichocarpa genotypes, providing valuable information for scientists studying plant genetics. Researchers have generated this dataset using whole-genome DNA short-read sequencing on the Illumina Genome Analyzer, HiSeq 2000, and HiSeq 2500 platforms. This sequencing effort ensured a minimum expected sequencing depth of 15×. The dataset comprises more than 9.7 million single nucleotide polymorphisms (SNPs) and indel variants. The combined annotation files are derived from P. trichocarpa v3.0 and v3.1. We merged these files to create a comprehensive annotation file used for GWAS analysis. In total, 38,830 genes overlapped between the two versions. For overlapping genes, we defined the start as the smaller and the end as the larger among the two versions to increase the likelihood of locating candidate genetic loci. Additionally, we included 2,505 unique genes from v3.0 and 4,120 unique genes from v3.1, resulting in a total of 45,455 genes in the updated annotation file.},

  doi          = {10.25983/2352478},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Tue May 21 04:00:00 UTC 2024},

  month        = {Tue May 21 04:00:00 UTC 2024}

}

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DOI: https://doi.org/10.25983/2352478

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