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

Dataset · Tue May 21 04:00:00 EDT 2024

DOI:https://doi.org/10.25983/2352478· OSTI ID:2352478

Shu, Meng Jun ^[1]; Yates, Timothy ^[2]; Cai, John ^[2]; Jawdy, Sara ^[1]; Tuskan, Gerald ^[1]; Chen, Jin-Gui ^[1]; Muchero, Wellington ^[3]

---

1. Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
2. University of Tennessee, Knoxville
3. Oak Ridge National Laboratory

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.

• 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: 2352478
• Country of Publication: United States
• Language: English

Related Subjects

09 BIOMASS FUELS
Populus Trichocarpa SNPS GWAS