Octoploid Strawberry DNA Variants from Genotyping-By-Sequencing Experiments

A study by Mitchell J. Feldmann of UC Davis demonstrates Genotyping-By-Sequencing (GBS) for variant discovery in octoploid strawberry. The dataset includes variant call format (VCF) files from two restriction enzyme combinations, PstI-MseI and HindIII-MseI, sequenced on an Illumina HiSeq 4000. The HindIII-MseI protocol discovered 491,811 variants, 2.5-fold more than the PstI-MseI protocol's 199,486 variants.

Use Cases

• High-precision genetic mapping in octoploid strawberry based on the dense genome-wide landscape of DNA variants.
• Identification of DNA variants associated with agriculturally important phenotypes using the discovered single nucleotide polymorphisms (SNPs).
• Genomic-enabled breeding programs leveraging sub-genome specific variant calls enabled by the reference genome.
• Benchmarking bioinformatic pipelines for variant discovery in polyploid species using the provided SLURM scripts.

Strengths

• Includes 491,811 discovered variants from the HindIII-MseI enzyme combination, a 2.5-fold increase over the PstI-MseI combination.
• Provides two distinct VCF files from different experimental protocols, allowing for methodological comparison.
• The study reports mapping rates of 51.41% to 55.56% for reads, resulting in over 1.5 million unique mapping locations.
• Accompanied by documented SLURM scripts detailing the bioinformatic pipeline from demultiplexing to variant calling.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download from the VCF files.
• Row count is unknown, which may limit suitability assessment for specific modeling tasks.
• Last update date is unknown; freshness unverified.

Provenance

Source

University of California, Davis

Collection Method

Genotyping-by-sequencing (GBS) on diverse strawberry accessions, using Illumina HiSeq 4000 sequencing and a custom bioinformatic pipeline.