Genotypic Data for GWAS Study on Black Rice with 31,501 SNPs

31,501 single-nucleotide polymorphisms (SNPs) from a diversity panel of black rice accessions. The data was generated via Genotyping-By-Sequencing by The Elshire Group Ltd and processed using the GBSV2 pipeline and TASSEL 5.0 for a genome-wide association study (GWAS) on grain pigmentation. Author Truong Duc Nguyen uploaded the dataset to figshare in May 2026.

Use Cases

• Identify quantitative trait loci (QTL) linked to grain pigmentation based on the SNP data.
• Perform genome-wide association studies (GWAS) on secondary metabolite profiles in black rice.
• Analyze genetic diversity within a panel of black rice accessions based on the 31,501 SNP markers.
• Investigate the genetic response to UV exposure in rice using the genotypic data.

Strengths

• Contains 31,501 SNPs, providing a substantial number of markers for genetic analysis.
• Data underwent quality control using the established TASSEL 5.0 software pipeline.
• Genotyping was performed by a named commercial provider, The Elshire Group Ltd, using Genotyping-By-Sequencing.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for certain analyses.
• The description does not specify the number of rice accessions in the diversity panel.

Provenance

Source

The Elshire Group Ltd (genotyping), Truong Duc Nguyen (author/researcher).

Collection Method

Genotyping-By-Sequencing (GBS), SNP calling via GBSV2 pipeline, quality control in TASSEL 5.0.

Time Range

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Freshness

Last updated 2026-05-06 11:23:43; freshness should be verified.

Geography

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