Tomato Fruit Malic Acid GWAS Results and SNP Markers

A 200-line tomato inbred line population was used in a genome-wide association study to identify genetic loci for fruit malic acid content. The study identified 90 significant SNP loci on chromosome 6 and annotated 17 candidate genes, with five prioritized for their association. The dataset includes SNP variants and genotyping results for marker-assisted selection.

Use Cases

• Correlate SNP genotypes from the five candidate genes (e.g., Solyc06g072910.2) with measured malic acid phenotypes to validate associations.
• Use the 90 significant SNP loci on chromosome 6 for linkage disequilibrium block analysis and fine-mapping of malic acid-related genomic regions.
• Apply the developed penta-primer amplification refractory mutation system (PARMS) primers for genotyping the six selected SNP loci in other tomato populations.
• Annotate the 17 candidate genes within associated regions using Pfam and Swiss-Prot database information to study gene families like ALMT or ABCB transporters.

Strengths

• Dataset is derived from a defined population of 200 advanced-generation tomato inbred lines, providing genetic diversity for association mapping.
• GWAS analysis identified 90 significant SNP loci with a specific chromosomal localization, offering high-resolution genetic targets.
• Results include annotation for 17 candidate genes and specific primers for six SNP loci, enabling direct experimental follow-up.

Limitations

• The dataset is small (1.5 MB) and likely contains summary results rather than raw sequencing or phenotypic data for the full population.
• All identified SNP loci are confined to chromosome 6, which may not capture the full genetic architecture of malic acid content.
• Phenotypic data (malic acid content) is from a single measurement at the red-ripening stage, lacking temporal or environmental replication.

Provenance

Source

Figshare, authored by Shanshan Wang.

Collection Method

Genome-wide association study (GWAS) conducted on a natural tomato population using DNA resequencing, variant detection, and phenotypic measurement.

Freshness

Last updated March 2026.