Tomato Malic Acid GWAS Candidate Genes and SNP Markers

A genome-wide association study identified 90 significant SNP loci and 5 candidate genes associated with malic acid content in tomato fruit. The analysis used a population of 200 advanced-generation tomato inbred lines and developed primers for six SNP loci for genotyping. The data provides molecular markers for marker-assisted selection in tomato breeding programs.

Use Cases

• Validate the association between the nine SNP variants within the five candidate genes and malic acid content phenotypes.
• Use the 90 significant SNP loci on chromosome 6 for linkage disequilibrium block analysis in tomato populations.
• Employ the primers developed for six SNP loci for penta-primer amplification refractory mutation system (PARMS) genotyping in other tomato lines.
• Investigate the functional roles of the identified ALMT family, ABCB transporter family, and NAC domain-containing protein genes in malic acid metabolism.

Strengths

• The GWAS analysis is based on a defined population of 200 advanced-generation tomato inbred lines.
• Identifies a specific set of 90 significant SNP loci and 5 candidate genes with functional annotations.
• Includes developed primers for six SNP loci, enabling practical application for genotyping.

Limitations

• The dataset is very small at 251.5 KB, likely containing summary results rather than raw genomic or phenotypic data.
• All significant SNP loci are reported only on chromosome 6, which may not capture the full genetic architecture of the trait.
• The underlying raw phenotypic measurements for the 200 inbred lines are not included in this data sheet.

Provenance

Source

figshare, authored by Shanshan Wang.

Collection Method

Genome-wide association study (GWAS) conducted on a natural population, with variant detection from DNA resequencing.

Freshness

Last updated March 24, 2026.