ArticleBMC plant biology2025
Association mapping of tomato fruit quality for weight, firmness, brix, and color using GWAS.
Article in BMC plant biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Domestication-associated reduction of methyl salicylate in tomato root and its significance for resistance to root-knot nematode.The New phytologist · 2026Article
- Multi-variant GWAS and genomic prediction dissect the genetic architecture underlying tomato fruit weight.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Identification of candidate genes for malic acid content in tomato fruits and development of associated SNP markers.Frontiers in plant science · 2026Article
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7 authors.
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Abstract
backgroundFruit quality traits such as fruit weight, firmness, total soluble solids content, and color strongly influence consumer acceptance, market value, postharvest shelf life, and processing efficiency in tomato. Therefore, these traits are central to breeding programs but remain challenging to dissect due to their polygenic and pleiotropic nature.
resultsWe evaluated 167 accessions from the Varitome collection, encompassing Solanum pimpinellifolium, Solanum lycopersicum var. cerasiforme, and Solanum lycopersicum var. lycopersicum. The Varitome collection represents a rich source of genetic and phenotypic diversity, making it a powerful resource for mapping complex traits. Genome-wide association studies (GWAS) were conducted using the FarmCPU and Blink models, utilizing a dataset of 3,879,252 SNPs, 831,152 INDELs, and 11,447 structural variants (SVs). Six fruit-quality traits were phenotyped: fruit weight, firmness, total soluble solids, lightness (L*), chroma (C*), and hue (h°). Our multi-variant GWAS uncovered both known and novel determinants of fruit quality. Known loci such as PSY1 and fw11.3/CSR were validated, while robust new signals were detected on chromosomes 1, 4, 6, 8, and 12 for °Brix and on chromosome 7 for fruit weight. Several pleiotropic hotspots were identified, particularly on chromosomes 1, 5, 6, and 8 for fruit color, supported by convergent SNP, INDEL, and SV associations. Candidate genes included biosynthetic enzymes (PSY homologs, LIN5), sugar transporters (SWEETs, SUTs, and sugar facilitator proteins), transcriptional regulators (MADS-box, bHLH, TCP, NAC, and MYB families), and genes linked to plastid remodeling, light signaling, and oxidative turnover. Integration of INDELs and SVs across models improved mapping resolution and robustness, enabling the detection of loci that would remain hidden in SNP-only scans.
conclusionsThis study demonstrates the multilayered genetic networks governing tomato fruit quality and expands the catalog of loci contributing to polygenic traits. By using SNPs, INDELs, and SVs with FarmCPU and Blink models, we provide validated and novel targets for marker-assisted breeding, genomic selection, and functional validation. These findings establish a framework for accelerating the development of tomato cultivars with enhanced fruit weight, sweetness, firmness, and color, thereby supporting both market competitiveness and nutritional quality.
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