SABER: a multiparental tomato population leveraging wild relative diversity for high-resolution QTL mapping
4 affiliations
- 1Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, PD Italy
- 2Institute of Plant Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
- 3Panora SpA, Fidenza, PR Italy
- 4Council for Agricultural Research and Economics (CREA) - Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, AP Italy
Abstract
Background: The narrow genetic base of cultivated tomato (Solanum lycopersicum L.) represents a major constraint on crop improvement, necessitating the exploitation of wild relatives to broaden allelic diversity. Here we present SABER (Solanum lycopersicum Allele Biodiversity Enriched Resources), a novel eight-founder Multiparent Advanced Generation Intercross (MAGIC) population that, for the first time, incorporates the Galápagos wild relative Solanum cheesmaniae as a founder alongside seven elite S. lycopersicum lines.
Results: Following a structured crossing scheme and Single Seed Descent (SSD) advancement, F6 recombinant inbred lines were genotyped at 5,850 high-confidence SNP markers using Single Primer Enrichment Technology (SPET). Population structure analyses confirmed low residual heterozygosity, limited substructure among offspring, and successful introgression of S. cheesmaniae alleles across all twelve chromosomes. Mapping performance was validated through three Mendelian traits with known genetic determinants, all of which resolved to genomic positions consistent with the literature. Quantitative Trait Loci (QTL) mapping identified known loci for fruit epicarp and flesh color, and two novel QTLs for days to flowering, number of leaves before flowering, and soluble solids content.
Conclusions: Together, these results demonstrate that SABER is a powerful and reliable platform for high-resolution QTL mapping and candidate gene discovery, and establish a replicable framework for integrating wild germplasm into multiparental tomato breeding resources.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12870-026-09726-w.
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BibTeX
@article{gabelli2026saber,
title = {{SABER: a multiparental tomato population leveraging wild relative diversity for high-resolution QTL mapping}},
author = {Giovanni Gabelli and Leonardo Caproni and Fabio Palumbo and Anna Giulia Boni and Giulia Ferrari and Maria Lucia Prazzoli and Marina Malatrasi and Sara Sestili and Matteo dell’Acqua and Massimiliano Beretta and Gianni Barcaccia},
journal = {BMC Plant Biology},
year = {2026},
month = aug,
doi = {10.1186/s12870-026-09726-w},
url = {https://doi.org/10.1186/s12870-026-09726-w},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - SABER: a multiparental tomato population leveraging wild relative diversity for high-resolution QTL mapping
AU - Giovanni Gabelli
AU - Leonardo Caproni
AU - Fabio Palumbo
AU - Anna Giulia Boni
AU - Giulia Ferrari
AU - Maria Lucia Prazzoli
AU - Marina Malatrasi
AU - Sara Sestili
AU - Matteo dell’Acqua
AU - Massimiliano Beretta
AU - Gianni Barcaccia
PY - 2026
DA - 2026/08/15
JO - BMC Plant Biology
DO - 10.1186/s12870-026-09726-w
UR - https://doi.org/10.1186/s12870-026-09726-w
AB - Background: The narrow genetic base of cultivated tomato (Solanum lycopersicum L.) represents a major constraint on crop improvement, necessitating the exploitation of wild relatives to broaden allelic diversity. Here we present SABER (Solanum lycopersicum Allele Biodiversity Enriched Resources), a novel eight-founder Multiparent Advanced Generation Intercross (MAGIC) population that, for the first time, incorporates the Galápagos wild relative Solanum cheesmaniae as a founder alongside seven elite S. lycopersicum lines. Results: Following a structured crossing scheme and Single Seed Descent (SSD) advancement, F6 recombinant inbred lines were genotyped at 5,850 high-confidence SNP markers using Single Primer Enrichment Technology (SPET). Population structure analyses confirmed low residual heterozygosity, limited substructure among offspring, and successful introgression of S. cheesmaniae alleles across all twelve chromosomes. Mapping performance was validated through three Mendelian traits with known genetic determinants, all of which resolved to genomic positions consistent with the literature. Quantitative Trait Loci (QTL) mapping identified known loci for fruit epicarp and flesh color, and two novel QTLs for days to flowering, number of leaves before flowering, and soluble solids content. Conclusions: Together, these results demonstrate that SABER is a powerful and reliable platform for high-resolution QTL mapping and candidate gene discovery, and establish a replicable framework for integrating wild germplasm into multiparental tomato breeding resources. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12870-026-09726-w.
SN - 1471-2229
ER -