Identification of a QTL region for tomato brown rugose fruit virus resistance in Solanum pimpinellifolium

Authors: Jaiswal, Namrata; ZIA, BAZGHA - Oak Ridge Institute For Science And Education (ORISE); Chanda, Bidisha; Gilliard, Andrea; SHI, AINONG - University Of Arkansas; Ling, Kai Shu

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/30/2025
Publication Date: 7/22/2025
Citation: Jaiswal, N., Zia, B., Chanda, B., Gilliard, A.C., Shi, A., Ling, K. 2025. Identification of a QTL region for tomato brown rugose fruit virus resistance in Solanum pimpinellifolium. Theoretical and Applied Genetics. .. https://doi.org/10.1007/s00122-025-04974-0.
DOI: https://doi.org/10.1007/s00122-025-04974-0

Interpretive Summary: Tomato is one of the most important vegetable crops in the United States and around the world. Tomato brown rugose fruit virus (ToBRFV) is an emerging virus, which was first identified in Jordan and Israel in 2014-2015 and has since spread to at least 25 countries around the world, including the USA. This seed-borne virus is capable of breaking the common resistance genes for tobamoviruses in tomato, thus poses a serious threat to tomato production. Developing new tomato cultivar with resistance to ToBRFV is one of the most important strategies to combat this emerging virus. In screening a core collection of the US tomato germplasm, we have identified a new source of resistance to ToBRFV in Solanum pimpinellifolium. In the present study, in collaboration with a collaborator in University of Arkansas, USDA-ARS scientists at the U.S. Vegetable Laboratory conducted quantitative trait locus (QTL) mapping and identified single nucleotide polymorphism(SNP) markers associated with ToBRFV resistance in tomato. The associated single nucleotide polymorphisms (SNPs) could be used by public and private breeders for marker-assisted selection to accelerate the development of new tomato cultivars with resistance to ToBRFV.

Technical Abstract: Tomato (Solanum lycopersicum L.), one of the most widely grown vegetables in the world, has been seriously impacted in the last decade by the emerging tomato brown rugose fruit virus (ToBRFV). ToBRFV is a seed-borne tobamovirus, with ability to overcome the commonly used Tm-2^2 resistance gene in tomato. The objective of this study was to conduct quantitative trait locus (QTL) mapping and identify single nucleotide polymorphism (SNP) markers associated with ToBRFV resistance in tomato. Two F2 populations were used for QTL mapping: one derived from a cross between S. pimpinellifolium USVL333 (PI 390718) × USVL332 (PI 390717) and another from ‘Moneymaker’ × USVL332 (PI 390717), with population sizes of 195 and 79 plants, respectively. The resistance trait was derived from the S. pimpinellifolium accession USVL332 (PI 390717). A major QTL for ToBRFV resistance was identified on chromosome 11 (SL4.0ch11), with the peak located at approximately 46.84 Mbp. This QTL spans a 22-kb interval between 46,825,788 bp and 46,847,421 bp, as determined through both genome-wide association study (GWAS) and QTL linkage mapping. Three SNP markers, SL4.0ch11_46825788, SL4.0ch11_46847421, and SL4.0ch11_46850215, demonstrated the most significant association with high LOD values (LOD = 13 in the Blink model) in GWAS analysis. In this genomic region, two disease resistance gene analogues, Solyc11g062150 (TIR-NBS-LRR resistance protein, Toll-Interleukin receptor) and Solyc11g062180 (disease resistance protein, leucine-rich repeat), were identified, which may serve as candidates for ToBRFV resistance. The QTL identified in this study could be valuable for plant breeders in facilitating tomato breeding with ToBRFV resistance.