TBRFV resistant tomato plant

Hamed Rashidi, De Lier (NL); Jonathan Kalisvaart, De Lier (NL); Roel Hamelink, De Lier (NL)

USPTO: us-12628751 · published 2026-05-19 · patents · A01H 1/126· A01H 1/045· A01H 5/08· A01H 6/825· C12N 15/8283

TBRFV resistant tomato plant

Roel Hamelink, De Lier (NL) , Jonathan Kalisvaart, De Lier (NL) , Hamed Rashidi, De Lier (NL) This is my paper

Pith reviewed 2026-05-21 00:02 UTC · model grok-4.3

classification patents A01H 1/126A01H 1/045A01H 5/08A01H 6/825C12N 15/8283

keywords tomatoTBRFV resistanceQTL mappingchromosome 11chromosome 12marker-assisted selectionSolanum lycopersicumvirus resistance

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The pith

A tomato plant resists Tomato brown rugose fruit virus through two defined QTLs on chromosomes 11 and 12.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper establishes that stable resistance to TBRFV in Solanum lycopersicum arises from the simultaneous presence of one QTL interval on chromosome 11 and a second QTL interval on chromosome 12. These intervals are delimited by specific nucleotide sequences and are tracked by tightly linked DNA markers that co-segregate with the resistance phenotype. The same intervals occur in two deposited breeding lines whose seed stocks serve as the reference source for the trait. If the claim holds, breeders can introduce durable field resistance into commercial varieties by marker-assisted selection without needing the full genome of the source lines.

Core claim

A Solanum lycopersicum plant that is resistant to Tomato brown rugose fruit virus comprises a QTL on chromosome 11 located between SEQ ID NOS 1 and 9 and linked to markers SEQ ID NOs 4 and 5, together with a QTL on chromosome 12 located between SEQ ID NOS 10 and 15 and linked to markers SEQ ID NOs 12, 13 and 14; both QTLs match those present in the deposited lines NCIMB 42885 and NCIMB 42887 and together confer the resistance phenotype.

What carries the argument

Two quantitative trait loci (QTLs) on chromosomes 11 and 12, each bounded by stated sequence intervals and tracked by co-segregating SNP markers, whose joint action produces TBRFV resistance.

If this is right

Breeders can introgress the resistance into elite lines using only the listed markers without phenotypic screening at every generation.
Commercial varieties carrying both QTLs should maintain resistance across diverse growing environments where TBRFV pressure is high.
The deposited seed stocks serve as a public reference for verifying the presence of the resistance haplotypes.
Stacking these QTLs with other known disease-resistance loci becomes straightforward once the chromosome positions are fixed.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

Marker assays based on SEQ ID NOs 4, 5, 12, 13 and 14 could be deployed in high-throughput genotyping platforms for large-scale nursery screening.
If the QTLs act additively, pyramiding them with resistance sources from wild tomato relatives may extend the durability of protection against evolving TBRFV strains.
The same intervals could be edited directly with CRISPR once the causal genes inside each QTL are identified.

Load-bearing premise

The two QTL intervals and their linked markers are sufficient by themselves to produce stable, commercially useful resistance without additional unidentified genetic factors or environmental interactions that could break the phenotype.

What would settle it

A plant that carries both marker sets yet develops typical TBRFV symptoms under controlled inoculation, or a plant that lacks one or both marker sets yet remains fully resistant, would falsify the claim that these QTLs alone confer the resistance.

read the original abstract

1 . A Solanum lycopersicum plant that is resistant to Tomato brown rugose fruit virus (TBRFV), which plant comprises a QTL on chromosome 11 and a QTL on chromosome 12, wherein the QTL on chromosome 11 is located between SEQ ID NOS. 1 and 9 and linked to co-segregating markers having the sequences of SEQ ID NOs: 4 and 5; and the QTL on chromosome 12 is located between SEQ ID NOS. 10 and 15 and linked to co-segregating markers having the sequences of SEQ ID NOs: 12, 13, and 14, wherein the QTL on chromosome 11 and the QTL on chromosome 12 are as comprised on chromosome 11 having the sequences of SEQ ID NOs: 4 and 5, and chromosome 12 having the sequences of SEQ ID NOs: 12, 13, and 14 in the genome of a Solanum lycopersicum plant, representative seed of which was deposited with the NCIMB under deposit number NCIMB 42885 and NCIMB 42887, and wherein the QTL on chromosome 11 and the QTL on chromosome 12 confer resistance to TBRFV.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Desk Editor's Note private letter to a colleague

This patent stakes a claim to two defined QTL intervals plus their marker sequences for TBRFV resistance in tomato, anchored by seed deposits, but supplies no phenotypic or segregation data to show those intervals are enough.

read the letter

The core of the filing is a precise description of two QTL regions—one on chromosome 11 between SEQ IDs 1 and 9, tagged by markers 4 and 5, and one on chromosome 12 between SEQ IDs 10 and 15, tagged by markers 12-14—together with the NCIMB deposits that carry them. That level of sequence-level definition tied directly to deposited material is the main concrete addition; most earlier TBRFV work has stayed at the level of broad linkage groups or phenotypic screens without releasing the exact intervals or the living reference lines. Breeders who want to introgress the trait via marker-assisted selection will find the marker sequences and interval boundaries immediately usable for tracking. The limitation is obvious and material: the text asserts that these two QTLs confer resistance but shows no virus-challenge results, no segregation ratios, and no near-isogenic comparisons. Without that evidence it is impossible to judge whether the intervals are sufficient on their own or whether additional loci or specific backgrounds are required for stable commercial performance. The circularity risk is moderate; the claim rests on the deposited lines rather than on any derived prediction, so the deposits themselves become the primary proof. This work is mainly of interest to tomato breeding programs and IP teams that need the exact markers and access to the deposited germplasm. It does not rise to the level of a data-driven genetics paper, but the marker definitions are clear enough that a serious editor could send it for review focused on utility and enablement rather than desk-reject it outright.

Referee Report

1 major / 2 minor

Summary. The manuscript claims a Solanum lycopersicum plant resistant to Tomato brown rugose fruit virus (TBRFV) that carries a QTL on chromosome 11 (bounded by SEQ ID NOs 1–9 and tagged by co-segregating markers SEQ ID NOs 4 and 5) together with a QTL on chromosome 12 (bounded by SEQ ID NOs 10–15 and tagged by markers SEQ ID NOs 12, 13 and 14). Both intervals are stated to be identical to those present in the deposited accessions NCIMB 42885 and NCIMB 42887 and are asserted to confer the resistance phenotype.

Significance. If substantiated, the identification of two discrete, marker-delimited QTL intervals that together confer stable TBRFV resistance would be of immediate value to tomato breeding programs, enabling marker-assisted introgression without reliance on the full deposited genetic background.

major comments (1)

[Abstract/Claim 1] Abstract/Claim 1: the assertion that the two QTL intervals “confer resistance to TBRFV” is unsupported by any phenotypic data, segregation ratios, virus-challenge results, or near-isogenic line comparisons within the manuscript; the genotype–phenotype correlation therefore remains unshown.

minor comments (2)

[Abstract] The description of the deposited lines should explicitly state the accession numbers and any available phenotypic or genotypic characterization data that accompany the deposits.
[Abstract] Marker sequences (SEQ ID NOs 4, 5, 12–14) are referenced but their physical positions or primer sequences are not tabulated, hindering immediate use by other laboratories.

Simulated Author's Rebuttal

1 responses · 0 unresolved

We thank the referee for highlighting the need for clearer linkage between the claimed QTL intervals and the TBRFV resistance phenotype. We address the single major comment below.

read point-by-point responses

Referee: [Abstract/Claim 1] Abstract/Claim 1: the assertion that the two QTL intervals “confer resistance to TBRFV” is unsupported by any phenotypic data, segregation ratios, virus-challenge results, or near-isogenic line comparisons within the manuscript; the genotype–phenotype correlation therefore remains unshown.

Authors: The QTL intervals are delimited precisely by the sequences present in the deposited accessions NCIMB 42885 and NCIMB 42887, which are explicitly described in the specification as TBRFV-resistant. In the context of this patent application the resistance phenotype is therefore tied directly to the presence of those exact intervals and their co-segregating markers; the deposits themselves constitute the working examples that demonstrate the correlation. No additional segregation tables or challenge data appear in the published claim language because the legal definition of the invention rests on the deposited material and the marker boundaries. revision: no

Circularity Check

0 steps flagged

No derivation chain or predictions; claim is purely descriptive of deposited accessions

full rationale

The document is a patent claim that directly identifies two QTL intervals and their linked markers by reference to the sequences present in the deposited lines NCIMB 42885 and NCIMB 42887. No equations, fitted parameters, predictions, ansatzes, or uniqueness theorems appear anywhere in the text. Because there is no derivation step that could reduce to its own inputs, no circularity exists.

Axiom & Free-Parameter Ledger

0 free parameters · 1 axioms · 0 invented entities

The patent rests on the unproven premise that the listed markers perfectly tag functional resistance alleles and that no other loci modify the phenotype under commercial growing conditions.

axioms (1)

domain assumption The deposited lines contain no additional unlinked resistance factors that contribute to the observed TBRFV resistance.
Abstract asserts that the two QTLs alone confer resistance.

pith-pipeline@v0.9.0 · 5809 in / 1188 out tokens · 23422 ms · 2026-05-21T00:02:24.644488+00:00 · methodology

discussion (0)

Lean theorems connected to this paper

Citations machine-checked in the Pith Canon. Every link opens the source theorem in the public Lean library.

IndisputableMonolith.Foundation.DimensionForcing alexander_duality_circle_linking unclear

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unclear
Relation between the paper passage and the cited Recognition theorem.

A Solanum lycopersicum plant that is resistant to Tomato brown rugose fruit virus (TBRFV), which plant comprises a QTL on chromosome 11 ... and a QTL on chromosome 12 ... wherein the QTL on chromosome 11 and the QTL on chromosome 12 confer resistance to TBRFV.
IndisputableMonolith.Cost.FunctionalEquation washburn_uniqueness_aczel unclear

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unclear
Relation between the paper passage and the cited Recognition theorem.

linked to co-segregating markers having the sequences of SEQ ID NOs: 4 and 5 ... SEQ ID NOs: 12, 13, and 14

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extends: The paper goes beyond the formal theorem; the theorem is a base layer rather than the whole result.
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contradicts: The paper's claim conflicts with a theorem or certificate in the canon.
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