Tomato plants resistant to ToBRFV, TMV, ToMV and ToMMV and corresponding resistance genes
Pith reviewed 2026-06-03 23:32 UTC · model grok-4.3
The pith
A TM-2-2 protein variant carrying Y/F/W at position 767 plus one of three specific substitution patterns at sites 822/825/848 confers tomato resistance to ToBRFV.
A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.
Core claim
A TM-2-2 protein variant that confers resistance against at least ToBRFV infection in tomatoes contains a tyrosine (Y), phenylalanine (F) or tryptophan (W) at the position corresponding to tyrosine 767 together with one of three substitution patterns at residues 822, 825 and 848.
What carries the argument
TM-2-2 protein variant defined by the residue-767 aromatic substitution plus one of the three listed substitution triplets at 822/825/848.
Load-bearing premise
The listed amino-acid combinations are sufficient to produce functional virus resistance when the variant protein is expressed in tomato plants.
What would settle it
Infection assays on tomato plants engineered to carry only the described TM-2-2 variant alleles showing no reduction in ToBRFV symptom severity or viral titer compared with susceptible controls.
read the original abstract
1 . A TM-2-2 protein variant, which confers resistance against at least ToBRFV infection in tomatoes, and wherein said TM-2-2 protein variant comprises a tyrosine (Y), a phenylalanine (F) or a tryptophan (W) at the position corresponding to tyrosine 767 of SEQ ID No:8, and one of the following substitutions: a) an arginine (R) at the position corresponding to cysteine 848 of the TM-2-2 protein (SEQ ID No:8), an asparagine or a serine at the position corresponding to asparagine 822 of the TM-2-2 protein (SEQ ID No:8) and a serine at the position corresponding to serine 825 of the TM-2-2 protein (SEQ ID No:8); b) a cysteine (C), a phenylalanine (F), a methionine (M), a tyrosine (Y) or a tryptophan (W) at the position corresponding to asparagine 822 of the TM-2-2 protein (SEQ ID No:8), a cysteine at the position corresponding to cysteine 848 of the TM-2-2 protein (SEQ ID No:8) and a serine at the position corresponding to serine 825 of the TM-2-2 protein (SEQ ID No:8), and c) a histidine (H), a lysine (K) or a threonine (T) at the position corresponding to serine 825 of the TM-2-2 protein (SEQ ID No:8), a cysteine at the position corresponding to cysteine 848 of the TM-2-2 protein (SEQ ID No:8) and an asparagine at the position corresponding to asparagine 822 of the TM-2-2 protein (SEQ ID No:8).
Editorial analysis
A structured set of objections, weighed in public.
Referee Report
Summary. The manuscript (US patent 12642203) claims a TM-2-2 protein variant that confers resistance to at least ToBRFV (and listed tobamoviruses) in tomato. The variant is defined by the presence of Y/F/W at the position corresponding to Tyr767 of SEQ ID No:8 together with one of three enumerated substitution patterns at positions 822/825/848 (Claim 1 / abstract). The remainder of the document enumerates additional claims for nucleic acids, plants, breeding methods and further virus combinations that rest on the same sequence definition.
Significance. A validated set of minimal sequence changes that convert TM-2-2 into a functional ToBRFV-resistance allele would be of direct utility for tomato breeding. No such validation data, however, appear in the document.
major comments (1)
- [Claim 1 / abstract] Abstract / Claim 1: the central assertion that the three listed substitution patterns (plus Y/F/W at 767) are sufficient to confer ToBRFV resistance is stated without any supporting infection assay, transgenic complementation result, or functional readout. No table, figure or methods section supplies phenotypic data for any of the enumerated sequence variants.
Simulated Author's Rebuttal
We thank the referee for the review. The document is a granted US patent (US12642203) whose claims define a TM-2-2 variant by specific amino-acid substitutions. Patent documents are legal instruments whose sufficiency is judged under 35 USC 112 enablement rather than by the evidentiary standards of a research article. Below we address the single major comment.
read point-by-point responses
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Referee: [Claim 1 / abstract] Abstract / Claim 1: the central assertion that the three listed substitution patterns (plus Y/F/W at 767) are sufficient to confer ToBRFV resistance is stated without any supporting infection assay, transgenic complementation result, or functional readout. No table, figure or methods section supplies phenotypic data for any of the enumerated sequence variants.
Authors: We agree that the patent text contains no infection assays, transgenic data or phenotypic tables. US patent practice permits claims to be supported by a written description that enables a person skilled in the art to make and use the invention without undue experimentation; the application supplies the exact residue positions and substitution patterns together with the reference TM-2-2 sequence (SEQ ID No:8). Whether this description meets the legal enablement standard is a matter for patent examination, not for the scientific peer-review criteria applied to journal manuscripts. revision: no
- Absence of any wet-lab validation data for the claimed sequence variants; such data cannot be added to the already-granted patent without a new filing.
Circularity Check
No derivation chain or quantitative predictions; patent consists solely of sequence claims
full rationale
The document is a patent whose central content is an enumerated list of amino-acid substitutions in a TM-2-2 variant (Claim 1 / abstract). No equations, fitted parameters, first-principles derivations, or predictions appear anywhere in the text. Consequently none of the six enumerated circularity patterns can be instantiated; the functional-resistance assertion is an unsupported assertion rather than a derived result that reduces to its own inputs.
discussion (0)
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