Author Topic: New tomato disease  (Read 1520 times)

reed

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New tomato disease
« on: 2020-02-10, 06:15:12 AM »
Has anyone else heard of this new threat to tomatoes? I had not until I got my 2020 catalogue from Seeds from Italy. Their blog says this about it.
Quote
A bit of background on the problem: The disease called Tomato Brown Rugose Fruit Virus (ToBRFV) was first found in tomatoes in Jordan in 2015. It has since been found in California, Mexico, Germany, Italy, Spain, Netherlands, United Kingdom, China, Saudi Arabia, and Greece. The virus is harmless to humans and animals. It affects only tomatoes and peppers, and it causes fruits to get brown wrinkled spots that make the crop unmarketable. ToBRFV is very contagious and can be transmitted on workers’ hands, clothing, tools, and so on. There are no resistant varieties.
You can read the whole thing here https://www.growitalian.com/blog/import-restrictions-on-tomato-pepper-seed/

William S.

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Re: New tomato disease
« Reply #1 on: 2020-02-10, 06:58:05 AM »
https://patents.google.com/patent/EP3409106A1/en

Was wondering about resistance. Only found the words "no commercial variety" in regards to resistance and this creepy Google patent.
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bill

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Re: New tomato disease
« Reply #2 on: 2020-02-10, 05:48:29 PM »
It is a Tobamovirus, which is generally a pretty nasty group of viruses.  The most famous one is Tobacco Mosaic Virus.  They spread easily by contact.  These are among the most stable viruses and can survive on surfaces and in debris for years at moderate temperatures.  Decontamination is challenging.  The viruses also often infect the seed coat, sometimes penetrating sufficiently to prevent easy sterilization.  Even seeds treated with bleach or TSP can sometimes transmit the virus at a low rate.  Dry baking seeds at 170 degrees F for 72 hours is often sufficient though.

Here is some general info about controlling Tobamoviruses:
https://www.intechopen.com/online-first/aspects-in-tobamovirus-management-in-intensive-agriculture
« Last Edit: 2020-02-10, 06:08:24 PM by bill »

William S.

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Re: New tomato disease
« Reply #3 on: 2020-02-10, 08:36:23 PM »
It sounds like we should be cautious before importing seeds or fruit from impacted areas.

I would really like to know where we can find resistance genes for sure. Some of us have so much tomato diversity in our gardens we are liable to have some already, but its hard to know, there is far more germplasm than we can ever work with individually. I worked with nine species or hybrids thereof last year and got seed back for eight. There are at least four more species and lots of accessions out there. Somewhere in that incredible diversity there hopefully is good resistance.

Those of us in the US will hopefully have a while before we get hit. Sounds like it might be pretty widespread already in Europe and Asia.
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bill

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Re: New tomato disease
« Reply #4 on: 2020-02-10, 09:56:44 PM »
The tm-1 gene from S. habrochaites provides resistance to several Tobamoviruses, but I couldn't find any information about ToBRFV, probably because it is new and little studied.

bill

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Re: New tomato disease
« Reply #5 on: 2020-02-10, 10:02:24 PM »
Never mind:

Quote
The genus Tobamovirus currently includes 37 species, one  of  which  includes  the  type  member  research  model  tobacco  mosaic  virus  (TMV)  [10].  Most  tobamoviruses  are considered to be severe pathogens, e.g., tomato mosaic virus (ToMV) and tomato mottle mosaic virus (ToMMV) with worldwide distribution (Mexico, United States, China, Brazil, Jordan and Iran) [11–18], pepper mild mottle virus (PMMoV) in plants belonging to the family Solanaceae, and cucumber green mottle mosaic virus (CGMMV), which is found mostly in plants belonging to the family Cucurbita-ceae (cucurbits). Tobamoviruses are known to cause up to 30%, 20%, and 15% yield losses in pepper, tobacco, and cucumber, respectively [10, 19–21]. Since the 1960s, tomato yield  losses  attributed  to  tobamoviruses  have  decreased  dramatically due to the discovery and deployment of three genes: Tm-1, Tm-2, and Tm-22, which control resistance to TMV and ToMV infection [20, 22].

The single-stranded (ss) RNA genome of tobamoviruses encodes the small and large subunits of the viral replicase (Rep), which includes RNA-dependent RNA polymerase (RdRP) and helicase domains, as well as a coat protein (CP) and a movement protein (MP) [23]. The Tm-1 gene sup-presses infection via interactions with the helicase domain of the viral Rep [24, 25], whereas Tm-2 control is effected via an interaction with the viral MP [26]. Studies of mutations causing resistance breaking in viruses have demonstrated that this phenotype is mediated by a few mutations in a sin-gle viral gene (CP, MP, or Rep) [27, 28]. This applies to ToMV strains that can circumvent the resistance controlled by the Tm-2 and Tm-22 alleles via two point mutations in their MP [26, 29, 30]. In contrast, genomic sequencing of emerging resistance breakers has demonstrated that they can differ by 9–15% from known viruses (e.g., comparing ToMMV to TMV and ToMV). These differences may result from the innate mutability of the tobamovirus RNA genome [3].  Thus,  the  identification  of  possibly  rare  resistance-breaking mutations is hindered by a significant background of changes in their genomic sequences.

Recently,  a  new  tobamovirus  that  can  break  the  Tm-2/Tm-22 (and Tm-1) resistance of tomato was detected in Israel [31]. Genome sequence analysis and comparison to other sequences in the GenBank database showed this virus to be an Israeli isolate of tomato brown rugose fruit virus (ToBRFV-IL) with 99% genomic sequence identity (99% coverage) to a new tobamovirus ToBRFV that was reported in 2016 in Jordan [16]. Considering that previous studies have demonstrated that a few nonsynonymous substitution mutations can result in resistance breaking [26, 29, 30], we hypothesized that the resistance phenotype of this new virus is primarily a result of a few mutations. To facilitate identification  of  these  mutation  “needles”  in  a  genomic  “haystack”, and to understand the evolutionary path lead-ing to the emergence of this new resistance-breaking virus, we performed a comprehensive genomic comparison and phylogenetic analysis of different tobamoviruses. Empow-ered by the large number of sequences from members of different species, the relationships between their hosts, and the number of variants per species used in this study, these approaches were found to be suitable for identifying resist-ance-breaking mutations. Our phylogenetic analysis local-ized all three ToBRFV genes between ToMV and RheMV/TMV host-shifting clades, and this, together with a relatively low mutation rate, suggests that a host shift contributed to the emergence of this new virus. Our comparative genomic analysis identified 12 potential resistance-breaking muta-tions in the MP gene, the primary target of Tm-2 resistance, and nine more in the Rep. Finally, molecular modeling of the helicase further confirmed the potential functional role of one of these mutations and enabled the identification of three more potential resistance-breaking mutations.

https://link.springer.com/article/10.1007/s00705-018-3819-5

Nicollas

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Re: New tomato disease
« Reply #6 on: 2020-02-11, 12:20:40 AM »
What a wise and smart move is the promiscous tomato project initiated by Joseph ...
« Last Edit: 2020-02-11, 08:08:43 AM by Nicollas »

Andrew Barney

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Re: New tomato disease
« Reply #7 on: 2020-02-11, 06:06:46 AM »
What a wise and smart move is the promiscous tomato project initiated from Joseph ...

True that!

It is interesting how one project to increase genetic diversity for one form of biotic / abiotic factors will automatically increase it for others. I have high faith that the wild tomato genomes have what we need.

But I think Joseph is on to something specific: it might be better to create domestic-like tomatoes from the wild species rather than trying to create domestic tomatoes with wild genes using introgression lines, etc.

The wild genomes have what is termed "genetic drag", but it is sometimes this "genetic drag" exactly what we need/want. Maybe not all of it, but as much as possible without tasting odd, poisonous, or have other negative traits. Whenever possible I think it is best to preserve these wild genomes as intact as possible while introducing cultivated domestic genes like large tasty fruit.

It may require adjusting some expectations about what a tomato is or should be. Maybe we shouldn't be breeding for "tomatoes", maybe we should be breeding for Tomatoes 2.0 or the "post-tomato".
« Last Edit: 2020-02-11, 06:08:37 AM by Andrew Barney »

William S.

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Re: New tomato disease
« Reply #8 on: 2020-02-11, 07:02:59 AM »
What a wise and smart move is the promiscous tomato project initiated from Joseph ...

The possibility of resistance in the promiscuous population is greater but not guaranteed and more work may be required occasionally to introduce a needed resistance.

As Andrew says the wild tomato genomes probably have what we need, but have we yet incorporated the right populations into the promiscous project? Maybe not, we are by the necessity of a garden to small farm scale working with a small subset of available wild populations in the form of wild tomato accessions. It would help in a case like this if we had some publication that identified a few promising accessions from a researcher with some funding. 

« Last Edit: 2020-02-11, 04:05:02 PM by William S. »
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William S.

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Re: New tomato disease Brown Rugose Fruit Virus (ToBRFV)
« Reply #9 on: 2022-01-11, 06:10:38 AM »
https://link.springer.com/article/10.1007/s41348-021-00535-x?fbclid=IwAR3hD1ln84sVLhKA8lY4nNhjb_yeMkRJg9xKdxQXT99ppRrBHkKTxHXkDqE

https://link.springer.com/content/pdf/10.1007/s41348-021-00535-x.pdf

New article about (ToBRFV) The Brown Rugose Fruit Virus listing some resistance that has been found.

In Solanum pimpinillifolium a long list of accessions they said 26 but I counted 19.

In Solanum habrochaites two accessions.

In Solanum chilense accession LA1932 which is already a notable accession for its ability to be crossed with domestic tomato. It is also an accession which I personally have not been able to get to set seed yet. Perhaps I should try growing it entirely indoors and in the greenhouse. 

In Solanum ochranthum which is very difficult to utilize except perhaps by somatic hybridization. Though this was the most interesting resistance they found because the plant in two cases seemed to have the ability to recover from the virus.

It seems that all domestic plants are susceptible?! Which doesn't bode well should the virus spread.

I went a little round looking for updates about this virus and the wikipedia article led me to this company which already is breeding for resistance.

https://www.enzazaden.com/news-and-events/news/2021/update-on-hr-tobrfv-tomato

Still doesn't bode well for heirloom tomatoes should the virus become widespread and common place. A similar effort to what Carol Deppe proposed for Late Blight could be necessary. Take either resistant strains of say Solanum pimpinillifolium or maybe resistant hybrids such as those being produced by the company above and cross those with heirlooms to spread the resistance into heirloom type fruits.
« Last Edit: 2022-01-11, 07:50:36 AM by William S. »
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Tim DH

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Re: New tomato disease
« Reply #10 on: 2022-01-11, 07:33:14 AM »
Another thing to worry about!  ...  Oh Joy!!

There was a British breeder whose mission statement included these words:

''Breeding objectives were focused on the amateur market, where there is a real need for modern, high quality open pollinated varieties.''

All six of their varieties are listed as ''ToBRFV free'', which, to my mind suggests that seed transmission is a problem!

https://www.gourmetgenetics.com/tomato/tomatoes.html

Tim DH


William S.

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Re: New tomato disease
« Reply #11 on: 2022-01-11, 07:54:06 AM »
Yeah, I am not sure even how concerned to be. Is this a disease that will rapidly be in all of our gardens or is it a disease that may never spread to most of us?

Sounds like it is transmitted via seed.

Here is a link where we can track its spread:

https://gd.eppo.int/taxon/TOBRFV/distribution?fbclid=IwAR25vRzS57fJmFsUjlwOqBFD0IGxJYtLMJwSDmv5nyOa50MyUH8wxmW8Vu8
« Last Edit: 2022-01-11, 11:34:41 AM by William S. »
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Garrett Schantz

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Re: New tomato disease
« Reply #12 on: 2022-01-11, 04:16:41 PM »
Attempting to breed for resistances would require us to have the virus to infect plants with.

Markers could help as well if we knew what genes were resistant.

I have heard of tobamovirus problems concerning tobacco and potatoes.

Fruit, leaves, seed - even touching leaves can trasmitt these viruses into a sterile room very easily.

Taking cuttings from very new growth might remove the virus, but it would probably return if it enters an area.

William S.

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Re: New tomato disease
« Reply #13 on: 2022-01-11, 05:13:54 PM »
It may be eventually the case that the virus comes to us, but until then I am very happy it isn't here yet. I think it would be a good idea to wait for markers. Let university facilities deal with disease containment systems if needed. It looks like it maybe isn't spreading too fast and there will be resistant hybrids offered fairly soon. Then we can desegregate those hybrids to make our own open pollinated resistant tomatoes. Sort of crazy to think that we are often only one tomato pandemic away from not being able to grow tomatoes or what have you - basically insert the name of any crop in lieu of tomato.
« Last Edit: 2022-01-11, 05:25:38 PM by William S. »
Western Montana garden, glacial lake Missoula sediment lacustrian parent material and shallow 7" silty clay loam mollisoil topsoil sometimes with added sand in places. Zone 6A with 100 to 130 frost free days