Open Source Plant Breeding Forum

General Category => Plant Breeding => Tomatoes => Topic started by: reed on 2020-02-10, 06:15:12 AM

Title: New tomato disease
Post by: reed 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.
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
Title: Re: New tomato disease
Post by: William S. on 2020-02-10, 06:58:05 AM

Was wondering about resistance. Only found the words "no commercial variety" in regards to resistance and this creepy Google patent.
Title: Re: New tomato disease
Post by: bill 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:
Title: Re: New tomato disease
Post by: William S. 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.
Title: Re: New tomato disease
Post by: bill 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.
Title: Re: New tomato disease
Post by: bill on 2020-02-10, 10:02:24 PM
Never mind:

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.
Title: Re: New tomato disease
Post by: Nicollas on 2020-02-11, 12:20:40 AM
What a wise and smart move is the promiscous tomato project initiated by Joseph ...
Title: Re: New tomato disease
Post by: Andrew Barney 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".
Title: Re: New tomato disease
Post by: William S. 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.