Single Flower Truss

[Fred Hempel]

Has anyone here worked with Single Flower Truss lines?

[maf]

I remember discussing this gene online some time ago, probably not on this board. It is my understanding that it has been patented. I know the patent was applied for some years ago, but now it may have been granted?
United States Patent 8,865,970

The invention claimed is:

1. A method for producing an angiosperm hybrid plant showing at least one yield-related heterotic phenotype, comprising: a. providing a mutant parent inbred angiosperm plant comprising a single mutation in a SINGLE FLOWER TRUSS (SFT) gene, wherein the mutation is such that it reduces SFT gene function when homozygous; b. providing a parent inbred angiosperm plant, homozygous for wild-type alleles of the SFT gene, the wild-type gene encoding a protein having the amino acid sequence set forth in SEQ ID NO:1; and c. crossing the mutant parent inbred angiosperm plant with the parent inbred angiosperm plant, homozygous for wild-type alleles of said SFT gene; thereby producing a heterozygous hybrid angiosperm plant comprising said wild-type SET allele and a mutated sft allele, wherein the heterozygous hybrid angiosperm plant shows at least one yield-related heterotic phenotype that is superior compared to a homozygous angiosperm plant having two wild-type alleles of said SFT gene.

[Fred Hempel]

It is not clear to me whether that is a provisional patent number, or a final number. In the link there is no date of issuing.

What is really unclear to me is how you can patent a loss of function mutation, when you did not discover the mutation. This article, published well before the patent filing date, makes no mention of any of the 3 patent authors.

I really hope this patent application was rejected.

The sft mutant is available from the Tomato Genetics Resource Center at UC Davis.

The mutant is listed as a spontaneous mutant.

[Fred Hempel]

There is a publication on sft from 1982.

Kerr EA (1982) Single flower truss "sft" appears to be on chromosome 3. Rep Tomato Genet Coop 32:31

How can you have a patent on a loss-of-function mutation, and even if you can, how can you patent a mutation that someone else "discovered"?

[ChrisK]

It is granted (2014) and the first 10 claims (and others) were cancelled. The patent is about using the specific alleles with a particular sequence in the heterozygous state, which was the novel observation described in your linked Nature paper.

Claims:

1.-10. (canceled)

2. 11. A mutant parent inbred plant homozygous for the mutant sft gene comprising the nucleic acid sequence set forth in SEQ ID NO:4, conferring at least one heterosis-related phenotype to a hybrid offspring.
3. 12. An isolated polynucleotide encoding a mutant sft protein having an amino acid sequence as set forth in SEQ ID NO:3.
4. 13. The isolated polynucleotide of claim 12, having the nucleic acid sequence set forth in SEQ ID NO:4.
5. 14. A method for producing a hybrid plant showing at least one heterosis-related phenotype, comprising:a. providing a mutant parent inbred plant comprising a single mutation in a SINGLE FLOWER TRUSS (SFT) gene;b. providing a non-mutant parent inbred plant, homozygous for wild type copies of the gene; and c. crossing the mutant parent inbred line with the non-mutant parent line;thereby producing heterozygous hybrid plant showing at least one heterosis-related phenotype that is superior compared to the phenotypic performance of at least one of the parent plants.
6. 15. The method of claim 14, wherein the heterozygous hybrid plant shows at least one heterosis-related phenotype that is superior compared to the phenotypic performance of the best parent plant.
7. 16. The method of claim 14, wherein the at least one heterosis-related phenotype is yield-related.
8. 17. The method of claim 14, wherein the hybrid plant shows at least one heterosis-related phenotype compared to the non-mutant parent plant.
9. 18. The method of claim 14, wherein the non-mutant parent plant is isogenic to the mutant parent plant.
10. 19. The method of claim 14, wherein the gene is tomato SINGLE FLOWER TRUSS (SFT) gene or an ortholog thereof.
11. 20. The method of claim 14, wherein the hybrid plant comprises a structurally intact and functional wild-type SFT gene copy and a mutated sft copy, wherein the mutation in the sft copy is such that it reduces SFT gene function when homozygous, and wherein said hybrid plant shows at least one yield-related heterotic phenotype compared to a homozygous plant having two functional wild-type copies of the SFT gene.
12. 21. The method of claim 20, wherein the wild type SFT gene encodes a protein having the amino acid sequence set forth in SEQ ID NO:1.
13. 22. The method of claim 21, wherein the wild type SFT gene comprises a nucleic acid sequence as set forth in SEQ ID NO:2.
14. 23. The method of claim 20, wherein the mutated sft gene encodes a protein having the amino acid sequence set forth in any one of SEQ ID NO:3, SEQ ID NO:5 and SEQ ID NO:7.
15. 24. The method of claim 23, wherein the mutated sft gene comprises a nucleic acid sequence as set forth in any one of SEQ ID NO:4, SEQ ID NO:6 and SEQ ID NO:8.
16. 25.-28. (canceled)
17. 29. The method of claim 20, wherein the plant is a tomato (Solanum lycopersicum) plant.
18. 30. A hybrid plant produced according to the method of claim 14.
19. 31. A hybrid plant comprising a structurally intact and functional wild-type SFT gene copy and a mutated sft copy, wherein the mutation in the sft copy is such that it reduces SFT gene function when homozygous, and wherein said hybrid plant shows at least one yield-related heterotic phenotype compared to a homozygous plant having two functional wild-type copies of the SFT gene.
20. 32. The hybrid plant of claim 31, said plant comprising a wild type SFT gene having the nucleic acid sequence set forth in SEQ ID NO:2 and a mutant sft gene having a nucleic acid sequence selected from the group consisting of SEQ ID NO:4, SEQ ID NO:6 and SEQ ID NO:8.
21. 33. The hybrid plant of claim 32, wherein the mutant sft gene comprises a nucleic acid sequence as set forth in SEQ ID NO:4.

[ChrisK]

Here is the full Nature Genetics paper in case anyone is interested. Think it's been posted in other threads, too.

http://pba.ucdavis.edu/files/165467.pdf

[maf]

Originally Posted by Fred Hempel

How can you have a patent on a loss-of-function mutation, and even if you can, how can you patent a mutation that someone else "discovered"?

Yes, sorry, I did not mean to suggest the gene itself was patented, just its useful function which is the increase in yield in the heterozygous state, as Chris referred to above.

It should be noted that the heterosis effect is only observed in a determinate (sp) background.

[Cole_Robbie]

My background is law, not science, but on the subject of patents, the entire system is full of gray areas. Patent law is the highest-paid legal specialty. Attorneys call patent litigation 'the sport of kings.'

There are a lot of patents granted because high-priced attorneys push them through. At the same time, there are also a lot of patents granted that are so shaky, those same high-priced attorneys could get them declared irrelevant to their own clients. Whoever has the most money wins; even if they're wrong, they win by outspending the other side.

[Fred Hempel]

In looking at the plants, it makes sense now that the heterosis is only evident in determinates. Essentially, it by making the plant more vegetative, it makes a determinate plant grow a bit bigger, instead of stopping.

Of course no tomato cultivar is truly determinate, but that is another point for another day.

Another point for another day is how will they enforce this patent. Mutants are clearly available. The patent, to me, seems like a big waste of time. And pretty unenforceable.

Originally Posted by maf

Yes, sorry, I did not mean to suggest the gene itself was patented, just its useful function which is the increase in yield in the heterozygous state, as Chris referred to above.

It should be noted that the heterosis effect is only observed in a determinate (sp) background.

[Fusion_power]

Fred, it is not just vegetative habit that is changed. Flower set is increased. If you want more details, Kctomato has a few lines with this gene and has made several crosses.

I found a different but much more useful set of genes that sorted out in the Big Beef X Eva Purple Ball cross. It results in 50% higher production on compact indeterminate plants. If you want a few seed to trial, send me an address and I'll put them in the mail. I've described the results of using this line a few times. Short story is that I picked 80 pounds of tomatoes from each F1 plant in my garden. The effect holds in most crosses I've made over the last 5 years. I'm growing out Aunt Ruby's German Green X (BB X EPB) this year in an attempt to stabilize a green when ripe with the enhanced fruiting genes.

[Fred Hempel]

That makes sense. I too have been more and more aware of combinations of parents that give high yield -- and many of them seem to be combinations of over-vegetative lines with over-flowering lines. That balance between vegetative vigor and flower production/fruit set is critical.

I think this is an area where hybrids are very promising, compared to OP lines -- because you can balance "flower production" mutations like multiflora with a second parent. Multiflora is useful for producing flowers, but it also leads to the early cessation of vegetative growth. So reducing it's effect is sometimes desired.

Originally Posted by Fusion_power

Fred, it is not just vegetative habit that is changed. Flower set is increased. If you want more details, Kctomato has a few lines with this gene and has made several crosses.

I found a different but much more useful set of genes that sorted out in the Big Beef X Eva Purple Ball cross. It results in 50% higher production on compact indeterminate plants. If you want a few seed to trial, send me an address and I'll put them in the mail. I've described the results of using this line a few times. Short story is that I picked 80 pounds of tomatoes from each F1 plant in my garden. The effect holds in most crosses I've made over the last 5 years. I'm growing out Aunt Ruby's German Green X (BB X EPB) this year in an attempt to stabilize a green when ripe with the enhanced fruiting genes.

[Fred Hempel]

And I hope KC Tomato is on the lookout for Isreali patent-enforcement crews.

[jmsieglaff]

Originally Posted by Fusion_power

I found a different but much more useful set of genes that sorted out in the Big Beef X Eva Purple Ball cross. It results in 50% higher production on compact indeterminate plants. If you want a few seed to trial, send me an address and I'll put them in the mail. I've described the results of using this line a few times. Short story is that I picked 80 pounds of tomatoes from each F1 plant in my garden. The effect holds in most crosses I've made over the last 5 years. I'm growing out Aunt Ruby's German Green X (BB X EPB) this year in an attempt to stabilize a green when ripe with the enhanced fruiting genes.

80 lbs, impressive! Is the BB x EPB a stable line you cross withe various other tomatoes? When you say that the production increase holds into the majority of subsequent crosses (e.g. Tomato Y x (BB x EPB)), does that hold true when growing many generations and stabilizing those new lines?

I really need a huge place to grow tomatoes. Crossing tomatoes sounds like a lot of fun, but also needs a lot of room for a lot of plants! Then what to do with all those tomatoes is another matter.

[Fusion_power]

The production increase in the F1 with most of the crosses gave similar results. I made one cross that did not show an increase. It was similar to the BBxEPB parent which is highly productive, but not to the tune of 80 pounds per plant. I'm working on 3 different lines segregating and selecting for increased production. One is a bicolor, one is green when ripe, and one is red fasciated. I also have the Aunt Ruby's German Green cross to grow F1 plants this year. Green when ripe is tough to work with. I have to grow 16 plants to get just one that segregates back to the green color.

[maf]

Originally Posted by Fred Hempel

In looking at the plants, it makes sense now that the heterosis is only evident in determinates. Essentially, it by making the plant more vegetative, it makes a determinate plant grow a bit bigger, instead of stopping.

Yes, there is an interaction of some kind between the two mutations that increases tomato production beyond what you would expect.

I think this is an area where hybrids are very promising, compared to OP lines -- because you can balance "flower production" mutations like multiflora with a second parent. Multiflora is useful for producing flowers, but it also leads to the early cessation of vegetative growth. So reducing it's effect is sometimes desired.

Yes, I am on record as not appreciating the multiflora trait in the homozygous condition, but as a parent for F1's with the heterozygous trait I can absolutely see the value.