Disease resistance testing

[ChrisK]

What about approaching an academic lab for a collaborative project?

[Boutique Tomatoes]

Chris, I'd been looking up the people in the University of Wisconsin programs who might be approached about something like this on the 'it never hurts to ask' theory.

Mark, if you could PM me where you got that pricing I'd be interested in looking into it. Perhaps if a few people wanted to pool samples to be tested...

[frogsleap farm]

Originally Posted by ChrisK

What about approaching an academic lab for a collaborative project?

I was thinking there may be a grant opportunity, without some funding I think it would be tough to get a university collaborator interested.

[Boutique Tomatoes]

Interesting, this just caught my attention.

http://www.todaystmj4.com/news/local....html?lc=Smart

Wisconsin Specialty Crop Block Grant Program

http://datcp.wi.gov/Farms/Crops_and_...ops/index.aspx

USDA link - Specialty Crop Block Grant Program - Farm Bill
http://www.ams.usda.gov/AMSv1.0/scbgp

Perhaps a creative grant application for the development of specialty tomato varieties intended for the small market grower?

[ChrisK]

Yep, agreed, that would be part of the discussion.

No idea what the business case or ROI for these tomatoes would be but what about one of the crowd sourcing investment programs like kickstarter?

Originally Posted by frogsleap farm

I was thinking there may be a grant opportunity, without some funding I think it would be tough to get a university collaborator interested.

[Fusion_power]

6 markers on 200 plants = $1500; double the price if same analysis on 1000 plants

The number of markers is the rub. You would need to work with at least 24 markers i.e. to sample for a round dozen traits with one marker on each side of the target gene region. This would mean quadrupling your stated price to $6000.

Since the same markers would have to be evaluated multiple times, the cost of marker evaluation would work out to about $36,000.00 to fix 12 traits.

I can see a pitfall of doing this and it must be something university work has already encountered. You would have to be able to pick out the best lines for future breeding work based on:
1. Which genes are closely positioned on the same chromosome.
2. Which plant contains more of the target genes
3. Which plant has the most target genes that are homozygous.
4. Which plant exhibits the best genetic envelope i.e. best package of non-target genes.

By selecting the best possible parents, the total cost of running the markers can be kept to a minimum. Poorly chosen parents could result in double the cost.

I should be able to write a program in Excel that would take most of the work out of the process. It would have to contain the entire tomato genome as a base and would have to be capable of estimating linkage values and determining the probability of crossovers. If we could evaluate multiple traits and then pick out the desirable variations, the total cost could be brought down significantly. In other words, it is more efficient to run markers for 12 traits than it is to run markers for a single trait looking for a single crossover event.

Thinking this through at a much higher level, this would need to be done with at least 100 total lines in order to develop a breeding population with sufficient variation. In other words, $17,000,000.00 just for running the markers in a big enough program. Lets say you needed to grow 1200 plants for each gene to be introgressed. This would infer a total of 14,400 plants that would have to be grown to select for 12 traits and by extension for 100 lines, would require 1,440,000 total plants.

This is purely speculative of course, but gives an idea of the scale a large program would entail.

DarJones

[Boutique Tomatoes]

It would be interesting to develop that Excel package and then see if it could be translated into a web application so that other breeders could play with the data as well.

I think looking for holy grail tomato lines that include all of the currently available disease tolerance/resistance genes is probably not realistic given the sheer numbers as you illustrate. But incorporating stronger disease resistance into lines targeted toward the home gardener or market growers would still be a good thing.

[frogsleap farm]

Most labs are using SNP markers and have identified a SNP that is very closely linked to the gene/allele of interest. There is no need for two markers, one in each flanking region. SNPs will also tell you whether the SNP is homozygous or heterozygous at the particular locus. One SNP should be adequate to determine accurately whether the gene/allele of interest is present in the plant for which you have supplied DNA, and if so - if it is heterozygous or homozygous. The problem as I see it is that informative SNP markers have only been identified for a handful of disease resistance traits, the large breeding companies claim to be identifying markers associated with genes/alleles associated with improved flavor - but these will be confidential. In my breeding program it would be useful to be able to identify which plants in a segregating population have resistance to Fusarium, Verticillium, LB and TSLW (possible today), but also Septoria, rin, atv, gs ....
which may or may not ever be available at a contract lab.

There was a slug of USDA $$ allocated to specialty crops research last year, so grants in that area generally are attractive - but sequestration may eat up much of that.

[ChrisK]

Plenty of software packages already out there for free.

Originally Posted by marktutt

It would be interesting to develop that Excel package and then see if it could be translated into a web application so that other breeders could play with the data as well.

I think looking for holy grail tomato lines that include all of the currently available disease tolerance/resistance genes is probably not realistic given the sheer numbers as you illustrate. But incorporating stronger disease resistance into lines targeted toward the home gardener or market growers would still be a good thing.

[Boutique Tomatoes]

Originally Posted by frogsleap farm

There was a slug of USDA $$ allocated to specialty crops research last year, so grants in that area generally are attractive - but sequestration may eat up much of that.

Well, because my curiosity is peaked I've asked an aquantance who is a grant application writer to research this and give me an idea of what it would take to submit a solid application. I'll be curious to see what she comes up with.

[DKelly]

rin is easy look for the sepals!
Grants are brutal just did one USDA...they wanted to see the matching funds...brutal but the paperwork was even more so! then a six month wait to boot.
I would like to test for resistance to tylcv are there markers for that one Mark?

[Fusion_power]

There is no need for two markers, one in each flanking region.

I disagree on this. Here is why.

In order to select for a unique gene, you must have a marker that is near that unique trait and only exists in one of the breeding lines. It does not matter what the other line has at that location, all that matters is that one line or the other is unique. Then you have to consider the other end of the gene. If you are introgressing a trait and a huge segment of a chromosome crosses over, then you are going to be stuck with whatever genetic contribution that chromosome segment includes. Therefore I reiterate that in order to introgress a gene, you MUST have 2 markers, one on each side of the gene. Otherwise linkage drag will make your breeding efforts useless.

More importantly, with some traits where crossovers are rare, you might want to use 4 or even 6 markers so you can progressively narrow down the trait.

DarJones

[Boutique Tomatoes]

Originally Posted by DKelly

rin is easy look for the sepals!
Grants are brutal just did one USDA...they wanted to see the matching funds...brutal but the paperwork was even more so! then a six month wait to boot.
I would like to test for resistance to tylcv are there markers for that one Mark?

Well, I've done a fair amount of work with various governments and large companies, so the hurry up and wait is old hat by now. (I spent last week in DC for a project and ended up flying back after accomplishing almost nothing, I kept having to remind the two project managers I was working with that we've been at this a while and sometimes this is just how it goes.) Did one grant project once upon a time, so I have an idea what kind of a paper tiger that involves as well.

The way to set this up for the matching funds issue seems simple enough, at least on the surface. Establish a business entity (possibly apply for a 501c status) to apply for the grant, fund it with the 25% needed to satisify the grant conditions then draw that back out as an administration salary/expenses making it just an accounting exercise.

I have the idea that this could be set up as an umbrella organization for multiple cooperating breeders to be able to use the grant fund resources, but haven't talked to our attorney or anyone who could tell me if I'm crazy yet.

It's something that could do some good for specialty crop development which is the purpose of the program. Plus the idea of helpng facilitate some tax money going to something I think is important is appealing, so I think I'll put in a little effort to investigate it.

[Boutique Tomatoes]

Originally Posted by Fusion_power

I disagree on this. Here is why.

In order to select for a unique gene, you must have a marker that is near that unique trait and only exists in one of the breeding lines. It does not matter what the other line has at that location, all that matters is that one line or the other is unique. Then you have to consider the other end of the gene. If you are introgressing a trait and a huge segment of a chromosome crosses over, then you are going to be stuck with whatever genetic contribution that chromosome segment includes. Therefore I reiterate that in order to introgress a gene, you MUST have 2 markers, one on each side of the gene. Otherwise linkage drag will make your breeding efforts useless.

More importantly, with some traits where crossovers are rare, you might want to use 4 or even 6 markers so you can progressively narrow down the trait.

DarJones

I will not pretend to have the level of understanding that you or Mark McCaslin have in this area, but my intuition tells me what you are describing is accurate when introgressing new genes from a a wild species.

However, in the case of genes that have already been introgressed into established breeding lines or the hybrids such as Iron Lady being used as sources of the genes, wouldn't that genetic cruft have already been dealt with?

[frogsleap farm]

Originally Posted by marktutt

Well, I've done a fair amount of work with various governments and large companies, so the hurry up and wait is old hat by now. (I spent last week in DC for a project and ended up flying back after accomplishing almost nothing, I kept having to remind the two project managers I was working with that we've been at this a while and sometimes this is just how it goes.) Did one grant project once upon a time, so I have an idea what kind of a paper tiger that involves as well.

The way to set this up for the matching funds issue seems simple enough, at least on the surface. Establish a business entity (possibly apply for a 501c status) to apply for the grant, fund it with the 25% needed to satisify the grant conditions then draw that back out as an administration salary/expenses making it just an accounting exercise.

I have the idea that this could be set up as an umbrella organization for multiple cooperating breeders to be able to use the grant fund resources, but haven't talked to our attorney or anyone who could tell me if I'm crazy yet.

It's something that could do some good for specialty crop development which is the purpose of the program. Plus the idea of helpng facilitate some tax money going to something I think is important is appealing, so I think I'll put in a little effort to investigate it.

Tomato breeding is a welcome escape from the bureaucratic complexities of my work life - you are a brave man to suggest this Mark.