Winter Reading

[Hermitian]

Originally Posted by ChrisK

A masters thesis on the genetics of grafting success.

Thanks for the pointer.

The only tie between genetics and this study are the 4 strains of tomato used (p.36). Otherwise, the paper goes no deeper. In my years of reviewing, I would rank the work as acceptable for MA Horticulture or BS Horticulture.

I did not check all the references. But because of my interest in rootstocks for perennial fruits, I am disappointed that there are a number of citations listed on p.83 that are not found in the references, and the reverse is true - the latter is permitted by several standards.

[aclum]

Hi Chris,

Thanks for posting the link to the paper on grafting. I just skimmed the abstract and it looks VERY interesting - particularly the part about the genetic basis for grafting failures and the use of adhesives. Can't wait to read the whole thing!

Anne

[ChrisK]

The cyanoacrylate (superglue) part is what jumped out at me but I confess I haven't read it (yet) so don't know the overall quality. I do know that my 1 attempt at grafting with superglue worked perfectly.

Originally Posted by aclum

Hi Chris,

Thanks for posting the link to the paper on grafting. I just skimmed the abstract and it looks VERY interesting - particularly the part about the genetic basis for grafting failures and the use of adhesives. Can't wait to read the whole thing!

Anne

[ChrisK]

Chapter 4 (starts pg 81) is the QTL analysis of graft success. Very low resolution.

Originally Posted by Hermitian

Thanks for the pointer.

The only tie between genetics and this study are the 4 strains of tomato used (p.36). Otherwise, the paper goes no deeper. In my years of reviewing, I would rank the work as acceptable for MA Horticulture or BS Horticulture.

I did not check all the references. But because of my interest in rootstocks for perennial fruits, I am disappointed that there are a number of citations listed on p.83 that are not found in the references, and the reverse is true - the latter is permitted by several standards.

[aclum]

Hi Chris,

Besides the superglue thing, another thing that popped out at me as I scanned the first parts of the thesis, was how the rootstock could affect the fruit quality and flavor - things like Brix, lycopene, and vitamin C content, etc. I had been under the impression that rootstock didn't affect the fruit quality in that way.

Most of the article was too technical for me and I haven't read (or scanned) most of it, but I'll keep plugging away. Lots of little "aha" moments popping out here and there as well as basic stuff like healing environment info, etc.

Anyway..... very interesting - even for someone like myself who is pretty clueless on the genetics part of it all.

Anne

[Hermitian]

Originally Posted by aclum

Hi Chris,
Besides the superglue thing ...

At (mostly independent) nurseries where tools and supplies are sold for grafting hardwoods, you will find some of the usual suspects such as knives and grafting tape - but you may also find beeswax. As long as you don't interfere with the cambian layer, placing beeswax around the graft and then enclosing with grafting tape is a good choice for slow or stubborn plants (e.g., Diospyros), and for plants that ooze a lot (e.g., Ficus).

[aclum]

Chris (or anyone else who knows the answer),

Starting on page 21 of the thesis (or page 32 of the PDF), the author discusses the 3 different alleles resistant to TMV. She mentions Tm-1, Tm-2, and Tm-2a.

As I briefly mentioned in the Fusarium Wilt J3 thread, I was confused by the TMV codes used for RST-04-105-T and RST-04-106-T rootstocks from DP Seeds where they use the codes Tm/+, Tm2a, Tm2/+ as shown in the following link:

http://www.dpseeds.com/rootstock

Can you "translate" the DP codes into the codes used in the thesis for me? I guess, basically, I want to know what the "/+" indicates.

Thanks,
Anne

[ChrisK]

The "+" designates the wildtype or "normal" allele. So in the case of TM2/+ the line is heterozygous for the TMV resistance gene. It has the dominant resistance allele on one chromosome and the wildtype allele on the other chromosome.

I would assume that a genotype listed as TM2a is homozygous for the resistance allele and is just not written TM2a/TM2a.

You can read about gene naming conventions in tomato here in sections 3 & 4: http://tgc.ifas.ufl.edu/genelist.htm

Very similar to the fruit fly naming convention, from what I remember.

Hope that helped!

Originally Posted by aclum

Chris (or anyone else who knows the answer),

Starting on page 21 of the thesis (or page 32 of the PDF), the author discusses the 3 different alleles resistant to TMV. She mentions Tm-1, Tm-2, and Tm-2a.

As I briefly mentioned in the Fusarium Wilt J3 thread, I was confused by the TMV codes used for RST-04-105-T and RST-04-106-T rootstocks from DP Seeds where they use the codes Tm/+, Tm2a, Tm2/+ as shown in the following link:

http://www.dpseeds.com/rootstock

Can you "translate" the DP codes into the codes used in the thesis for me? I guess, basically, I want to know what the "/+" indicates.

Thanks,
Anne

[aclum]

Hi Chris,

Yes - that helps a lot ! And thanks for the link - should be quite helpful.

Anne

[Hermitian]

Originally Posted by ChrisK

... It has the dominant resistance allele on one chromosome and the wildtype allele on the other chromosome. ...

Chris, is this determined statistically from macroscopic observation of a population, or by sequencing?

And as a follow-up, how easy or "routine" is it nowadays for a genetic biologist to obtain a sequence for one or more samples of tomato or other annual fruit crop?

[ChrisK]

Could be either but since the gene is known and has been cloned a direct sequencing or PCR based test could be easily designed.

Obtaining a sequence is trivially easy and can be done in high throughput in microtiter plates with tiny pieces of tissue (a few mg). The samples are processed by robotic instruments. This kind of analysis has been reduced to push button science. Push the button and come back in the morning for your data. Assuming the robot doesn't break down that is!

Originally Posted by Hermitian

Chris, is this determined statistically from macroscopic observation of a population, or by sequencing?

And as a follow-up, how easy or "routine" is it nowadays for a genetic biologist to obtain a sequence for one or more samples of tomato or other annual fruit crop?

[ChrisK]

Advanced genetic tools for plant biotechnology

[Hermitian]

Originally Posted by ChrisK

Advanced genetic tools for plant biotechnology

Thank you, very interesting.

A friend of mine holds several patents on GMO algae. In a suitable medium they will break down specific types of plastics into liquid compounds that can be separated and reconstituted into plastics. Some municipalities have stopped sorting recyclables by hand: they just dump it all in the tank.

[ChrisK]

http://www.nature.com/ng/journal/vao...l/ng.2877.html

[Hermitian]

Originally Posted by ChrisK

http://www.nature.com/ng/journal/vao...l/ng.2877.html

Thanks, another genomics milestone.

The authors mention "The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species." An interesting omission is that over 80% of the world's hot pepper crop is grown for pesticide extract used in boat paint, cable casings, etc. and in this commercial activity proprietary strains of peruvian lineage are typical. The production farms are mostly in Bangladesh, Burma, and south China.