Winter Reading

[ChrisK]

Not really tomato specific but might be of interest to some. I wonder if anyone is putting significant effort into genome wide association mapping/studies and genomic selection in tomato. Still the domain of the "big guys" since it takes significant capital investment.

Can genomics boost productivity of orphan crops?

[Fusion_power]

A better question to ask would be: Which university currently has full genome mapping capabilities?

To my knowledge, the only access currently is by sending off samples to an external lab.

DarJones

[ChrisK]

Several do and it's getting cheaper every year. Genotyping By Sequencing is an inexpensive method of finding several hundred thousand SNPs. It would be interesting to know if any of the big University breeding programs are thinking about this.

http://www.maizegenetics.net/gbs-overview

Originally Posted by Fusion_power

A better question to ask would be: Which university currently has full genome mapping capabilities?

To my knowledge, the only access currently is by sending off samples to an external lab.

DarJones

What is the complexity of mapping a tomato genome compared to mapping a primate genome?

Ted

[Fusion_power]

Current cost to map a human genome is a bit over $1000. When it gets below $100, most people at some point in life will have theirs done.

Mapping a tomato genome is comparable in many ways but also very different. There are a few cheaper ways to manipulate plant cells than there are for human cells. Some tests can now be done to map the genome of a tomato plant for about $35 each. Note that there are problems with this method, it is not as detailed as is really needed.

I need to dig into this deeper, it has been about 5 years since I looked at it last. The technology has changed dramatically.

DarJones

[ChrisK]

The difficult step is the first genome of any organism. Once you have that, the next one can be assembled using it as a template. A new genome requires much more sequencing to get a good assembly.

The cost and complexity is driven by the end purpose. The inexpensive methods Darrel refers to are good for finding markers but not so good for putting a brand new genome together, which is still a bit laborious.

De novo genome assembly: what every biologist should know

You think GM plants are controversial, wait until we have $100 genome technology available.

With my limited knowledge of genetics, it would seem easiest to map a genome to compare markers for comparison to another organic cellular structure of similar origins. It would seem more difficult to map a genome or multiple genomes to identify and compare functions and structures such as cognitive ability and reproduction.

How far off base am I?

Ted

[Fusion_power]

How far off base am I?

Ted, the best I can tell, you are somewhere over in left field.

Here are a few articles with significant info about cold tolerance.

Introgressed from S. Habrochaites
http://link.springer.com/article/10..../fulltext.html

PI 120256 might be an interesting line with some cold tolerance.
http://link.springer.com/content/pdf...A1012616231637

Inheritance patterns for cold tolerance.
http://www.tuinbouw.nl/files/page/Bi...10450-04_1.pdf

DarJones

[frogsleap farm]

Originally Posted by ChrisK

The difficult step is the first genome of any organism. Once you have that, the next one can be assembled using it as a template. A new genome requires much more sequencing to get a good assembly.

The cost and complexity is driven by the end purpose. The inexpensive methods Darrel refers to are good for finding markers but not so good for putting a brand new genome together, which is still a bit laborious.

De novo genome assembly: what every biologist should know

You think GM plants are controversial, wait until we have $100 genome technology available.

The tomato genome sequence was published this summer. It's a great start, but connecting DNA sequence to gene function (functional genomics) or breeding value (whole genome prediction) will take time and money. I believe there is ongoing research on both in industry and in the public sector. More readily available are molecular markers associated with simply inherited traits of value. The sequenced genome will facilitate generating these markers and enable use of other applied genomic tools (e.g. TILLING) in tomato improvement. Molecular markers associated with key disease resistance genes are already routinely used in tomato breeding, and markers for quality traits (such as flavor) are a hot research topic.

[frogsleap farm]

TILLING is a "reverse genetics" approach to generating novel genetic variation. There are several groups that have developed TILLING populations in tomato (e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845601/). TILLING uses molecular tools to identify specific mutations in specific genes in mutagenized populations. It is widely viewed as an alternative to genetic engineering in developing novel traits in plants.

[frogsleap farm]

Here's a recent functional genomics project on tomatoes - the results of which were widely published in the general media.

http://www.news.cornell.edu/stories/...toesRipen.html

[frogsleap farm]

Arcadia BioSciences in Davis, CA has had a TILLING program on tomatoes for several years. They recently announced they had generated novel mutants in one or more of the delayed ripening regulatory genes (e.g. rin/nor), that are improvements over the current mutant alleles used by breeders.

http://www.arcadiabio.com/extendedshelflife

[ChrisK]

Yep, that's the power of TILLING, when you know what you are looking for. GWAS can help elucidate the unknown genetic architecture of a trait or trait component.

[Fusion_power]

This article delves into the chemistry of cold tolerance in tomatoes. It is a fascinating article.
http://onlinelibrary.wiley.com/doi/1...4.02176.x/full

DarJones

[ChrisK]

Alteration of the interconversion of pyruvate and malate in the plastid or cytosol of ripening tomato fruit invoke diverse consequences on sugar, yet similar effects on cellular organic acid, metabolism and transitory starch accumulation


Abstract

The aim of this work was to investigate the effect of decreased cytosolic phosphoenolpyruvate carboxykinase (PEPCK) and plastidic NADP-dependent malic enzyme (NADP-ME) on tomato (Solanum lycopersicum) ripening. Transgenic tomato plants with strongly reduced levels of PEPCK and plastidic NADP-ME were generated by RNA interference gene silencing under the control of a ripening-specific E8 promoter. While these genetic modifications had relatively little effect on the total fruit yield and size, they had strong effects in fruit metabolism. Both transformants were characterized by lower levels of starch at breaker stage. Analysis of the activation state of ADP-glucose pyrophosphorylase correlated with the decrease of starch in both transformats, which suggest that is due to an altered cellular redox status. Moreover, metabolic profiling and feeding experiments involving positional labelled glucoses of fruits lacking in plastidic NADP-malic enzyme and cytosolic PEPCK activities revealed differential changes in overall respiration rates and tricarboxylic acid (TCA) cycle flux. Inactivation of cytosolic PEPCK affected the respiration rate which suggests that excess of oxaloacetate OAA is converted to aspartate and reintroduced in the TCA via 2-oxoglutarate/glutamate. On the other hand, the plastidic NADP-malic enzyme antisense lines were characterized by no changes in respiration rates and TCA cycle flux and together with an increase of pyruvate kinase and phosphoenolpyruvate carboxylase activities indicates that pyruvate is supply through these enzymes to the TCA cycle. These results are discussed in the context of current models of the importance of malate during tomato fruit ripening.