mtDNA/cpDNA and choice of male/female parent plant?

[bower]

In animals, mitochondrial DNA is passed on by the female parent only.
After a good bit of searching, I found that tomato inheritance of organelles (plastids, chloroplasts and mitochondria) is likewise "strictly uniparental-maternal".

What are the known traits affected by organelle DNA's in tomatoes, that would affect the choice of maternal parent in a cross?

I know there are not a lot of traits governed by the organelle DNA, but some of the plant characteristics like UV-tolerance, metabolic rate, adaptibility to low light conditions, etc. come to mind. Has anyone noticed that these traits are inherited from the female parent in a cross?

[pittaro90]

The only trait influenced by chloroplasts i know is the variegation of the leaves (there's a variegated tomato variety)

[bower]

I did see that commented in my search. At least it's an easy trait to spot!

I also read, the Cytoplasmic Male Sterility (CMS) gene which is commonly used in hybrid production is of course, passed on exclusively by the female parent. So anybody using a commercial hybrid for a cross would not want to use the hybrid plant as the female parent, to avoid passing on this sterility gene to your cross.

(In the F1 product, the CMS gene is over-ruled by using the Restore fertility Rf gene in the nuclear DNA - which has normal segregation). Some of what I read was about corn, but I think the same applies to tomato hybrid production, afaik. So the CMS gene wouldn't be weeded out just by making the offspring male sterile, necessarily.

It's possible that the general metabolic traits I was looking for are also over-ruled by more dominant traits in nuclear DNA, I suppose. There seems to be a fair bit of confusion (or should I say, laissez-faire) in the plant world, where genetic material is passed around between chloroplasts, mitochondria, and the nuclear genome. (!)

[Tom Wagner]

I know that in my long time breeding work resulting in tens of thousands of distinct tomato lines/varieties…that many trace back to a distant matrilineal seed parent. I know the maternal line of my Green Zebra traces back to the 1930’s…but there is no record of its ancestry before that. I suspect many varieties could be traced back to just a handful of varieties. When I cross tomatoes with many dozens of varietal inputs…even a variety with over one hundred varieties in the crossing …only one maternal ancestor carries the mitochondrial genetic information outside of the nuclear genetic material.
I find almost a magical/romantic connection by introducing a new variety into my germplasm bank by using the new variety as a female…I feel the female parent imparts an occasional combining ability that is linked to that maternal cytoplasm. By selfing the hybrid to get to the various filial generations…I am still maintaining that maternal cytoplasmic magic. But as I continue to make crosses with these unique lines, I am invariably using them often as male parents…thus losing that female impact. Green Zebra has been used so many times by me to create new varieties it measures high as an ancestral pollen parent as well as a cytoplasmic parent….no matter how many generations of crosses are made.

I have made some notes due to an internet search. I don’t profess to know much about mtDNA…my experience and knowledge is mostly self taught….I had a course of graduate level cytogenetics back 45 years ago but that is literally worthless today. I am including a few links and quotes of links to help others undertand the topic better. There is no central authority for this information…alas.


Tomato mitochondrial genome sequence

Fernando Carrari's lab has released a first draft of the mitochondrial genome sequence. [October 12, 2008]

The mitochondrion is the organelle within the eukaryotic cell that is primarily concerned with the synthesis of ATP in respiration. Current hypothesis traces it origins to an endosymbiotic event to form a cell lineage containing two independent genomes. Full comprehension of the mitochondrial (mt) genome structure is of fundamental importance not only for it evolutionary implications but also for a better understanding of biochemical processes that take place into this organelle in crop model species. Several mt genome sequences have been recently released from higher plants. We present here the tomato mitochondrial genome and a web-interface resource for plant mitochondrial comparative genomics.

Provisional Map

[IMG]http://i.imgur.com/12Szg.png[/IMG]
http://mitochondrialgenome.org/
http://www.ndsu.edu/pubweb/~mcclean/plsc431/maternal/maternal3.htm
http://www.ndsu.edu/pubweb/~mcclean/plsc431/maternal/maternal4.htm
http://www.ndsu.edu/pubweb/~mcclean/plsc431/maternal/maternal2.htm
All of the organelle DNA that is found in an embryo is from the female.

The egg cell is many times larger than the pollen cells, and contains both mitochondria and chloroplasts. Pollen is small and is essentially devoid of organelles, and thus organelle DNA. So any trait that is encoded by the organelle DNA will be contributed by the female.

http://www.ncbi.nlm.nih.gov/bioproject/67471
http://www.scientificjournals.org/jo...icles/1058.htm

Genetics Today, 1963 p. 242-243
13.94. Some Biochemical and Physiological Properties of Plant ReciprocalHybrids.
S. I. Issaev and V. V. Vartapetyan (Moscow, U.S.S.R.)

Content of sugar and vitamin C in fruits of reciprocal tomato hybrids was higher in the case, where the variety with high level of these substances was taken as maternal plant. The choice of the maternal plant influenced also the degree of heterosis. Heterosis of a certain property increased, when the maternal plant of the pair was characterized by the same property.

http://pubs.aic.ca/doi/pdf/10.4141/cjps80-022

From this experiment, we concluded that
under normal growing temperature regimes,
the cytoplasmic effect was less important
than the nuclear effect; however, under the
stress of cool temperature conditions, the
cytoplasmic effect may reveal some importance
especially for the earliness of several
growth component stages. It is advisable,
therefore, that the cytoplasmic effects and
genic-cytoplasm interactions should be
studied by plant breeders working on tomato
selection for earliness under stress temperature
conditions.

http://www.nrcresearchpress.com/doi/...urnalCode=cjb1

Pigmentation differences in fruit of the reciprocal hybrids were detected.

http://www.deepdyve.com/lp/springer-...and-I76qb0H05G

The article above hints to a difference to Fe usage due to maternal effects in a tomato hybrid testing the difference in reciprocals.

http://www.ncbi.nlm.nih.gov/pmc/arti...48/pdf/437.pdf

Observation of mean differences of reciprocal crosses in table 17 indicates
that there might be some maternal influence acting in these hybrids
causing them to respond to potassium deficiency somewhat in the same
manner as their maternal parent. A direct comparison of these reciprocals
is given in table 19.

Genetic diversity and relatedness tomatoes via maternal dna
T

he genetic diversity of a variety is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity.

drought resistance, Lycopersicon, , Solanum pimpinellifolium, Solanum lycopersicum var. cerasiforme.

Adaptation to local environment has long been considered a major factor driving phenotypic change and speciation
coastal regions for S. pimpinellifolium, etc.
Note that several “coastal” populations of S. l. cerasiforme were originally
collected from sites in close contact with human settlement

Modern breeding of tomatoes has all descended from European stock, however, there is a LOT of diversity in the Americas that has not yet been tapped. Even though a tremendous introgression of will species of tomatoes has occurred to obtain disease resistance…my bet is that the majority of improved inbred and subsequently…hybrids still use a narrow maternal DNA haplogroup.

The founder effect looms large when it comes to tomatoes...we save seed from a tomato often disregarding the pollen parent, thus many varieties are created in time from a single variety over time.
Founder effect

The establishment of a new population by a few original founders (in an extreme case, by a single fertilized female) which carry only a small fraction of the total genetic variation of the parental population [Ernst Mayr, 1963]. The result is that a given allele, gene, chromosome, or part of a chromosome found in members of the population can be traced back to one ancestral individual.

Even though I have created thousands of tomato varieties, my knowledge of potato breeding is perhaps more expansive. Even as far back as 1932, it was estimated that 230 varieties of potatoes in Europe and North America trace back to ROUGH PURPLE CHILI, and the resultant male sterility inherited from the maternal line. Since 1932, the varieties created with ROUGH PURPLE CHILI is probably in the thousands. I am on a personal vendetta to move away from maternally descended potato clones from ROUGH PURPLE CHILI, GARNET CHILE, EARLY ROSE, RUSSET BURBANK, etc. Fertility/fecundity on the female side allows me to expand the growth of diversity through both the female line and the male line.


Tom Wagner



What is of unbelievable significance is that we have such diversity of tomatoes today, regardless of the limited founder varieties and the limited mitochondrials from those early tomato favorites. Is there a "Eve" tomato line from the Americas? Allow the genome folks to ansswer that to the best of their ability.

[bower]

Thank you so much for this, Tom. Absolutely fascinating, and very instructive for the choice of the female parent.

About potatoes: Our family spent some years in Colombia SA in the early seventies, where the diversity of potatoes is astounding. It came as a shock to us - our humble farmer lineage on the island had access to a mere handful of varieties, on which we survived for ~ 400 years. I have no doubt that your potato breeding is as exciting as the tomato.

[loeb]

So, if i want to work with tomatoes like lutescent or variegated or tigerette cherry, I should use them as a maternal parent? I'm going to work with tomatoes as an ornamental plants, I love the way they smell, this is reason nr 1 to grow them, for me. I guess I've made my first cross last year accidently in right way : snow white cherry x f1 from my friend, mom was the sweeter one I hope it will work. I will read very carefully this material that Tom Wagner gave here.. This is very interesting thread, thanks for asking Bower And I will plant some TPS this year, and try to breed some other veggies, so knowing what to do is really helpfull.

[bower]

Originally Posted by loeb

So, if i want to work with tomatoes like lutescent or variegated or tigerette cherry, I should use them as a maternal parent?

If you are concerned about the colour, I think maternal parent would only have an effect in a few cases where the colour effect is specifically produced by nuclear DNA acting upon the 'plastome' DNA in the chloroplast, which is also the chromoplast in the ripe fruit.

The rin gene study which Tom linked is a good example of this, and I also found another while reading today: the hp or 'high pigment' genes - which are in the nuclear genome and equally distributed by the male or female parent - produce their effects, at least in part, by affecting the gene expression of the chloroplast DNA inherited from the mother. So presumably some differences in that maternal DNA could contribute to the final phenotype result.
This study found that the number of copies of chloroplast DNA was increased by the HP gene. So when HP high pigment is expressed, the larger number of chloroplasts (becoming chromoplasts) in the fruit would cause more intense colour in the fruit.
http://www.springerlink.com/content/p8f77vyhf1jenbq9/
A second study involving a hp-2 allele also found increased chloroplast size and number was present from early stage of fruit development.
http://www.plantphysiol.org/content/145/2/389.full

Other than the 'pigment container' chromoplast expression effects, there seems a relatively small potential for fruit colour to be affected by maternal cDNA. Most of the chloroplast DNA is strongly downregulated in ripening fruit, except for one gene (accD) which is involved in fatty acid biosynthesis for the membranes of the chromoplasts which will contain the pigments, according to this article: http://www.plantcell.org/content/20/4/856.full.

On the other hand, the majority of colour related genes are in the nuclear genome. There's a good section on colour genetics and pigment chemistry in tomatoes and peppers in this article, which is nicely written in fairly plain english.
http://jxb.oxfordjournals.org/content/58/14/3841.full
Another overview of the major colour genes in tomato nuclear genome is found here: www.oardc.ohio-state.edu/tomato/jashs1098.pdf

Red/yellow fruit colour is not affected by maternal DNA, according to reciprocal cross results: http://www.scielo.br/scielo.php?pid=...pt=sci_arttext

[Tom Wagner]

BOWER,

For someone who just joined this forum, you sure are involving yourself with rather complicated subjects as such as the mtDNA vernacular.

That said, one of the reasons I work with maternal parents as a priority is that I am constantly loading up tomato lines with new recessives regardless of the mtDNA phenomenon. Crossing these true breeding clones as the flower parent with hybrids, four way crosses, etc as pollen parents allows me a better handle or looking at the segregates at the F-2 level. That means I treat maternal lines as a starting point and rarely , if ever, worry about the perfect multi-generation maternal line.

[Dutch]

Originally Posted by Tom Wagner

That said, one of the reasons I work with maternal parents as a priority is that I am constantly loading up tomato lines with new recessives regardless of the mtDNA phenomenon. Crossing these true breeding clones as the flower parent with hybrids, four way crosses, etc as pollen parents allows me a better handle or looking at the segregates at the F-2 level. That means I treat maternal lines as a starting point and rarely , if ever, worry about the perfect multi-generation maternal line.

Thanks Tom, my grow outs should be interesting again this year. I'll post some pictures again later in the summer.
Dutch

[bower]

Originally Posted by Tom Wagner

BOWER,

For someone who just joined this forum, you sure are involving yourself with rather complicated subjects as such as the mtDNA vernacular.

Tom,

To say that I'm struggling with the vernacular is an understatement. I'm not even sure about proper usage of the terms gene/allele/locus in that post, although I do understand what they mean. But what a mess of terms I found out there: cytoplasmic DNA, mtDNA, cDNA, chloroplast DNA, plastome, etcetera. The reason for naming or using them in my post, is not to appear knowledgeable when I'm not, but to make a list of search terms which might make the difference between finding, or not finding, some information that is sought.

I have three reasons for making such a long post with comments and links to what I read about a subject in which I have no practical experience.
1.) I hope if I've made errors that an expert here will point em out. I have no shame in that - I just want to learn.
2.) The material I found might be useful to someone else in the forum, so it's good to share the links.
3.) From a purely selfish point of view, making a post with links to resources on the internet is a way of organizing the material I found, so I can return to this thread when I need to re-read some information.

If this is not how it works here, and isn't an appropriate use of the forum, let me know. I realize that experts and professionals are busy, and there may be other reasons such as social delicacy, for not boldly correcting a post that is wrong. If that's the case, I will keep my comments to a minimum in future.

[Dutch]

bower thanks for starting this thread and all your links. While most of it went over my head, I did learn a few things and I think so will some others.
Dutch