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Bemidji Minnesota

I’ve just been doing second hand research on what VNTR is, and this is my offhanded theory (I type fast so it got long to read) on how this relatively new area of genetics may be applied, and likely has been for quite some time, to Atlantic Giants, even without our knowing of it. One quick search for tandem repeats, or VNTR in the search function came up with nothing, so this may be the start of this discussion here. Like I said, I am still learning about this, but I find it fascinating.

If any of this information is wrong, then sorry, I am still reading up on it, and some of you here may have far more extensive knowledge on the subject than I. If I got any of it wrong, please correct me, and I will not take it as an insult.

Tandem Repeats, or variable-number-tandem-repeat (VNTR), are basically repeating codes that exist on certain traits in genetics.

For example, if say a hypothetical sunflower gene for taller height is WTNSD, then the shorter varieties would have WTNSD WTNSD, where a much taller one would have WTNSD WTNSD WTNSD WTNSD WTNSD WTNSD WTNSD WTNSD WTNSD WTNSD, and the more it has, the bigger it gets.

3/25/2009 12:04:26 PM

Bemidji Minnesota

From what I have been able to gather, VNTR, exist in plants as well as animals. The more or less copies for a specific trait, the more or less exaggerated the trait is.

For years plant and animal breeders have been utilizing these, without knowing what they truly were, or even that they existed. They just knew that 2 big dogs bred together could result in even bigger dogs, and that dogs with long faces bred together could result in even longer faces. The opposite is also true, by mating parents together with a smaller version of a feature, one could breed to reduce a certain trait even more.

Now the VNTR could be applied to all the features of the AG in theory, that we have seen able to breed for. From color, to shape, to having dill rings and internal cracks, to being flawless bomb proof wonder fruits. There may be certain tandem repeats for over all volume of fruit, as well as for thickness, or “going heavy”.

What is so interesting about VNTR is that it shows there is not a set IF or THEN in genetics, but that a feature can be compounded over many generations. Meaning there is not just a gene for big or small, or hybrid vigor via an F1 or something like that which guarantees large size, but what could be happening is that through selective breeding AG growers have been simply increasing the amount of VNTR for size. Not to mention all the ways VNTR may control plant vine growth as well.

This may be why with AG starting with a limited gene pool, we have now so many different lines, colors, body shapes, and sizes. Different lines are exhibiting different numbers of VNTR. Perhaps why when one with a large volume is bred to a thick one, the result could be one with a thickness and a huge volume, was that the case with the 1068?

3/25/2009 12:04:52 PM

Bemidji Minnesota

In practice we can even see the results of this when one compares the good looking bright orange pumpkins compared to the salmon colored record breakers. More often than not, new larger size shows up in ones that are being bred for size/weight/sturdiness, as that is what all the effort in increasing those traits is put into. What is happening is that every generation is a concentrated effort to increase these tandem repeats.

Now since these traits are for the most part accumulative, that would mean orange can be bred back into one that has achieved great size. These orange ones will however be a generation or two behind the salmon colored monsters, as by the time the seeds with combined high numbers of size VNTR with bright orange color are planted, the new generation of salmon colored monsters has already moved on to having even more VNTR for size. Which can be easily observed with how really Orange pumpkins with really pretty shape like the 1317 Rose are just not quite as heavy as say the 1689 Jutras. Now its possible that one day there will be one as good looking and red as the 1317, with the same volume, weight, and as many VNTR for size as big and heavy as the 1689 Jutras, but again, by that time the WR would likely be a salmon colored 1 ton freak.

3/25/2009 12:05:17 PM

Bemidji Minnesota

Now this does not mean it is impossible to get an orange WR, as there is a small chance that an orange one could pass on all of its VNTR for size along with its color, but the likely hood of passing on more VNTR goes up with the one that already has more of them to give.

This would also mean that breeding for making hybrid vigor, may actually be irrelevant, when we could still increase the amount of VNTR with close relatives, or even self pollinating. The key would be to then select the best performing offspring and repeat, because those with the most of the desired trait, would also be the ones with the most VNTR for the trait. Also those with the least problem traits, would have the least VNTR for those as well.

Just take a look at how many common ancestors show up many times in the genetics of champion lines. What I think is happening is that they simply had more VNTR for size, and even bred with themselves, passed on more VNTR for size. This could be why some 800 pound x 800 pound seeds still grow 1200 pound offspring, instead of just throwing fruit no bigger than themselves. Now there is a chance they will sometimes have offspring that get less VNTR than desired too, and you can tell them easy by under-producing seeds. That is why it is selective breeding. Those that consistently fail and are not planted, probably had less VNTR than we wanted, or perhaps too many for vine growth resulting in massive flat vine tangled abominations.

Anyhow, here is some reading for you plant genetic detectives out there, who are more interested in this than I:

3/25/2009 12:05:28 PM

Bemidji Minnesota

Rogstad, S. H. 1996. Assessing genetic diversity in plants with synthetic tandem repetitive DNA probes. In, Genomes of Plants and Animals, J. P. Gustafson and R. B. Flavell, editors, Plenum Press, New York, New York. Pp. 1-14.

Rogstad, S. H. 1994. Inheritance in turnip of variable number tandem repeat genetic markers revealed with synthetic repetitive DNA probes. Theoretical and Applied Genetics 89: 824-830.

Rogstad, S. H., J. C. Patton, and B. A. Schaal. 1988a. M13 repeat probe detects DNA minisatellite-like sequences in gymnosperms and angiosperms. Proceedings of the National Academy of Science USA 85: 9176-9178.

Nybom, H., B. A. Schaal, and S. H. Rogstad. 1989. DNA "fingerprints" can distinguish cultivars of blackberries and raspberries. Acta Horticulturae 262: 305-310.

Nybom, H., and S. H. Rogstad. 1990. DNA "fingerprints" detect genetic variation in Acer Negundo (Aceraceae). Plant Systematics and Evolution 173: 49-56.

Rogstad, S. H., H. Nybom, and B. A. Schaal. 1991. The tetrapod "DNA fingerprinting" M13 repeat probe reveals genetic diversity and clonal growth in quaking aspen (Populus tremuloides). Plant Systematics and Evolution 175: 115-123.

Pelikan, S. and S. H. Rogstad. Provisionally in press, pending minor modifications. Improved estimation of heterozygosity from VNTR multilocus probe data. Molecular Biology and Evolution.

3/25/2009 12:05:33 PM

Eastern Washington State

Meathead, the VTNR that you are referring to are primarily used for genetic marker analysis (ie dna fingerprinting). The consensus opinion is that for the most part they do not appreciably change the function of the genes to which they are linked. Of course there are the exceptions such as Huntingtons Chorea in humans. However the AG size trait comes from somewhere, so why not your VTNR? My feeling is however that most of the traits in AG , especially thinks like color, shape and plant vigor are run of the mill genetic variation that is not strongly selected for by growers.

You have an inquiring mind, I think you would find Steve Tanskley's work on Tomatoes very interesting. It explains how just a few genetic loci make the difference between a thumnail sized wild tomato and a 2 lb beefsteak cultivated variety. Sound familiar?

3/25/2009 1:48:21 PM

Eastern Washington State

Also your thoughts on selfing plants to get the traits you want consistently are correct. It’s probably the best approach, and the way most breeding programs work. However there’s a danger in that inbreeding also brings out deleterious traits in some of the progeny. Most of us here don’t want to take that kind of risk with only the space to grow a few plants. I’m new to this hobby and will never be a contender for size, so that’s the approach I will be taking. Several generous growers have sent seed that has good size/shape/color potential. I’ll be selfing everything and carrying forward that material that looks the best. In a few generations I’ll either get frustrated and go do what works for everybody else, or I’ll have seed lines that will behave consistently. We’ll see!

3/25/2009 1:57:37 PM

Midway, UT

Interesting stuff.

3/25/2009 4:52:49 PM

Bemidji Minnesota

Thanks for you thoughts on the matter Brian.

It would make sense that color is not controlled by a VNTR then, but the theory of having to take out a generation to add it into an existing line of salmon colored giants would still put it 1 gen behind the rest in terms off accumulated tandem repeats for size alone.

I definitely think its a safe bet that the size of AG is controlled by these VNTR's. This would explain how from basic Hubbard types with a little orange thrown in, some of the best selective breeders in the world have grown fruit in excess of 1600 pounds, with very consistent chances of fruit over 1000 pounds. 20 years ago that was as fantasy as candy land.

I will look up Steve Tanskley's work, I grow tomatoes too, and I find this type of information very fascinating. Hmm, haven’t used my GI bill yet, maybe I should go to school for botany and genetics since I got interest in it? Put my tandem repeat theory for AG size to the test.

3/25/2009 5:15:03 PM

Rhode Island

huh????????????????????? if growing a giant pumpkin gets this involved ill go back to growing field pumpkins,peppers and tomatoes. lol

3/26/2009 5:08:24 PM

Pembroke, New Hampshire

Great reading guys.
Pap- whether you know it or not, you're already a botanist(heavy on the applied, less on the theoretical).

3/26/2009 5:27:41 PM

President - GPC

NIce!

3/26/2009 5:39:27 PM

Bemidji Minnesota

Ok, shorter version for Pap’s convenience.

Giant size could very well be caused by the genes accumulating to higher numbers for the trait of size and growth.

Meaning that if a seed gets the “BIG” genes from both its parents, added up together, will give even bigger fruit.

You already knew that, and have been putting in into work.

This theory above is an explanation of what has been going on instead of hybrid vigor or mutation.

3/26/2009 7:28:38 PM

Eastern Washington State

Pap you crack me up!

Please expect in the mail soon a humble request ($ included) for a Dicks Tips II. Because I respect your expertise!

brian

3/26/2009 7:55:27 PM

Cincinnati,OH

Heres a link i found interesting on inherited fruit color
http://cuke.hort.ncsu.edu/cgc/cgc26/cgc26-15.pdf

3/26/2009 7:58:52 PM

Rhode Island

i knew that --lol that explains why the 1450 was such a great producer in a limited quantity ( so few seeds in the pumpkin ) 1068 x 1068 sib. heavy into heavy
thanks
pap

3/27/2009 8:23:22 AM