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AG Genetics and Breeding

Subject:  Genetic question for Joe Ailts

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Dustin

Morgantown, WV

Joe, since you're assembling this project, I wanted to ask at what point you thought selfing might become detrimental? I understand the reasoning to self, and am not questioning the project, but asking if you have come across anything to suggest when inbreeding might become too inbred?

Is there ever a point where the genes get too similar, or does it eventually just get stabilized as they do in flower seeds to produce specific color varieties?

What are your thoughts on how it works?

4/9/2019 9:58:22 AM

cjb

Plymouth, MN

I can't speak from experience with plant breeding, but for laboratory animals inbred lines are generated by crossing brothers with sisters for a minimum of 20 generations. At this point, essentially all genes in the organism are homozygous.

Since some plants can be self fertile (e.g. pumpkins), alleles should be fixed even more quickly. AGs being as inbred as they are should also expedite the process.

There isn't anything about selfing itself that I would expect to be detrimental. If you were able to select for the best growing progeny that had the characteristics you want, eventually you'll fix the best possible genes.

I think the main limitation with breeding giant pumpkins is the small number of progeny that get grown from a single plant. A small number of seeds get planted. These plants then get a lot of grower love to make it to the scale. Because grower input and local weather conditions have a massive effect on fruit size, it's hard to objectively evaluate which progeny have the best genetic potential. A small scale breeding program runs the risk of selecting for deleterious traits quite by accident, just by merit of the bottleneck of the low number of progeny that are grown per generation.

4/9/2019 11:27:26 AM

Dustin

Morgantown, WV

Wow Craig! :)

You gave me a lot of points to think about. Perhaps the biggest downfall of continual selfing is simply carrying and strengthening an undesired trait that accompanies a quality trait like low disease resistance being carried with size, or a less vigorous plant also being carried with the darker color gene. Just loose examples, not sound theory.

I agree that the sample size limits the potential of any project, again one of the reasons I think Joe's Army will make better progress together than anyone will alone.

Do you think tissue culture could be used to maintain quality genetics that have already been harvested and weighed? The plant would obviously not be as vigorous as a tap rooted plant from seed, but could offer a re-visit to special genetics for an additional season for breeding purposes?

I think an additional issue affecting the limit of genetic selection here is that we treat for so many diseases as a preventative measure rather than an integrated threshold measure. The breeding projects at my university abuse plants on purpose to find the ones who survive, but that is not the mentality here, leading to increased chemical use and ineffectiveness. What do you think?

4/9/2019 11:08:58 PM

irischap

Guelph, Ontario

With some crops , like corn. you can get inbreeding depression with subsequent generations. This has been looked at with the pumpkin family (Cucurbitaceae) and there seems to not exist in this group.

Having said this, there is another factor called 'Heterosis' which is scientific name for hybrid vigour. Meaning that with some plants you get hybrids of two lines that show exceptional vigour, bypassing both parents. Again some plants like corn hybrids produce this, but no real evidence it happens with pumpkin/squash family. In any case , it is usually a result of crossing two lines that have a long history of being selfed.

Last year I selfed a large number of AG, as I'm doing genetic experiments and this involved about 20 plants.

Yes,I have plant breeding and genetic training.

4/10/2019 7:47:31 AM

Dustin

Morgantown, WV

Thank you Irishchap, I understand heterosis, but thought it came more from interbreeding species, like crossing pumpkins with squash rather than pumpkin to pumpkin? Are you saying that they can be same species, but generally unrelated, and still produce heterosis?

Additionally, so many orange pumpkins can be traced to a common relative at some point of their lineage. I tried to search back to find anything unrelated to what I have, but it's a rather tiresome search. Are you suggesting that one or two generations within many is not enough to worry about being closely related to each other?

4/10/2019 8:34:13 AM

irischap

Guelph, Ontario

Hybrid vigour is from same species.Generally unrelated lines, Not from interspecies crosses , which are a completely different thing. With inbred lines of pumpkins there is not expected to be problems. But I would always start several seeds and keep the best grower(s). I did look at literature of inbreeding with curbits, not seen as a problem. But if you did it for several generations and selected most vigorous plants, you would end up in a dead end as in you would reach a big weight, but all subsequent plants would be in a small variation around that. So no inbreeding depression, but a limit on progress. So to get bigger sizes you will have to go back to outcrosses.That is breed to another line or unrelated plant.

4/10/2019 10:09:46 AM

cojoe

Colorado

Iris, keep up the genetics discussion.For those newer to the hobby growers tried crossing the two biggest fruit in 2006/2007? which was the 1446 eaton and 1420.5 laRue.Several people made that cross and the reverse.One seed, from those parents the 998.6 pukos grew a worid record. It can be done with orange-just some participation to get a large sample size and keep egos out of it.Prob have a orange cross that consistently will have potential for orange 2000lbers by three generations.

4/10/2019 11:34:03 AM

Dustin

Morgantown, WV

Thank you for clarifying heterosis for me.

So if I understand the selfing statement correctly, the "bottleneck" would simply be the potential of that combinations limit rather than any specific detrimental issue? Not necessarily anything wrong, but only as strong as it will get without a new combination from outside source?

4/10/2019 5:51:57 PM

irischap

Guelph, Ontario

Yes. Combination of genes working well with each other

With modern AG breeding, it has been a hit or miss , accidental method. No particular planning based on known breeding methods. AS in people tend to cross large with large. It works as there is a large pool to pick from. So better gene combinations do get selected.

When you have established best gene and gene combinations in an inbred line, you can get improvement from a good out cross . But only if you get best one. Best one would be more likely to be from another one from a selected, independent line of selfed pumpkins selected.

For best selection you need to grow a number from each cross and select best.

4/10/2019 6:56:02 PM

cjb

Plymouth, MN

I'd really like to see exactly how inbred some of today's top genetics are (inbreeding coefficient). I suspect it's not that big of a gene pool, and with the small numbers of progeny that gets grown there's an increased risk of accidentally carrying on bad traits.

Size, color, shape are easy to select for. Could probably breed out undesirable vine characteristics. Beyond that, it's hard to track undesirable traits. I think it'd be a favor to the community if seed fate tracking were a bit more elaborate than what exists now. For every seed that gets grown, it'd be useful to know if it made it to scale, what it taped at the end, if it blew, etc.

As an aside, I happened to be at an awards banquet last night where the breeders who developed First Kiss and Honeycrisp got honored. 1 in 10,000 crosses go on to become a commercially viable variety.

4/10/2019 10:09:01 PM

Joze (Joe Ailts)

Deer Park, WI

Great discussion. I agree with all of irischap's points. While there may not be concrete evidence of inbreeding depression in cucurbits, I do believe that as the tree of genetic diversity narrows, primarily do to the "herd mentality" of the majority of growers planting seeds with nearly identical parental lines (2145 McMullen for example), we may be isolating unfavorable characteristics associated with those lines.

That sentence was a mouthful, allow me to illustrate metaphorically. Let's say we agree MJ was the greatest basketball player ever and that we wanted to populate Earth with MJ kiddos to create even better basketball players. So MJ gets to breed with women everywhere, including the female version of himself (self crossing) to create more progeny with MJ DNA. Presumably, whatever genetic gifts endowed him with basketball prowess would be passed along. Let's also assume that MJ also carried some genetic traits that made him susceptible to various diseases...heart disease, alzheimers, etc. By perpetuating his DNA, we get both his basketball offensive skills and the potential for poor defensive health genes.

That's essentially what I believe is going on in AG genetics. we continue to breed for offense (size) without any consideration for defense (disease resistance). We can prop up weak defense through the excessive use of chemistry (insecticides, fungicides, etc). But I do believe that we could be heading for a future scenario where these plants may be so weak, we cannot limp them to higher offensive heights.

The reason? we continually select for offense without any regard for defense. When was the last time anyone chose a pollinator purely for its perceived resistance to a disease?

By virtue of a plant appearing "healthy" at pollination, one may argue that we are reinforcing strong defense, as a plant that goes down to disease pre-pollination obviously will not contribute to the gene pool.


4/11/2019 5:58:08 PM

Joze (Joe Ailts)

Deer Park, WI


however, this is not the same type of selective breeding that traditional breeders would employ to reinforce defensive characteristics.

So, Dustin, to answer your question directly, it is possible that somewhere down the line continued self crossing could become detrimental. But, quite frankly, I have no way to predict when that may be the case. make sense?

4/11/2019 5:58:15 PM

Dustin

Morgantown, WV

Thank you for joining in, I'm sorry to have singled you out in the first place Joe. I did not expect Craig, or Irishchap to come at me with what they did, so thank the two of them for that. I will be more open in my questioning moving forward. I hope that others have more to contribute, as it is making more sense than it did already.

Counterquestion... Would it be worthwhile to grow a quality genetic, on a mass scale, at an organic farm where nothing is sprayed, and heavy amendments aren't favored?

To ask further, there has been a disease resistance program here for decades with the WV '63 tomato developed by Dr. Mannon Gallegly. He recently released 2 new lines that are resistant to I think late blight, and one has increased sugar content. In 4 years of watching his trials, I have noticed one thing. He abuses his plants.

They are left on bare soil, they are crowded, and they are left to fend for themselves. The latest survivors are selected.

Short of the control of pruning to one pumpkin per plant, and pollinating at roughly the same time, could it be conceived that planting the same seed throughout a 20 or so plant trial, and selecting the best balance between time of disease versus overall gain, would be a quality experiment in selecting stronger overall genes than selecting simply the largest grown from the year?

Mouthful back to you, sorry. I invite anyone with suggestions to join :)

4/11/2019 9:14:28 PM

irischap

Guelph, Ontario

The end goal is large fruit at weight off. In terms of deleterious gens, there is a selection against. This happens as the plants with any deleterious genes do not produce heavy fruit successfully, so get selected out. Yes, there can still be carried in genetics, but over time become less common, as people look at offspring charts, and select accordingly. not best process, but works. If you were doing a line of selfed fruit, you would see this in a fruit, and not use that line to go forward. In a selfed line, you would keep several lines going and select after a few generations. You never put all of your eggs in one basket. As a fruit , Atlantic Giants genetics move forward, but only as genetic pool consists of so many growers. So selection is over a wide selection of plants. You are more likely to carry some deleterious genes then in a planned selfing lines, but generally select against, as bad plants do not produce award winning pumpkins.

4/12/2019 11:14:47 AM

Chris H

Ithaca, NY

I think it would be very challenging to breed for disease resistance in AGs. Cucurbits in general have very few resistance genes (R genes). I doubt modern AGs are even segregating for disease resistance. It is common practice to make crosses between cultivated squash species and wild squash species to bring in disease resistance. These crosses are difficult to make and many negative alleles come along for the ride (sometimes called linkage drag) and need to be purged through intense breeding efforts. However, it might be worth the effort. The US National Germpasm System is a good place to look for diversity https://npgsweb.ars-grin.gov/gringlobal/view2.aspx?dv=web_taxonomyspecies_view_accessionlist&params=:taxonomyid=12597, if you're feeling bold...

4/12/2019 11:17:43 AM

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