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Ithaca, NY

Hi,
I am a graduate student at Cornell University in the Department of Plant Breeding and Genetics. Currently, I work in a vegetable breeding laboratory and we do a lot of work with squash breeding. I first learned about giant pumpkin growing when I was a kid. The experience of growing giant pumpkins is what led me to pursue a career in plant breeding and genetics.
I'm still interested in giant pumpkins, specifically in the evolution of giant pumpkins. As part of the CucCap https://cuccap.org/genomic-tools/ initiative, we are DNA sequencing many diverse C. maxima (same species as giant pumpkin) lines including some giant pumpkin types. Basically, we are applying the same techniques used in human personalized medicine to better understand plants. I think it would be cool to obtain DNA information on a couple of hundred AGs, from older seed stocks to more modern stocks, and run some analysis to explore how thirty plus years of community-wide selection has shaped the squash genome.

9/29/2018 3:03:38 PM

Ithaca, NY

I would like to launch a project on https://experiment.com to help fund a giant pumpkin genetics experiment. Before I get started I need to establish interest and get an idea for the seeds that people would be willing to grow/donate for the experiment. If we get funding, we would ask growers to grow their seed, collect some trait data (rind color, shape, weight etc..) and we would send a small kit (coin envelope with desiccant) for growers to send us leaf tissue for DNA extraction. For very old seed that won’t germinate, we would ask growers to send us their seed, so we can extract DNA directly from the embryo tissue.
You can read a draft proposal of the project here https://docs.google.com/document/d/16DqgkNMM8kNrOQWDYsoRGOJh3zFIAqNa-KDlTqPjHAc/edit?usp=sharing . If you think you would be interested in participating in this project please fill out this form https://goo.gl/forms/iCcYpge5bDO6dK9E3, this isn’t a formal commitment we just want to gauge how many people would be willing to participate if we get funding.

9/29/2018 3:03:51 PM

Ithaca, NY

Feel free to shoot me an email at ch728@cornell.edu

9/29/2018 3:04:14 PM

Watlington, UK

Great idea! An excellent opportunity for the giant pumpkin community to get some real scientific analysis of AG genetic development. If this takes off who knows where it will take us? I hope we can get the 200+ growers you're asking for.

9/29/2018 3:52:07 PM

Grittyville, WA

Filled out the form.

9/29/2018 10:12:34 PM

Grittyville, WA

This could be the most interesting project we see for the next few years. Lets do our part to make it a success.

9/30/2018 1:51:48 PM

Guelph, Ontario

Did a number of crosses this year to sort out genetics of the white genes in giant pumpkins. I say genes , plural, as at this point it is obvious that there are at least two.

9/30/2018 2:00:48 PM

Grittyville, WA

Can you test any methods prior to scaling up? Do you have an advisor? Whats the minimum cost to get it set up to and ready to start getting results?

9/30/2018 2:01:24 PM

Ithaca, NY

Hi, yes I do have an advisor and I have extensive experience with the techniques needed to make this project work. I also have access to the latest genomics/computational technology, as well as to some of the minds that developed this technology. If you follow the link to the draft proposal I included above, you can see my budget. Basically, I am hoping to raise around ~$7,000 which should cover the majority of the project. I will be soliciting funds from multiple sources including University connections and from private industry. In my mind, the greatest challenge will be logistics but I'm confident that we can work it all out together. I anticipate this project yielding some scientifically interesting results and more practical results that the community can use for genetic improvement of AGs. All results would be made freely available to the community.

9/30/2018 4:24:09 PM

Ithaca, NY

Hi irischap, very cool. There are likely several genes that condition rind color. Old studies in C. maxima seem to point in this direction, but there has been very little work in mapping these genes with modern techniques.

9/30/2018 4:27:58 PM

Ithaca, NY

I hope to have some results to share soon. I am conducting a pedigree analysis of all AG records that I have access to. There are some issues with the naming system in giant pumpkins. Mostly, the pollinator listed is often not technically correct. I have some programming skills, so I am working on writing a small program to correct this problem. Then I can use standard methods to calculate a pedigree-based relationship matrix, which can be used to aid in crossing decisions.

9/30/2018 4:37:06 PM

Grittyville, WA

I think bathabitat may share your opinion about how the cross should be written. He posted about this... He would be a good contact maybe and I'm curious to know if you agree with him. I will try to find time to do my part to help. Busy time of year. Whats the timeframe for the project?

9/30/2018 6:22:20 PM

Ithaca, NY

Bathabitat was the one who first pointed out the issue to me, and he is correct. The pedigrees are not maintained correctly, and I have to make some assumptions to fix this. In the end the relationships may not be 100% correct but should be close enough to be useful. I'm hoping to have things in place before the next growing season.

9/30/2018 6:29:48 PM

Oak Grove, Mn

I am wondering if my many generation selfed pumpkin line could have any value. I would be curious to know how much genetic diversity is still left in the seeds.

9/30/2018 7:29:34 PM

Ithaca, NY

I'm not sure there would be a lot of value in selfing out lines. That is standard practice in squash breeding programs, but that's because the goal is to produce a uniform product. Hybrids are also common in squash breeding, but not because they display heterosis. More for variety protection reasons and public perception. I am also very curious to see how much genetic diversity is left in modern AGs. That is one of my goals with this project.

9/30/2018 10:15:00 PM

Bloomington, IN USA

I would hazard a guess that the amount of genetic diversity is rather low.

9/30/2018 11:40:46 PM

Guelph, Ontario

What is more interesting would be what genes contribute to the size, and what they do on molecular level.. So comparison to non giants would be useful. I have several crosses of AG with other C. maxima cultivars. Two grown this year and several crosses made for next years season. These will be very useful for teasing out genes and there effect. So Chris, are you interested in some of these comparison?

10/1/2018 7:16:49 AM

Ithaca, NY

Agreed Irischap, what cultivars have you crossed with AGs? As part of the CucCap project I mentioned we are sequencing hundreds of C. maximas from the USDA diversity collection. This collection includes squash from all over the world of all different shapes, sizes, levels of disease resistance and color. I will combine this data with the AG data that we generate. This may allow us to identify loci that contribute to size. Another approach is to use selection mapping. The idea is that regions that contribute to size lose genetic diversity as they are selected on over time. We may be able to detect these signatures of selection. Additionally, we can use the CucCap data to help determine the founders, the Adam and Eve so to speak, of modern giant pumpkins. This data can also be used to identify other squash that may merit crossing with modern AGS.

10/1/2018 8:35:41 AM

Guelph, Ontario

Orange Hubbard squash, a white decorative squash, a large grey-green decorative squash of unknown genetic origin, and a Blue hubbard. The Green squash versus AG shows strong powdery mildew resistance. They all show long fruit maturity growth, with large variability. Orange Hubbard shows AG plant habits (maternal ) but shorter fruit maturity time, but longer then hubbard.. Comparing sibs with different characteristics to parental material can sources out genes quicker then general genome comparisons. Time to develop fruit is a key gene to AG size. About 4-6 weeks for C. maxima versus 12-15 weeks of growth for AG

10/1/2018 9:44:39 AM

Plymouth, MN

I'm excited by the project and am happy someone with experience in plant breeding is taking it on. I'd be happy to participate, but don't know what I plan to grow and don't have a big seed archive.

A couple thoughts:
1) I know it's not up to professional standards, but am glad you're taking it on to yourself to clean up the available pedigree data and start there. Getting some quantifiable data on just how inbred the modern, 2000+ AG is would be useful in directing your project.
2) For your proposal for growing seeds: how informative is "weight" really going to be? There is so much heterogeneity in how the plants are grown, from feeding regimens to space the plant is allowed. I think you may get the most information looking at old (80-90's vintage seed, if available) vs commercial seed pack AG, vs today's heavy hitters.
3) Just what are you proposing to sequence and how many samples? I assume not whole genomes given your budget, so exons or specific loci? I'm not familiar with your 192-plex PstI Genotyping-by-Sequencing library prep. Given my experience with NGS, $7,000 can get spent awfully fast.

Keep us in the loop as you work on this. You may get more interest advertising over the winter, and particularly after the weighoff buzz dies down.

10/1/2018 9:58:12 AM

Ithaca, NY

Irischap, I agree that an F2 population of AG X smaller C. maxima would be a useful follow-up experiment for mapping/validating size related QTL.

10/1/2018 2:07:55 PM

Ithaca, NY

cjb, I'm glad you are interested. I will likely advertise again in the winter. I have also emailed the survey to some grower connections that I have to help distribute.

1) I agree. The pedigree analysis is an important first step. The relationship matrix derived from this analysis can be combined with weight and other data in a linear mixed model framework to calculate BLUPS for giant pumpkin lines and estimate the heritability of weight.
2) Genotype X environment interaction is a huge problem with AG weight data. My plan is to focus on comparisons between landraces, vintage AGs, and modern AGs.
3) Indeed WGS is not feasible as it is currently too pricey. GBS is a very popular reduced resprentation method used in many crop species https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019379. In squash we can run 192-384 samples on one lane of a sequencer. Depending on the diversity of the samples, this can yield 5-10 thousand genome wide markers. My plan is to sequence somewhere between 192-384 AG samples depending on how much participation I can get.

10/1/2018 2:25:13 PM