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Ithaca, NY

Hi everybody,

I think it would be really cool to make use of all available pedigrees to make a relationship matrix. I think having this information could help inform crosses, and it would allow us to look at population structure that has developed over time.
In order to do this, I need access to many pedigrees. It seems like Pumpkin Fanatic has this information, but I can't find a way to download all the pedigrees in a spreadsheet format. Does anybody know a way to get/have access bulk pedigree data?

5/28/2018 8:41:55 AM

Ithaca, NY

Relationship matrix background https://wiki.groenkennisnet.nl/display/TAB/Chapter+6.7.2%3A+Calculation+of+additive+relationships

5/28/2018 8:48:41 AM

Grittyville, WA

can copy and paste gpc results into a spreadsheet... I can maybe send you my edited formatted dataset if it would help

5/29/2018 2:35:22 AM

Ithaca, NY

I looked into scraping all the data off of the GPC info pages, but they only go back to 2009. Are older results available elsewhere? I guess I can start with what's available.

5/29/2018 8:58:43 PM

Western NY

Change the year in the URL, that should get you back to 2005.

5/30/2018 9:10:19 AM

Ithaca, NY

Thanks for the suggestion! I have all the data going back to 2005 now. I have to do some preprocessing to remove typos and naming inconsistencies, but If all goes well I'll have some results to share soon.

5/30/2018 6:23:41 PM

Willamette Valley, Oregon

Results from that would be interesting. There's a huge pitfall in the way the data are organized that will limit your success (and could lead you to the wrong conclusions).

The main thing is that the "pollinator" isn't the actual genetic father-pollinator but the seed or from a fruit perspective the Paternal grandmother. I wrote an article about it. I'll copy and paste here:

5/31/2018 2:10:00 AM

Willamette Valley, Oregon

An article for the PGVG Newsletter
What’s in a Name? Naming of Pumpkin Fruit and Pumpkin Seeds:
Potential Pitfalls in Understanding Giant Pumpkin Seed Genetics
By Scott Holub

Summary: Our current seed and fruit naming convention is potentially misleading in terms of the genetic potential of the offspring from that seed. Simple improvements can easily be implemented.

All giant pumpkin growers use a common practice for naming and referring to giant pumpkins and other fruit grown for weight or size. Let’s use Larry Nelson’s big AG fruit from this year for the rest of the example, since he asked this useful question. Here’s the shorthand for his fruit and the seeds that are in that fruit:

1468 Nelson ’12
where 1468 is the fruit weight, Nelson is the last name of the grower, and ’12 is the year.

On its most basic level it is useful shorthand in discussion and for easy reference. It does not tell the whole story genetically though, only 50% to be precise.

5/31/2018 2:11:37 AM

Willamette Valley, Oregon

Here’s another longer shorthand we often see, which includes the data GPC collects at weigh-offs:

1468 Nelson ’12 (1421 Nelson x 1661 Jutras)

The first important thing to recognize is that the main label (1468 Nelson) refers to either the fruit (as in the GPC database) or the seeds in the fruit, or sometimes both. That alone can be confusing. Recognize that the GPC database is labeled primarily as a FRUIT (mother) database and to a lesser extent a SEED (offspring) database. That’s the first step in understanding the potential for confusion. They are two very different perspectives, but both are important. Actually the standard shorthand label above does an inadequate job for both purposes (fruit or seed) in regards to the genetic history of either. For the purposes of interpreting genetic/familial relationships the above shorthand is exceptionally confusing, if not misleading (although unintentionally, of course). Read on…

Here’s a more detailed version of the fruit/seed description that some folks are now using (and I am in favor of). Note the extra information in the brackets [ ].

1468 Nelson ’12 (1421 Nelson x 1661 Jutras [1144 Nelson])

From the genetic perspective of the SEEDS within the 1468 Nelson fruit (as opposed to the fruit itself), here’s an explanation of the familial relationships to the seeds for all the numbers listed above:

Biological Mother (Maternal Grandmother x Paternal Grandmother [Biological Father])

5/31/2018 2:11:56 AM

Willamette Valley, Oregon

Figure 1. Family tree of the 1468 Nelson seeds with appropriate orientation of genetic relationships.

Paternal.Grandfather....Paternal.Grandmother....Maternal.Grandfather...Maternal.Grandmother
.....1466.Jutras.‘11......1661.Jutras.‘11...............Open............1421.Nelson.‘11....
..........|__________v__________|........................|________v________|...............
..............Father.(pollinator)...........................Mother.(Fruit).................
................1144.Nelson.‘12............................1468.Nelson.‘12.................
.....................|____________________v_____________________|..........................
.......................................Seeds...............................................
..............................1468.Nelson.‘12.x.[1144].....................................

5/31/2018 2:19:59 AM

Willamette Valley, Oregon

1468 Nelson is the biological mother of the seeds, but confusingly, it's what both the fruit and the seeds in the fruit are called for short (see Figure 1). It’s referred to as “weight” in the GPC database meaning fruit weight. The 1468 Nelson contributes 50% of the genetic material to the seeds within her.

1144 Nelson is the fruit weight from the biological father of the seeds. The biological father is often ignored entirely (which is a travesty genetically), but when recognized it’s called the "pollinator" or "the pollinating plant" to distinguish it from the 1661 Jutras “pollinator” (see below). The 1144 Nelson contributes 50% of the genetic material to the seed. It clearly deserves recognition, but is understandably difficult to track sometimes.

1421 Nelson is the maternal grandmother of the 1468 Nelson seeds, (but confusingly, the mother of the 1468 Nelson fruit itself.) The GPC data base calls this “Seed (mother)” in reference to the relationship to the fruit.

5/31/2018 2:20:24 AM

Willamette Valley, Oregon

1661 Jutras - Here’s a tricky one, so read slowly: 1661 Jutras is genetically the paternal grandmother of the 1468 Nelson seeds. As such, it is “the mother of the pollinating plant” and nothing more. The 1661 Jutras provides on average 25% of the genetic material to the seeds through its contribution to the 1144 Nelson pollinator. The GPC database calls the 1661 Jutras “Pollinator (father)”. Strictly speaking neither “pollinator” nor “father” is accurate from the fruit perspective of the GPC database or from the seed perspective of this discussion. 1661 Jutras is NOT the genetic pollinator/father (the 1144 Nelson is). Again, 1661 Jutras is the paternal grandmother to the seeds (and nothing more than a husband or mate to the fruit, with no influence on fruit (essentially the mothers “belly”) performance that year other than to spur growth, which any C. maxima pollen could do). - Ok read that again.

(As an aside: When referring to the fruit only, not the seeds: 1468 Nelson ’12 (1421 Nelson) seems a more appropriate shorthand. Leaving off the 1661 Jutras de-emphasizes it, since it really has no role in the fruit size that year. For example, news reports on the new world record fruit should really only report the fruit weight and the seed (mother) of the fruit. Pollinator is irrelevant unless the topic is future seeds.)

5/31/2018 2:20:48 AM

Willamette Valley, Oregon

The maternal and paternal grandfathers of the seeds (in this case Open and 1466 Jutras) are not shown at all in the shorthand, which again is misleading genetically since they are of equal importance to the grandmothers of the seed, which ARE shown. Any one of the maternal/paternal grandmothers/ grandfathers contributes on average 25% of the genetic material in the seeds. Including all these grandparents in the shorthand would be unwieldy in most cases though.

5/31/2018 2:21:40 AM

Willamette Valley, Oregon

------end of article

5/31/2018 2:22:30 AM

Willamette Valley, Oregon

So basically you need to know the info on the real plant that grew the real male flower that pollinated a female. Often you can figure that out, but it's not reported in a handy way in the GPC data. Often the father identity/quality is not known, if no fruit made it to the scale.

An example of why this all potentially matters is:
1623 Wallace '03 (1278 Goetze '11 x 1725 Harp '09 [2009 Wallace '03])

All 1623 Wallace offspring have half 2009 Wallace genes, but that's not obvious in the standard nomenclature. So 1623 Wallace seeds and 2009 Wallace seeds are half siblings.

5/31/2018 2:35:58 AM

Eastern Pennsylvania

I am totally on board with this Scott. It would also be a great benefit to see [HD] added when applicable.

5/31/2018 7:57:48 AM

Ithaca, NY

I hadn't immediately considered this, but you are right and it does complicate things. The pedigree conventions are different then what I'm used to. All seeds from the same fruit are genetically distinct full-sibs, and everytime a seed is grown it should be given a universally unique identifier and this is what should be tracked.

5/31/2018 8:38:05 AM