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Breeding Better Butternut Squash – and a Thanksgiving Recipe

After a long career as a science writer, textbook author, and genetic counselor, I’ve become an accidental authority on squashes.

I began volunteering at the largest food pantry in my small city in June 2020, where my husband Larry had been in charge of the plant and fungal kingdoms for years. It was the height of the pandemic. So gloved and masked, we shoved fruits and veggies into plastic bags, filled shopping carts with the bags, and wheeled them over to a window at which another masked, gloved volunteer quickly pushed the bags to the clients waiting outside.

Like most activities back then without human contact, it wasn’t much fun.

Nowadays, Larry and I help the clients choose fruits and veggies, and I share cooking and storage tips as well as recipes. I love the challenge of figuring out how to prepare something unfamiliar – plantains, Jerusalem artichokes, broccoli rabe.  

My favorite client is a 95-year-old Ukrainian woman. I know which days she’ll show up with her helper, so I assemble bags of bountiful beets so she can make borsht for her congregation. Schenectady has a large Guyanese community, and the ladies with whom I share tips and recipes call me “mommy.” I tell our Black clients how to make stuffed cabbage; they share how to cook collards.

But I’m still a biologist at heart. Here at DNA Science a few years ago, I shared The Peaceable Genomes of Pumpkins.

For this year’s Thanksgiving post, I came upon an article, Genomic Prediction and Selection for Fruit Traits in Winter Squash, published in G3: Genes, Genomes, and Genetics, from Michael R Mazourek of Cornell University and colleagues, from 2020.

The article focuses on butternut squash, which the folks at the food pantry call “pumpkins.” The tan, barbell-shaped vegetables are by far the most popular – the poor acorn and spaghetti squashes sadly pile up in their bins, unrequested. I pity the oddly hued and shaped squashes that are doomed to be ornamental only, but it’s fun to play with the smallish gourds that resemble ducks and geese. And of course Halloween pumpkins enjoy their special day.

Here’s a brief look at the genomics, then some cooking tips, in time for Thanksgiving.

Winter Squash 101

Late summer brings mountains of zucchini, and winter a variety of bulbous and multicolored squashes. Rather anthropomorphically, the designation “summer” or “winter” squash reflects the stage of maturity at which we eat them. We consume immature summer squash, but mature winter squash.

All squash belong to the same taxonomic family, Cucurbitaceae. They have small genomes and grow as vines.

The past two summers, some types of squash that I know we didn’t plant have festooned our garden. We deduced that they arose from seeds in compost, bird droppings, and perhaps diverse mammalian barf in response to a stinky concoction I placed on leaves to discourage deer. The vines seemed to have brains, growing over, under, and snaking around everything we intentionally planted, strangling the delicate tomato plants as well as the hardy beanstalks as they brought forth various round and oblong offspring.

Squash taxonomy is complicated. The Latin species designations cover more than one type of squash, and the same species can have multiple common names, depending on the culture of the cook.  

Five Cucurbita species are domesticated: butternut (C. moschata), summer squash aka zucchini (C. pepo subspecies pepo), Hubbard squash (C. maxima), cushaw squash and silver-seed gourd (C. argyrosperma), and C. ficifolia, also called  Asian pumpkin, black seed squash, chilacayote, cidra, fig-leaf gourd, and Malabar gourd.

My favorite squash is kabocha, which is a C. maxima from Japan. It’s related to the Caribbean Hubbard.  Kabocha resembles buttercup squash, which is C. maxima too, but is much sweeter, with thicker flesh. Hubbards are those gigantic, lumpy, gray things.

I also love the small, striped, delicata squash, which unexpectedly popped up in my garden this summer. It’s a cultivar of C. pepo, and also called peanut squash, Bohemian squash, or sweet potato squash. It cooks with the skin on, recipe below.

Genomic Prediction

Squash breeders aim to improve fruit quality. Not surprisingly, the article in G3: Genes, Genomes, and Genetics focused on butternut squash. Its coveted traits are carotenoid content (source of vitamin A) and free sugar content. Each trait is “complex,” which has a specific meaning in the language of genetics: the characteristic arises from contributions of many genes, to different degrees, most to a small extent.

Traditionally, geneticists have called the genes contributing to complex traits “quantitative trait loci.” But “QTLs” are more theoretical than practical, and difficult to translate into planting advice. I certainly didn’t think about them when planning and planting this year’s vegetable garden. 

But things are rapidly changing. Now that genome sequencing is not only possible but faster and cheaper, breeders are drilling down to specific parts of plant genomes that control desirable quantitative traits. The situation is a little like reading a book review or CliffsNotes (yes, they still exist) to get the main plot points (QTLs) compared to reading the entire book (the genome sequence).

Such a genome-level look at squash could enable more nuanced breeding programs, while also allowing “multi-trait selection” that balances the effects of specific traits based on economic importance, diminishing some while amplifying others. The approach has a rather unappealing acronym that sounds like a digestive disorder: GBLUP, for “Genomic Best Linear Unbiased Prediction.”

But genetics has never been known for decent acronyms and abbreviations (RFLP or VUS anyone?).

GBLUP sounds a little like presymptomatic genetic testing for a disease in humans. Predictive power might inform a gardener or plant breeder which shoots peeking up in May or June will yield the best squashes come October. That’s valuable intel because as any home gardener knows, squash plants can rapidly radiate, then snake up and around and even bolt from the garden altogether to traverse the lawn. They’re space hogs. It would be great to be able to identify those genetically destined to succeed, as well as to nurture the tastiest squashes. I feel badly when I have to ditch a squash that I’ve watched grow for months because it tastes soapy.

With genomic prediction, it “would also be possible to screen hundreds of seedlings for fruit quality traits in a greenhouse, which is impossible with traditional methods. This would allow two cycles of selection per year: one in the field and one in the greenhouse,” the researchers write.

But knowing too much of what to expect in a garden might take the fun out of it, ruin the surprise of an unidentifiable vine peaking out from under a leaf and spawning a rapidly enlarging, yet still-mysterious squash. I think that genetic prediction is sort of the same in people – sometimes it’s better not to know.


Peel the squash with a carrot peeler.

Lay the squash down and cut off the ends, then cut rounds, like slicing a salami.

Cut the rounds into bite-sized chunks. Towards the center, seeds will appear. Remove and toss into the compost bin for next year’s garden.

Place squash chunks in a baking pan along with about a cup of juice. I use apple, orange, mango, and apple cider. Add a teaspoon of honey. Let it sit for a few hours, turning the chunks.

Bake at 400 degrees for about 40 minutes, then turn the chunks. Enjoy!


The skin is edible! No need to peel.

Slice the squash longitudinally. Scoop out seeds and toss into compost bin.

Rotate the squash 90 degrees and slice along the shorter axis, creating C-shaped pieces about half an inch thick. Soak them in juice and bake in a bit of butter, not oil, for about 30 minutes.

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