Using genomics in organic seed breeding

Harvest time for trial squash at Cornell University’s certified organic test farm. The best plants are flagged, and then bagged in a mesh onion sack to be cured for yield and quality analysis. Seed from the plants that test the best will be planted next year.
Photo courtesy of Michael Mazourek.

“If we had psychic honeybees, we could have done this,” plant breeder Michael Mazourek says as he surveys the 2-acre squash patch at Cornell University’s 30-acre certified organic test farm. Under inspection are 80 plots filled with trials for a variety he’s currently referring to as “Honeynut 2.0.”

It’s the first week of October, and Mazourek wants to assess the storage trials before the frost hits. Honeynut 2.0 is a cross between butternut and buttercup that’s been in the making on and off since the 1980s, about a decade before Mazourek’s arrival at Cornell’s breeding program. The cross has an extra-rich, creamy, “beautiful” texture and flavor, according to Mazourek. The reasons for Honeynut’s slow development are varied.

Buttercup and butternut are different species. Crossing the two is a difficult and laborious process – unless, of course, you have psychic honeybees or an incredible stroke of luck. Started two generations of faculty members ago, the squash blossoms had to be hand-pollinated by the breeders to make the cross. Anyone growing Cucurbita maxima buttercup and butternut on their farm simultaneously could naturally get some cross-pollination, which would result in a naturally occurring hybrid plant, but it would be rare and often couldn’t reproduce itself. Such hybrids don’t tend to produce male flowers.

Honeynut squash is the result of a project started by two determined breeders, Dick Robinson and Molly Jahn. The initial result was a mini butternut with green skin that ultimately ripens to a caramel color. After developing an early version of the variety, the breeders put it on the shelf for a while. It didn’t fit the mainstream concept of what a butternut should be, and its initial reception was lackluster.

USDA-funded projects like the Public Seed Initiative and the Organic Seed Partnership distributed these seeds to interested growers across the country and within the Northeast. When the chef at a local on-farm restaurant started presenting Honeynut, things changed. Soon, High Mowing Seeds picked up the variety and doors opened. “We’ve had trials in places like Wisconsin. The growers there initially thought it was odd and strange, but they tasted it, then it started to take off,” says Mazourek.

Despite the variety’s initial success, Mazourek’s team has received requests for powdery mildew resistance and longer storage. Honeynut doesn’t get diseases in storage, as many squashes do; instead it dries out. To address these concerns, the breeders are crossing Honeynut with several other exceptional butternuts, early butternuts and compact butternuts to come out with Honeynut 2.0.

High-tech + tradition = look, don’t touch

In this phase of development, Cornell’s breeders are merging high-tech with traditional methods. All the breeding in Mazourek’s lab involves the techniques that the origins of agriculture were based on. “The thing we do that’s more advanced is our look-don’t-touch approach to the genome,” he explains.

Until recently, genetic testing and genome identification were mainly used in transgenic breeding. Transgenic breeding (also known as genetic engineering or GMO) involves isolating the DNA, taking the exact piece of DNA desired and inserting it back into the same plant or another organism. The process removes the gene in an artificial way. Reinsertion of the gene is semi-natural, as it involves bacteria that naturally move genes.

“We do think it’s wonderfully cool to be able to see what makes the plants tick inside,” says Mazourek. While he revels in the technological advancement, he uses genetic testing only to see the genetic makeup of a crop and to develop new tests that identify other traits. He elaborates, “We’re not using it to make the changes, but we’re using it to sift through the plants we have and be able to identify the plants we want.”

In one of Cornell’s other fields, Mazourek and his team are doing some crosses with peppers; some are hot and some aren’t. Since strong disease resistances come from wild, very hot peppers, and the breeder is not interested in burning his mouth in hundreds of taste tests, he uses genomics to protect himself. First, he segregates the population by whether or not the peppers are hot. Next, while the plants are still in the transplant trays, Mazourek snips off a small part of the leaf and conducts a DNA test on it to see whether it has the traits that make it spicy, pleasantly flavorful, etc.

Mazourek does a lot of work in peppers for flavor, novelty and disease resistance. He also works on winter squash, snap peas, summer squash, cantaloupes and cucumbers. His students find his multitask approach to breeding amusing. Most breeders focus on one crop at a time, sometimes one crop for their entire career. Mazourek chooses to focus on the fungal resistance or novel quality traits that can boost consumption, rather than specific crops.

The breeder has found a couple of intriguing plots in 2012’s Honeynut patch that he and his team will plant again in 2013. If one of those crosses is as promising as Mazourek expects, it will probably be released for grower trials in the next year, and then released to seed companies in 2014 or 2015. That could make Honeynut 2.0 commercially available as soon as 2016.

Until then, interested growers should watch for Honeynut 1.5, aka Amber Delight. This is a hybrid between Honeynut and another disease-resistant squash that seems to have married the best of both together. Mazourek anticipates the official release of Amber Delight in the horticultural journals in spring 2013. From there, it’s up to seed companies to pick up the variety and make it commercially available.

The author is a freelance writer based in Massachusetts and a monthly contributor to Growing.