Tag Archives: Cold Spring Harbor Laboratory

Designer groundcherries by CRISPR (clustered regularly interspaced short palindromic repeats)

I love the little things.. Groundcherries are just the right combination of sweet and tart.

Courtesy of Boyce Thompson Institute

They’re not in the stores very often and I wondered about that. Luckily, an  October 1, 2018 Boyce Thompson Institute news release by Mike Carroll (also on EurekAlert) explains why that is and how scientists are trying to overcome the difficulties,

You might not have heard of the groundcherry, or at least, never tasted one. But that could soon change thanks to research from the Van Eck Laboratory at Boyce Thompson Institute (BTI).

The groundcherry (Physalis pruinosa) is approximately the same size as a cherry tomato, but with a much sweeter flavor. The tropical-tasting fruit is also a powerhouse in terms of nutritional value. Packed with Vitamin C, Vitamin B, beta-carotene, phytosterols, and antioxidants, plus anti-inflammatory and medicinal properties, this tiny fruit might just be the next superfood.

“We feel there is potential for these to become a specialty fruit crop and to be grown on a larger scale in the US,” said Joyce Van Eck, associate professor at BTI.

However, even with their delicious flavor and nutritional value, groundcherries remain an underutilized crop in the United States. Several characteristics make them unsuitable for large-scale agriculture. [emphasis mine] In the October 1, 2018 issue of Nature Plants, Van Eck and colleagues present research which could change that and make groundcherries a common household name thanks to the genome editing tool CRISPR.

CRISPR has great promise for increasing crop productivity, especially for orphan crops such as groundcherries, which often contain undesirable characteristics resembling wild relatives. Leveraging knowledge from model crops (such as the tomato) can improve plant architecture (growth habit), flower production, fruit size, and more.

Selections for mutations in tomatoes have led to improvements in yield and Van Eck and her collaborator, Zach Lippman, at the Cold Spring Harbor Laboratory hypothesized that groundcherry genes could be similarly modified for immediate improvements. One concern with the groundcherry is its weedy growth habit. Genetic alterations have led to changes in the hormone that regulates flowering, producing plants which are more compact with fruit in clusters. They also targeted ways to increase fruit size and weight [emphases mine] through a CRISPR-generated mutation, leading to fifty-percent more fruit along a given stem and more seedy sections in each fruit.

“It’s exciting that we can take what we have learned in tomato and apply it to distantly related species,” said Van Eck.

Van Eck is also focused on fixing problems caused by fruit drop. [emphasis mine] Groundcherries drop to the ground, often before fully ripening.

This puts the fruit at risk for damage and creates a labor-intensive harvest process. In addition, fruit having to be gathered up from the ground causes concerns for food safety with potential for foodborne illness. A jointless mutation in tomatoes could provide the inspiration for using gene-editing to stop fruit drop in groundcherries.

“Physalis is the perfect candidate for looking at getting the fruit to not drop,” said Van Eck. “Gene editing might be the only way to fix this in the groundcherry.”

This study represents the first step towards improving the groundcherry and this work could be extended to target additional genes benefiting a range of consumer desirable traits.

Veronique Greenwood wrote an October 6, 2018 article for the New York Times about the scientists and the work featured in the October 1, 2018 issue of ‘Nature Plants’ and two scientists from Van Eck’s lab, Nathan T. Reem and Esperanza Shenstone, have written a November 14, 2018 essay about the work for The Conversation (h/t phys.org).

Here’s a link to and a citation for the research paper,

Rapid improvement of domestication traits in an orphan crop by genome editing by Zachary H. Lemmon, Nathan T. Reem, Justin Dalrymple, Sebastian Soyk, Kerry E. Swartwood, Daniel Rodriguez-Leal, Joyce Van Eck, & Zachary B. Lippman. Nature Plants volume 4, pages766–770 (2018) DOI: https://doi.org/10.1038/s41477-018-0259-x Published: 01 October 2018

This paper is behind a paywall.

CRISPR corn to come to market in 2020

It seems most of the recent excitement around CRISPR/CAS9 (clustered regularly interspaced short palindromic repeats) has focused on germline editing, specifically human embryos. Most people don’t realize that the first ‘CRISPR’ product is slated to enter the US market in 2020. A June 14, 2017 American Chemical Society news release (also on EurekAlert) provides a preview,

The gene-editing technique known as CRISPR/Cas9 made a huge splash in the news when it was initially announced. But the first commercial product, expected around 2020, could make it to the market without much fanfare: It’s a waxy corn destined to contribute to paper glue and food thickeners. The cover story of Chemical & Engineering News (C&EN), the weekly newsmagazine of the American Chemical Society, explores what else is in the works.

Melody M. Bomgardner, a senior editor at C&EN [Chemical & Engineering News], notes that compared to traditional biotechnology, CRISPR allows scientists to add and remove specific genes from organisms with greater speed, precision and oftentimes, at a lower cost. Among other things, it could potentially lead to higher quality cotton, non-browning mushrooms, drought-resistant corn and — finally — tasty, grocery store tomatoes.

Some hurdles remain, however, before more CRISPR products become available. Regulators are assessing how they should approach crops modified with the technique, which often (though not always) splices genes into a plant from within the species rather than introducing a foreign gene. And scientists still don’t understand all the genes in any given crop, much less know which ones might be good candidates for editing. Luckily, researchers can use CRISPR to find out.

Melody M. Bomgardner’s June 12, 2017 article for C&EN describes in detail how CRISPR could significantly change agriculture (Note: Links have been removed),

When the seed firm DuPont Pioneer first announced the new corn in early 2016, few people paid attention. Pharmaceutical companies using CRISPR for new drugs got the headlines instead.

But people should notice DuPont’s waxy corn because using CRISPR—an acronym for clustered regularly interspaced short palindromic repeats—to delete or alter traits in plants is changing the world of plant breeding, scientists say. Moreover, the technique’s application in agriculture is likely to reach the public years before CRISPR-aided drugs hit the market.

Until CRISPR tools were developed, the process of finding useful traits and getting them into reliable, productive plants took many years. It involved a lot of steps and was plagued by randomness.

“Now, because of basic research in the lab and in the field, we can go straight after the traits we want,” says Zachary Lippman, professor of biological sciences at Cold Spring Harbor Laboratory. CRISPR has been transformative, Lippman says. “It’s basically a freight train that’s not going to stop.”

Proponents hope consumers will embrace gene-edited crops in a way that they did not accept genetically engineered ones, especially because they needn’t involve the introduction of genes from other species—a process that gave rise to the specter of Frankenfood.

But it’s not clear how consumers will react or if gene editing will result in traits that consumers value. And the potential commercial uses of CRISPR may narrow if agriculture agencies in the U.S. and Europe decide to regulate gene-edited crops in the same way they do genetically engineered crops.

DuPont Pioneer expects the U.S. to treat its gene-edited waxy corn like a conventional crop because it does not contain any foreign genes, according to Neal Gutterson, the company’s vice president of R&D. In fact, the waxy trait already exists in some corn varieties. It gives the kernels a starch content of more than 97% amylopectin, compared with 75% amylopectin in regular feed corn. The rest of the kernel is amylose. Amylopectin is more soluble than amylose, making starch from waxy corn a better choice for paper adhesives and food thickeners.

Like most of today’s crops, DuPont’s current waxy corn varieties are the result of decades of effort by plant breeders using conventional breeding techniques.

Breeders identify new traits by examining unusual, or mutant, plants. Over many generations of breeding, they work to get a desired trait into high-performing (elite) varieties that lack the trait. They begin with a first-generation cross, or hybrid, of a mutant and an elite plant and then breed several generations of hybrids with the elite parent in a process called backcrossing. They aim to achieve a plant that best approximates the elite version with the new trait.

But it’s tough to grab only the desired trait from a mutant and make a clean getaway. DuPont’s plant scientists found that the waxy trait came with some genetic baggage; even after backcrossing, the waxy corn plant did not offer the same yield as elite versions without the trait. The disappointing outcome is common enough that it has its own term: yield drag.

Because the waxy trait is native to certain corn plants, DuPont did not have to rely on the genetic engineering techniques that breeders have used to make herbicide-tolerant and insect-resistant corn plants. Those commonly planted crops contain DNA from other species.

In addition to giving some consumers pause, that process does not precisely place the DNA into the host plant. So researchers must raise hundreds or thousands of modified plants to find the best ones with the desired trait and work to get that trait into each elite variety. Finally, plants modified with traditional genetic engineering need regulatory approval in the U.S. and other countries before they can be marketed.

Instead, DuPont plant scientists used CRISPR to zero in on, and partially knock out, a gene for an enzyme that produces amylose. By editing the gene directly, they created a waxy version of the elite corn without yield drag or foreign DNA.

Plant scientists who adopt gene editing may still need to breed, measure, and observe because traits might not work well together or bring a meaningful benefit. “It’s not a panacea,” Lippman says, “but it is one of the most powerful tools to come around, ever.”

It’s an interesting piece which answers the question of why tomatoes from the grocery store don’t taste good.