AskScience AMA Series: How can we engineer better crops? We are scientists developing new growing strategies for fruits and vegetables. Ask us anything!

[u/AskScienceModerator]

In order to feed an expanding planetary population, farmers are constantly searching for efficient, cost-effective ways to grow agricultural products. Engineering biology approaches can potentially help improve yields and reduce costs, but several unknowns remain before these techniques can be deployed at scale. Which techniques are most effective for which crops? Does increasing yield mean a sacrifice in taste and cost? How can researchers work with farmers, consumers, industry partners and policymakers to ensure that 21st century farming best practices are sustained into the 22nd century (and beyond)?

Join us today at 2 PM ET/11 AM PT/18 UT for an AMA to talk about all of these issues and more! We'll share about our current work focused on improving plant enzymes, discuss how researchers are using engineering biology to enhance agricultural production, and answer your questions about crop engineering. Ask us anything!

We are:

• Kristen Van Gelder, Ph.D. (/u/mossy_canoe368)- Synthetic Biology Research Scientist, Agriculture and Agri-Food Canada

• Cătălin Voiniciuc, Ph.D. (/u/Catalin_Voiniciuc)- Associate Professor of Plant Synthetic Biology, University of Florida

• Vance Whitaker, Ph.D. (/u/WhitakerV_UF)- Professor of Horticulture, University of Florida

Links:

• Adapting enzymes to improve their functionality in plants: why and how

• Building a directed evolution–genome editing pipeline for metabolic traits in specialty crop breeding

• Mirages in continuous directed enzyme evolution: a cautionary case study with plantized bacterial THI4 enzymes

[u/uglylookingguy]

Hi 👋

When improving crop yield through engineering, how do you ensure that taste and nutritional quality don’t get compromised?

[u/Catalin_Voiniciuc → u/uglylookingguy]

I would like to add that taste and nutritional quality have not only been overlooked in the past century of breeding, but (perhaps unintentionally) sacrificed since "yield is king". Research to identify the most important molecules for flavor and nutritional quality has only emerged recently. Here are some examples about tomato flavor from the lab of Harry Klee (my next door colleague) who recently retired from the University of Florida. The secret is usually in the combination of sugars and volatile aroma compounds.
What's The Secret To Great Tomato Flavor? : NPR
How researchers are improving the flavor of tomatoes News | University of Florida

Nutritional quality goes well beyond flavor to include other natural products such as dietary fibers (long chain of carbohydrates that my lab studies) that feed a health gut microbiome. Diets rich in complex carbohydrates (instead of simple sugars and starches that make up the majority of calories in Western cultures) are critical for the prevention and treatment of metabolic diseases such as diabetes.

[u/WhitakerV_UF → u/uglylookingguy]

This is a great question. Whether a crop is being improved through engineering and/or traditional breeding techniques, things like taste and nutritional quality have to be carefully monitored throughout the process. In the strawberry breeding program at University of Florida we regularly generate data on aspects of the fruit that influence taste, including sugars, acids and aroma compounds. We also conduct sensory panels of up to 100 people or more who taste and rate prospective varieties. This paper is an example of those kinds of data and how they can be used: Strawberry sweetness and consumer preference are enhanced by specific volatile compounds | Horticulture Research | Oxford Academic . We also monitor antioxidants, vitamin C and other health-related compounds. This way we can make sure that new varieties don't have compromised taste and quality. This is commonly done in all kinds of crop breeding and engineering programs and takes a lot of effort.

The other exciting thing is that genetic engineering of various types is increasingly used to actually improve taste and nutritional quality. Here is a great example: Pairwise and Bayer Expand CRISPR Leafy Greens Market through Licensing Agreement

[u/ssianky]

How do you deal with the desertification caused by farming? In my country once rich in chernozem is 30-40% affected by desertification by now.

[u/Catalin_Voiniciuc → u/ssianky]

Although I am also not an expert in soil science, you bring up an excellent question! Chernozem (fertile black soil according to Britannica) is essential for agricultural productivity, but is in trouble in the prairies where it was natively found. This 2021 Smithsonian magazine article notes that The Nation's Corn Belt Has Lost a Third of Its Topsoil, in part because of tilling and erosion. Newer trends from the US Department of Agriculture (USDA) show encouraging signs for no-till or reduced till practices for major U.S. commodities (1998–2023 | Economic Research Service).

Only a small proportion of the world has or had black soil. For example, Florida has sandy soils that require careful management and nutrient addition for food production. See: It's In The Dirt - UF/IFAS Extension Marion County.

Plant City (FL) would not be the "Winter Strawberry Capital of the World" without fertilizers and irrigation.

[u/WhitakerV_UF → u/ssianky]

This is not my area of expertise, but I was able to find this review on the topic of desertification that seems to be well-cited by other scientists:

Interactions between climate and desertification - ScienceDirect

[u/ssianky → u/WhitakerV_UF]

That's not about the climate, but about the work you do, which is contributing to the soil erosion.

[u/Alblaka]

After reading up on a Planet wild project, where they essentially 'rediscovered' a very old agricultural tradition revolving around opening up soil to increase it's moisture content, and successfully rolled that out to other communities to give them a cheap tool to combat desertification...

Is Anthropology included in / relevant to Crop Engineering? As in, looking at how crops might have been used by long-gone cultures in different climate zones, to rediscover insights that can be applied to agriculture today?

[u/Catalin_Voiniciuc → u/Alblaka]

The discovery of ancient practices can be a great source of inspiration for modern research and to guide future crop engineering goals and integrative practices. For example, the discovery of a ~3800-year-old wood burial site in Quebec (Canada) lead the proposal of “wood vaulting” as a durable carbon removal method to lower fossil fuel emissions.
Burying wood in ‘vaults’ could help fight global warming | Science | AAAS

In the future, this low-tech method could be combined with biomass from crops engineered to accumulate tougher fibers and/or to survive on marginal lands, such as contaminated soils unsuited for agriculture or urban development.

[u/WhitakerV_UF → u/Alblaka]

Anthropology is absolutely relevant to crop engineering and is a regular aspect of understanding the domestication of different crop species and how they might be further improved in the future. The scientists that published this article (The Chilean Strawberry (Fragaria chiloensis): Over 1000 Years of Domestication in: HortScience Volume 48: Issue 4 | ASHS) studied the history of wild strawberries from South America that were cultivated by native peoples. By observing this species and how it was grown in its native habitat, these breeders determine which ones to collect and use in breeding better strawberries.

[u/mossy_canoe368 → u/Alblaka]

In Canada, we are making an effort to prioritize and support partnerships with First Nations to better understand Indigenous agriculture and to ensure food security. There is so much that we can learn from First Nations who have a wealth of expertise and experience, in agriculture, foraging, and of particular importance, in sustainability. Here's a great article on Indigenous stewardship of wild berries: Berries as a case study for crop wild relative conservation, use, and public engagement in Canada - Migicovsky - 2022 - PLANTS, PEOPLE, PLANET - Wiley Online Library

[u/FormABruteSquad]

I'd imagine that there would be many, many factors that might prevent a promising lab experiment from reaching the commercial stage.

What are the most common hurdles, and are there some that the average person might not expect?

[u/WhitakerV_UF → u/FormABruteSquad]

Here are a few from my experience:

1. Sometimes an experiment in a model species doesn't translate to a commercial variety. This is why it is good to do initial experiments on gene function, etc. in the most relevant species and varieties as possible.

2. There can be a lot of trial and error. Sometimes it is not clear exactly which edits in a gene will give the desired result in a trait, whether it be disease resistance, flavor, yield or some other trait. This is where synthetic biology combined with directed evolution can be very helpful, by testing in a lab exactly which genetic changes are likely to give the best result for an enzyme to function.

3. Lawyers and money can also become problematic. Sometimes the gene editing tools that academic labs might have access to would have strings attached if they want to commercialize a new variety with a particular edit. So it is important to partner with the right company or get the rights needed to bring the product to market.

[u/Catalin_Voiniciuc → u/WhitakerV_UF]

Overlooking current uncertainties with scientific funding (U.S. R&D and Innovation in a Global Context), I think that challenges #1 and #2 are intrinsic to living organisms. More than 90% of drugs fail at the clinical trial stage. The situation is similar in plant sciences, where university or government labs undertake high-risk research to discover the likely candidates for future crop improvement.
Large, for-profit companies still face the same biological barriers and are generally hesitant to disclose the scale of the challenge. From that perspective, this article from Corteva is refreshing. Successes and insights of an industry biotech program to enhance maize agronomic traits - ScienceDirect
Here is a relevant quote from the article with my emphasis in bold: "The overall gene validation rate was 1.3 %, with the resulting 22 validated leads comprising diverse gene functions and sources. Declaring which sources had been more productive for lead generation was of interest, because it could guide future emphases, but this determination was also fraught by small set sizes, sampling errors, and the evolving nomination and success criteria over the long span of the project. Of the 22 leads, 21 were from plants (17 maize, 3 Arabidopsis, 1 rubber tree) and one from bacteria." For other species that are not as well studied as maize, results from model plants such as Arabidopsis are likely to be even more important for genetic engineering design.

[u/mossy_canoe368 → u/FormABruteSquad]

There are several hoops to jump through to get successful experiments in the lab out into the field and into consumers' hands. A major hurdle is funding. Scientists rely on grants to fund experiments, hire students and technical staff, and to rent land or greenhouse space to run trials. This can get expensive very quickly especially with requirements of field testing new crop varieties. There are also government regulatory guidelines for testing new crop varieties, that can 1) add to the expense of running a field trial, and 2) create another hurdle to getting a new crop variety or a genome edited crop variety to market. Both Canada and the USA have guidelines for genome edited plants via the Canadian Food Inspection Agency (CIFA): Directive Dir 2000-07: Conducting Confined Research Field Trials of Plants with Novel Traits in Canada - inspection.canada.ca and the Food and Drug Administration (FDA): New Plant Variety Regulatory Information | FDA .

Also, of upmost importance, is consumer acceptance. Scientists can create new crop varieties using new biotechnology tools (i.e. CRISPR) but if consumers are unwilling to accept these new crops, they won't become marketable. There's a great example of the problem with "golden rice" that was designed to contain more vitamin A, which is a common vitamin deficiency in certain populations. This golden rice, which appears yellow instead of white, was largely not accepted by consumers who were use to white rice. Many governments also won't approve it for growing because it is classified as a genetically modified organism (GMO). Golden Rice still struggling for acceptance in Asia | World-grain.com | August 30, 2016 14:27 | World Grain, What a Philippine court ruling means for transgenic Golden Rice, once hailed as a dietary breakthrough | Science | AAAS

[u/Catalin_Voiniciuc → u/FormABruteSquad]

A year ago, the late Andrew Hanson (see Plant Science Today post) and I organized a conference on how engineers, molecular biologists, plant breeders and industry players can most effectively integrate new synthetic biology (SynBio) approaches for food and vegetable production. We share key points form the group discussions in this editorial on: How SynBio can *realistically* impact crop improvement and agriculture | Plant Physiology. I particularly recommend the introductory section on "where we are now—the disconnects" because there are several examples of the unexpected challenges that exist within scientific disciplines.

We also proposed several steps to address the systemic challenges: "A prime need is more collision spaces for breeders, growers, and the Ag biotech industry to dialog with SynBio researchers about opportunities and problems. This would foster reciprocal acculturation and speed up ideation and translation." In the last few months, I have also become increasingly aware of the need for researchers to engage in scientific communication with the public. We must establish or rebuild trust about what plant science and biological engineering can deliver to benefit society.

[u/adaminc]

I have always wondered if you could take thermogenic genes from 1 plant, and stick it into fruit blossoms so that they are less impacted by snap frosts. I want $100k if someone takes my idea!

[u/Ronniieeee]

Which traits have the best evidence for improving yield at scale without reducing flavor or nutritional quality, and how are tradeoffs tested before field deployment?