The Physalis Improvement Project: blending research with community science

Abstract

The Physalis community science project shows how citizen science not just communicates with and engages people in research but also how it can inform and benefit the professional scientists.

The Physalis Improvement Project is an offshoot of our previous research on tomato to study the genetic control over plant growth, fruit size, and inflorescence architecture (Xu et al, ²⁰¹⁵). We used a reverse genetics approach using CRISPR/Cas to knock out gene expression followed by evaluation of the resultant phenotypes. Through this work we realized a great potential for CRISPR/Cas gene editing to fast‐track domestication of underutilized plant species to make them viable for agricultural production. To put this idea into practice, we chose to stay within the Solanaceae family—of which tomato is a member—and focus on a species that has had so far experienced little if any improvement through plant breeding. We chose to work with Physalis peruviana and P. grisea because, in addition to answering basic fundamental research questions, we believed there was untapped agricultural and economic potential of these fruit in the USA. However, both would require further improvements for agricultural production.

P. peruviana is commonly known as goldenberry (Fig 1) and P. grisea as groundcherry (Fig 2) because the ripe fruit fall off and need to be gathered from the ground. They can be grown in a wide variety of soil types with successful crop production even under poor, sandy conditions (Wolff, 1991). Goldenberry and groundcherry produce attractive, sweet, highly nutritious yellow to orange‐yellow berries surrounded by an inflated calyx (husk) (Fig 1). The fruit is mostly consumed fresh, although it can also be used to make jams, pies, juices, raisins, and snack products. Both have great potential as nutraceuticals or functional foods because the fruit is an excellent source of beta‐carotene, vitamin C, and vitamin B complexes, and they are rich in minerals (zinc, iron, magnesium, and phosphorous) and phytosterols (Ramadan & Morsel, 2003; Rodrigues et al, ²⁰⁰⁹; Shenstone et al, ²⁰²⁰). In addition, goldenberry and groundcherry also have untapped agricultural and economic potential, especially in the USA.

Figure 1. Goldenberry and groundcherry fruit surrounded by the typical inflated calyx (husk).

(A) Goldenberry. (B) Groundcherry.

Figure 2. Images from community scientist events.

(A) Coffee mugs given as thank you gifts in year 1. (B) Foods prepared with goldenberries and groundcherries by event participants. (C) Informational signage and fruit for taste testing at a local farmers market. (D) Reusable tote bag given as a thank you gift in year 2.

Establishing a community science program

As part of the Physalis Improvement Project, we needed firsthand information and experience from farmers and home gardeners growing goldenberry and groundcherry to help identify any undesirable characteristics that might prevent them from being adopted. In addition, we also believed that engagement with farmers and consumers would heighten the visibility of these plants. We therefore established a community science program to gather firsthand feedback in parallel with our research. It would give us access to a large amount of data across different growing regions and conditions that would not be possible to gain by our small research group.

Community science, also referred to as citizen science, engages volunteers from the general public to collect information beyond what is realistic for a single scientist or research group to accomplish. For example, a single scientist cannot possibly document the presence of a particular insect species in more than 200 locations every day, but 200 community scientists reporting to the scientist can. In turn, community scientists gain an understanding and appreciation for the scientific process. There are many opportunities for participation in various community science projects that are open for people of all ages and backgrounds.

…great potential for CRISPR/Cas gene editing to fast‐track domestication of underutilized plant species to make them viable for agricultural production.

During the first season of our community science program, we worked with 11 farmers in different counties in New York State that represented multiple geographical regions to investigate the effects of different growing conditions. These sites included traditional and organic practices, as well as high tunnel operations—low‐cost greenhouse systems where plants are grown directly in the ground—that are used to extend the growing season (Lamont, 2009). It is critical to invite growers’ input at an early stage and we therefore visited all the farms during the growing season to learn directly from the farmers about the traits they find attractive or unattractive to help focus our improvement efforts.

In addition, we had another 40 participants who represented home gardeners and public gardens. This first season we provided either plants or seeds of three different types (accessions) of each goldenberry and groundcherry. However, as the number of community scientists grew in subsequent years, we provided only seeds. We also gave them background information on each of the six accessions and best practices for growing them. All participants received surveys for entering their feedback on characteristics that included plant growth habit, fruit size, fruit drop, harvest times, flavor, diseases, and insect pests.

…we believed there was untapped agricultural and economic potential of these fruit in the USA.

To foster and sustain their engagement, we created a website with a blog (https://btiscience.org/our‐research/bti‐physalis‐project‐2/) as well as a Facebook page and Twitter account (@PhysalisProject). At the end of the season, we hosted a “Physalis Harvest Event” for participants to share their experiences and gave them a gift of a coffee mug (Fig 2A). Attendees were encouraged to bring food prepared with their goldenberry and groundcherry harvests: muffins, rice pudding, fruit compote, and granola with dried goldenberries (Fig 2B).

Expanding the number of community science participants

We continued the project for a second growing season to expand to other regions in the USA with approximately 65 participants from NY State and 17 other US states. In addition to groundcherry and goldenberry, we provided seeds from green and purple tomatillo to keep it interesting for the participants from the first year. One of the participants was a public garden that sponsors a summer camp for children who were responsible for taking data and observations on the groundcherry, goldenberry, and tomatillo plants. We visited the campers to get firsthand information and to tell them about our research. We also held an event at a local farmers market where we distributed educational materials about Physalis and offered a taste testing of goldenberry and groundcherry (Fig 2C). As in the first year, we hosted a harvest event that included arts and crafts activities for children, foods prepared with Physalis, presentations about our research, and an opportunity for participants to share their experiences. This time we gave reusable tote bags as thank you gifts (Fig 2D).

During the second year, we conducted a sensory evaluation in collaboration with Cornell University’s Sensory Evaluation Center with fruits from our field program to obtain data related to consumer preferences. A total of 102 participants from the local community were queried on characteristics such as flavor, color, size, and preference for fruit with or without the surrounding husk. These data have been key in focusing our efforts for desirable fruit characteristics. An additional benefit of the sensory evaluation is that the consumer preference information will serve as preliminary data for future grant proposals.

…we needed firsthand information and experience from farmers and home gardeners growing goldenberry and groundcherry to help identify any undesirable characteristics that might prevent them from being adopted.

Despite the pandemic, we were able to continue our community science project for a third season in 2020. In fact, several participants commented that having such an activity was a helpful diversion from the impact of COVID‐19. We had the largest group of participants with 750 participants from 43 different US states including Alaska and Hawaii, partly in response to an article about the project in the LA Times (Marantos, 2020). About 1400 people contacted us but we had to limit the number of participants to 750 because of the amount of seed available. These new community scientists enjoyed being part of the project and many had never heard of or eaten goldenberries or groundcherries.

Information gathered from community scientists

During the 3 years we received consistent feedback regarding the traits participants favored and those viewed as problematic. We learned that the wild, unmanageable growth habits made goldenberry and groundcherry challenging to grow both on a larger scale as well as in small gardens and pots on patios and decks. Based on our and others earlier work with tomato, we identified several candidate genes in goldenberry and groundcherry and used CRISPR/Cas to target three of these to modify plant growth habit in separate experiments. After genotyping lines for the intended edits, phenotypes of the E0 (first generation) are evaluated and plants with the desired growth habit modifications are self‐pollinated. Subsequent generations are genotyped for the expected edits, evaluated for growth habit, and analyzed for the presence or absence of Cas9.

It would give us access to a large amount of data across different growing regions and conditions that would not be possible to gain by our small research group.

Depending on where the community scientists lived, some had a good harvest of goldenberries, but others had only a few fruits or none at all by the end of the growing seasons indicating varied maturity time. Feedback also highlighted flavor preferences, which helps us focus on those traits that consumers would be most likely to purchase. Many of the community scientists liked the flavor of the groundcherries and the amount of fruit produced, but said the fruit drop at various ripening stages makes harvesting difficult and increases the risk of food‐borne illness when fruits have to be gathered from the ground. The reason for the fruit drop is a joint or abscission zone in the pedicel, and we are now studying gene expression in and cellular development of the pedicel with the aim to modify growth of that region to prevent abscission. To date, we have done RNA‐seq analysis of the abscission zone at three developmental stages—early, middle, and late—and are mining the data for potential target genes.

Insect interaction project

An additional problem revealed through the community science program during the three seasons was significant insect predation on goldenberry. We and our community scientists observed that the adult three‐lined potato beetle (Lema daturaphila) would lay eggs on both the groundcherry and goldenberry plants. The larvae fully developed and caused significant damage on goldenberry plants (Fig 3) but not on groundcherry. The other insect that caused damage on goldenberry was the subflexus straw moth (Chloridea subflexa), although it was not as prevalent across regions as the potato beetle. The moth is a specialist insect on Physalis that feeds on the fruit and causes extensive damage which makes the fruit unmarketable. As with the three‐lined potato beetle, the subflexus straw moth was not a problem on groundcherry.

Figure 3.

Three‐lined potato beetle (Lema daturaphila) larvae feeding on a goldenberry leaf.

As a result of this information, we added a new area of investigation to our Physalis improvement program focused on insect interactions. Plants in general employ morphological defenses against insects such as latex production, leaf toughness, and a greater number of trichomes (Howe & Jander, 2008). Their biochemical defenses include specialized metabolites that are toxic or affect a developmental stage of the insect life cycle (War et al, ²⁰¹⁸). We are now analyzing the metabolite differences between goldenberry and groundcherry to identify those that might be responsible for the insect interactions. The current focus is on withanolides, which are steroidal compounds that have been reported to be involved in insect interactions in the Physalis. Our goal is to identify the specific withanolides in groundcherry that fend off both the three‐lined potato beetle and C. subflexa. We are again using CRISPR/Cas9 to create loss‐of‐expression mutants for selected genes in the withanolide pathway. These mutants will be evaluated for withanolide content and challenged with the insects at different insect developmental stages. As the work progresses, we plan to investigate additional factors that either separately or synergistically with withanolides might be responsible for the differences in insect interactions between goldenberry and groundcherry. The results could again contribute to future breeding programs focused on insect resistance.

Science communication for community engagement

As a new activity during the third season, we built relationships with local chefs to expand our educational reach by providing fruit, background information on these species, and a few recipes. We hoped it would also increase market demand for locally sourced agricultural products and in doing so provide additional income for farmers. We learned from chefs that the best way for farmers to connect with them is to show up at the back door of their restaurants with produce, and that is what we did even if this was somewhat difficult owing to the pandemic. In lieu of a more extensive network of chefs who could create recipes, we invited a Cornell graduate student who is an avid baker to develop some recipes with fruit we provided—she posted her creations on Instagram and we invited her to blog about her recipes (https://btiscience.org/groundcherries‐galore‐what‐to‐do‐with‐all‐the‐fruits‐of‐your‐labor/).

Over the years, we have continued to develop our project website as a platform for science communication. Part of the communication has been through the blog, which has now 800 subscribers. Through our website and the blog, participants can not only follow the progress of the project but also learn about other aspects of plant biology and crop improvement. Subscribers can post comments and questions to our research group. We have received much feedback on their experiences growing groundcherry and goldenberry including photos of insects found on their Physalis and general questions related to the species.

The blog series also provides opportunities for undergraduate and graduate students and postdocs to gain experience in science communication and realize the importance of engagement with the general public to promote an understanding of science. They provided blog posts on subjects such as pollinators, what makes tomatillos sticky, aquaponics, and recipes from goldenberries and groundcherries. We also added a series called “Approaches for Crop Improvement” about plant breeding, mutagenesis breeding, and genome sequencing. Future posts will include background information on how genetic engineering and gene editing can contribute toward crop improvement.

During the three years we received consistent feedback regarding the traits participants favored and those viewed as problematic.

Establishing a community science program that allowed us to build relationships with farmers and the general public early in our research provided an excellent opportunity to gain firsthand information about what they liked, but more importantly, did not like about growing goldenberry and groundcherry. Their responses show a clear interest in expanding production if several problematic characteristics were corrected such as their wild, unmanageable growth habit, delayed maturity, and low productivity of goldenberry, fruit abscission of groundcherry, and insect predation. In collaboration with Zach Lippman at the Cold Spring Harbor Laboratory and Michael Schatz at Johns Hopkins University, we are now implementing a multifaceted approach that combines plant breeding, genome sequencing, and gene editing to improve or eliminate undesirable characteristics of goldenberry and groundcherry (Lemmon et al, ²⁰¹⁸; Kwon et al, ²⁰²⁰). Our approach of organizing a community science program in parallel with technologies to fast‐track improvement, which in the case of underutilized species can be viewed as accelerating domestication, could provide a model or establish guidelines for taking underutilized species from the lab to the farm to market. This could have economic and ecological impact if it expands the number of plant species beyond what we currently rely on for agricultural sustainability.

Conflict of interest

The author declares that she has no conflict of interest.

EMBO reports (2022) 23: e53918.