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Vonnie Estes

The power of genetics and environment in indoor agriculture

August 31, 2022

Editor’s Note: Vonnie Estes is VP, AgFood Tech Innovation at the International Fresh Produce Association (IFPA) and a regular contributor to AFN – see her previous posts here. IFPA represents companies from every segment of the global produce and floral supply chain.

This week, IFPA announced the creation of a new council focused on controlled environment agriculture – also known as indoor farming – to focus on the opportunities presented by the technology stack for the fresh produce industry.

A key area of focus of Estes and her colleagues is how CEA could enable new varieties of crops to bring better taste and characteristics for consumers, as she writes below.

In a world starved for water and arable land, where the notion of “food miles” conjures not only activist consumers, but also logistical challenges as well as rising fuel costs, the potential in CEA is seemingly massive. It represents a $50 billion market opportunity driven by the demand for fresh, local, sustainable produce year-round. The vision of a CEA farm is high tech; with plants growing under lights, with advanced automation, and AI. But despite all of the advances in the software and hardware within the plant factory operation, innovation of the most complex machine has been neglected – the plant itself. How can a crop’s biology be manipulated for higher profits in this fast-growing market through breeding?

Ever since early farmers started collecting seeds for propagation, they focused on varieties that performed best under unpredictable field conditions, not for highly controlled environments. Specifically, crop plants exude up to 40% of photosynthate into the soil to “feed” beneficial microbes and allocate additional resources to produce secondary products (with an unpleasant taste or texture, by “design”) to ward off pests and diseases. Unlocking the maximum potential of the seed for precisely controlled environments, where every day is a good day, will allow breeders to focus on plant traits that are enhanced when grown indoors, and to deemphasize issues that would be of top concern for outdoor production. As we get more control of the environment, we can design crops with traits to delight the consumer and improve the supply chain.  

What to breed for

Marc Oshima, co-founder of AeroFarms says, “For vertical farms, breeders can shift their focus to qualities of primary importance to consumers: taste, aroma, texture, and other attributes related to quality. It is also important to have plants that are efficient in their architecture, such that they can be easily maintained and harvested in our unique environment.”

The biggest breeding targets for field-grown fruits and vegetables are for disease resistance. Breeders are on a treadmill to stay ahead of the next disease in the field. It is not a matter of just swapping out disease-resistant genes for genes that confer good flavor, but CEA does allow breeders to not have to stay ahead of the next potentially devastating outdoor disease. Some diseases like powdery mildew are possible indoors but can often be controlled through management practices.  

The focus of breeding can shift to developing and accelerating the discovery of new crops, growing recipes, and efficiency improvements that can be replicated at a scale specifically designed for indoor systems. These changes benefit both producers and consumers. Growers will benefit from traits that allow for longer-lasting produce, quality, faster growing, and beneficial architecture. At the center of trait development for consumers is satisfying the need for flavor, taste, color, texture, and nutrition.

Scientists and entrepreneurs are speculating about the many possibilities of growing indoors like producing pharmaceuticals in plants, increasing the amount of specific nutrients and/or bioactives, higher protein, food for personalized diets to name a few.

Although there are many future possibilities for nutrition and health, at IFPA we want to encourage people to eat more produce NOW which will improve health!  

Who is breeding?

CEA growers are mostly not doing their own breeding. But breeding for indoor ag has been underserved by big seed companies. Bayer Crop Science saw this need. In 2020 Bayer Crop Science and Temasek formed Unfold as a separate company to serve the breeding needs of indoor farms. Unfold is offering seeds to all indoor farms and recently joined forces with Bowery Farming to accelerate the development of new plant varieties specifically for the vertical farming industry.  

Using a different business model, Kalera, one of the fastest-growing US vertical farming companies acquired Vindara a company that develops seeds designed for vertical indoor farm environments. Vindara is a fully owned subsidiary of Kalera. Dr. Jade Stinson, cofounder and president says she is breeding for a variety of traits across different crop programs. A few of the desired traits for agronomy are yield and architecture. Hedonic traits are flavor, color, and texture. They are also exploring phytochemicals for nutrition.  

Most CEA farms are looking to collaborate with outside breeders, universities and/or seed companies. Aerofarms has several active collaborations with outside breeders working with public, university, and commercial breeding programs. They are currently evaluating multiple third-party breeders’ proprietary plant genetics for strawberry and hops for suitability in fully controlled growing environment. As a founding member of the Precision Indoor Plants (PIP) consortium, AeroFarms is the Principal Investigator for the first project to co-optimize conditions for lettuce. AeroFarms joins project collaborators at Cornell, and other universities, as well as government agencies such as NASA, Department of Energy, and USDA. 

Sakata Seed America is an example of a progressive seed company working in controlled environment agriculture. In 2019, Sakata began to focus on existing genetics that showed promise for the indoor market. Now they are partnering with key indoor growers to trial Sakata genetics. They are breeding lettuce, arugula, basil, chard, beet greens, mustard, and pak choi to be used now and to start next-gen breeding projects. Breeders are looking for optimum yield, advantageous plant architecture, and flavor, color, and texture. Sakata is working through strategic collaborations with their genetics to supply quality seed to the sector.

Beyond leafy greens, strawberry is one of the crops getting the most interest in vertical farms. In October 2020, a joint project was announced between vertical farm Plenty and Driscoll’s. They are using Driscoll’s proprietary genetics and berry expertise with Plenty’s indoor farming technology and plant science expertise to grow and study Driscoll’s branded berries.

Scott Komar, senior VP of Global R&D at Driscoll’s says, “We have the largest portfolio of genetics to pull from and optimize for Plenty’s indoor growing environment, which gives us a significant advantage and head start over other smaller, less diversified breeding programs.” They are excited to see the initial fruition of the collaboration and look forward to expanding the relationship with a new vertical farm in the Northeastern US.

Breeding Tools

What tools are breeders using to breed for controlled environment agriculture? The genetics and breeding history in fruits and vegetables are not as well developed as in many of the row crops and there are a huge number of crops.

But we are catching up.

Breeders are using advanced breeding tools to meet the market need for produce that is nutritious, high-yielding, and delicious.  Tools at their disposal are genomics and computational biology, analytics and deep machine learning along with more traditional breeding methods like marker-assisted breeding and introgression. 

Many companies and breeders are interested in gene editing as a tool to make breeding quicker and more precise. In an uncertain global regulatory environment, most breeders are using gene editing as a breeding tool in non-commercial lines to find genes of interest quickly, to see what’s possible. They then can develop a similar trait using time- and resources-demanding traditional breeding.  Aside from a tomato producing higher levels of health-promoting gama-aminobutyric acid (which entered Japanese market last year), no gene-edited produce is currently in grocery stores today anywhere. Given that US consumers continue to be excited about bioengineered pink pineapple, non-browning apples and disease-resistant papaya, the future of gene-edited produce should be bright as well. 


With the market’s rapid growth, breeders and growers alike are placing a greater emphasis on developing varieties best suited for indoor production.

Focusing on the biology of the crop allows for the opportunity to create step changes in agronomic traits to improve unit economics, more consumer-focused traits create differentiated products, and ultimately for crops to be grown all year round that may not grow outdoors due to climate pressures.  

Dedicated breeding for vertical farms is a vast untapped opportunity. We are only at the beginning of learning how much is possible in breeding for indoor growers. 

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