DR.

KEVIN FOLTA (Orcid ID : 0000-0002-3836-2213)

Article type : Review Article

Accepted Article
Editor : A.Weber

Title: Breeding New Varieties for Controlled

Environments

Kevin M. Folta1,2
1
Horticultural Sciences Department, 1251 Fifield Hall, University of Florida, Gainesville, FL 32611
USA

2
Graduate Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL
32611

CORRESPONDING AUTHOR EMAIL: kfolta@ufl.edu

Abstract

Agricultural production in controlled environments is increasingly feasible, and may play an

important role providing nutrition and choice to growing urban centers. New technologies in lighting,
ventilation, robotics, and irrigation are just a few of the innovations that enable production of high-
value specialty crops outside of a traditional field setting. However, despite all of the advances in the
hardware within the plant factory operation, innovation of the most complex machine has been
neglected—the plant itself. Indoor agricultural operations typically rely on legacy varieties, plants
selected and bred for field conditions. In the field, phenotypic stability is paramount, as production
must be consistent in an unpredictable and changing environment. However, the controlled
environment affords focus on different breeding priorities, as environmental flux, pests, pathogens
and postharvest quality are less formidable barriers to production. To the contrary, breeding for
controlled environments shifts the focus to a completely different set of plant traits, such as rapid
growth, performance in low light environments, and active manipulation of plant stature. Instead of
breeding for phenotypic stability, plants may be bred to maximize genetic plasticity, allowing specific

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 traits to be presented as a function of the quality of the ambient light spectrum. In this scenario plant
varieties may be grown with optimal size, supporting a focus on consumer traits like flavor or
accumulation of health-related compounds. Gene editing may be a central technology in the
Accepted Article
production of designer plants for controlled environments. This review considers the opportunity for
breeding for controlled environments, with a focus on a revision of priorities for controlled-
environment breeders.

Introduction

You never hear of a dogsled race won with a team of Chihuahuas. Dogs have been bred for

specific applications, forever changed from a common canine ancestor to meet specific human needs

and to perform optimally in discrete environments. Their size, body type, color, and ability to tolerate

environmental extremes have shaped dog genetics to match the desires of their human breeders.

The same thing happened with plants. Just as animals related to the gray wolf genetically

transformed to the Chihuahua or the Alaskan Malamute due to human association, humans have also

domesticated plants, shaping their genetics, and aligning their form and function to best fit human

demands while adapting to prevailing environmental constraints. Most current cultivars were bred to

perform in the field, growing rapidly, navigating biotic and abiotic stressors, and ultimately yielding a

valued product at a time dictated by weather, market windows, or labor availability.

So why are we surprised when plants created for the field do not perform well when grown in

a closed or controlled environment? Controlled plant environments are becoming a greater interest in

filling an important agricultural niche. These environments may range from greenhouses to

completely closed artificial-light facilities and share the common feature of precise control of

environmental conditions. For the purposes of this review controlled environment primarily refers to

artificially illuminated closed plant production systems (Kozai et al., 2015; Jansen et al., 2016), where

light, temperature, humidity, fertilizer, and other factors are tightly regulated in a thermally insulated

and almost airtight environment (Kozai, 2013).

These controlled environments are often referred to as “plant factories” or “zero-acreage

farms” as they do not encroach on, and instead complement, existing limited farmland or urban open

space. Ironically, while a stark departure from pastoral scenes and a distal artificial insult to

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 agroecology, this kind of literal factory farm is generally viewed positively by the consumer (Jansen

et al., 2016; Coyle and Ellison, 2017). Growth facilities are being constructed in urban centers that
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permit local production of high-value specialty crops (Ehrenberg, 2008; Vogel, 2008). The short

supply chain may positively affect product quality and postharvest performance. These protected

agricultural operations offer potential to repurpose unused urban space, provide jobs for city-dwellers,

generate local produce in population centers and potentially widen specialty crop availability to

remedy nutritional deficits of food deserts (Kozai et al., 2015). Social benefits connect consumers to

local food, enhancing community food security, with a greater potential for transparency, although

these benefits are not always realized, especially for the food insecure (Bohm, 2017). There also are

potential benefits in water usage, recycling of organic wastes, and a reduction in supply chain carbon

emissions (Kozai et al., 2015; Specht et al., 2015).

While the vision of indoor year around agriculture has many potential benefits, it requires

considerable investment in setup and operation (Kozai and Niu, 2015). Establishment of these systems

requires careful attention to lighting, climate control, water, nutrients, and pest management. These

costs are not trivial and are described as a principal limitation of the approach (Banerjee and

Adenaeuer, 2014). There has been a creeping evolution of the hardware to establish these systems, led

in part by the engineering acumen of companies that realize a potential business opportunity in

horticultural specialty crop space. Substantial considerations have shaped the development of lighting

systems, irrigation, hydroponics, HVAC systems, robotics, and stacking strategies to maximize space

(Grift et al., 2008). However the most important and complicated machine in the process has been

sorely underestimated—the plant itself.

Flipping the G x E Equation

Plant productivity is dictated by a dynamic interaction between genetics and environment.

Plants bred for the field carry the genetics favoring phenotypic stability in the presence of ranging

environmental variation. Breeders select genotypes that suppress variation under duress, striving for

predictable growth and development, consistent yield, and performance that is agnostic to prevailing

conditions (Allard and Bradshaw, 1964; Mickelbart et al., 2015). The question of stability has been

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 considered to be a central hindrance in variety improvement (Hill, 1975). The attribute of stability is

important because growers can’t control the weather or disease incidence, yet demand season-to-
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season predictability that fits their production capacity and market windows.

On the other hand, plants bred specifically for a controlled environment offer the opportunity

to reconsider breeding priorities for a completely different theatre (see Table 1). When the

temperature is stable, the light environment is tuned to optimal, threats from pests and pathogens are

marginalized, and the postharvest interval is short, there is more opportunity to produce varieties that

don’t simply need to satisfy basic horticultural production expectations (Figure 1). In a tightly

regulated environment GxE interactions are constrained or even optimized for a given crop over a

particular developmental period. Today it is possible to breed and select for varieties explicitly

intended for the controlled environment, producing new varieties that broaden the sensory experience

for consumers, enhance profitability for growers, and decrease the energy requirement for their

production. The goal is high-value fresh produce, and the new genetics of crops-in-a-box should

match well with the demands and opportunities of this contrasting growth environment.

In short, there are two basic ways to control G x E. Breeders may constrain the G to not

respond to E, providing some specific output. By definition controlled environments offer the

opportunity to completely eliminate variation in E, so that G is expressed predictably. One set of

genes, one environment, one predictable product. However, can the ability to manipulate E offer even

more opportunity? What if one G may function well in a variety of E’s, so that multiple products may

be derived from one G, based on different prevailing E’s? Controlled environments offer the potential

to turn plant breeding upside down, as now breeding for the maintenance of fundamental traits in a

variety of E becomes a priority, and genetic plasticity is desired over phenotypic stability.

Different Priorities: Energy Input Cost

Plant traits for controlled environments may be grouped into two areas, traits that constrain

production costs and traits that increase value at retail. Several aspects govern production costs, such

as speed of production. Sprouts (seedlings at the cotyledon stage) may only require several days in a

controlled environment before becoming market ready. The production of microgreens (a young

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 seedling with its first two true leaves) occurs on the order of weeks. Small leafy vegetables, such as

high-value lettuces, can be grown in several weeks, while aromatic herbs may reach a significant
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market size within a month’s time. These kinds of plants, where the vegetative growth is harvested,

offer a more rapid turnaround than crops that require flowering to produce fruits like tomatoes or

strawberries, and also command a relatively high market value. The rapid cycling limits input costs.

Of course, established and productive fruit-bearing plants may not need to be replanted, offering the

capacity to simply trigger flowering with discrete light treatments (covered in following section).

A plant that resides in controlled environment space requires energy spent on illumination, as

well as management of ambient temperature, usually meaning costs both in supplying photons, as

well as the cost of managing the heat associated with supplying photons (Al-Kodmany, 2018).

Whether done by circulating air, specialized air handlers or water cooling, there is an energy

investment in producing light. With this in mind the optimal plant materials would germinate rapidly

and move quickly to market.

Several factors independently influence plant growth in a controlled environment, including

temperature, humidity, substrate and nutrition. But of all external factors, light may be controlled

with the greatest agility, as wavelength and fluence rate may be controlled instantaneously. Together

with photoperiod, these light attributes may be individually adjusted and may have a profound role in

maximizing productivity while investing fewer photons.

Future genotypes may be selected to grow optimally in low light conditions (< 100 µmol·m-2·

s-1, about 1/20th of full sunlight). The model plant Arabidopsis thaliana has provided a number of

mutants and natural variants exhibiting light hypersensitive phenotypes, where growth and

development are enhanced under low-light conditions (Maloof et al., 2001). Natural genetic variants

have been identified that exhibit differences in photosynthetic efficiency (van Rooijen et al., 2015).

Other genotypes are developmentally hypersensitive to light, leading to enhanced deetiolation, leaf

expansion and stem-growth inhibition in lower light environments, such as plants featuring mutations

in the Lrb genes (Christians et al., 2012). The genetic basis of light hypersensitivity is well

understood, as light responses are typically orchestrated by opposing forces that negatively and

positively affect gene expression. Elimination of negative genetic regulators of light responses may

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 allow seedlings to develop more rapidly with lower light inputs. Selection of such materials may

provide new genotypes that can reach market quality with fewer photons applied.
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Exploiting Plasticity

Plants are environmentally modified organisms, meaning that their form and functions are

dictated by cues from their surroundings. One of the most important inputs is light (Carvalho and

Folta, 2014). The pull of light on plant biology has been well explored for centuries, and the genetic

basis of photocontrol of discrete plant processes has been unraveled in Arabidopsis thaliana

(reviewed in Briggs and Huala, 1999; Lin, 2002; Quail, 2002). The basic findings from the model

organism can now be translated to a multitude of species, including high-value crops grown in

controlled environments.

Historically, candidate genes and loci identified in controlled environments have not

translated well to the field (Cabrera-Bosquet et al., 2012; White et al., 2012). The reason is obvious,

as the stability afforded by any protected environment biases selection away from traits that could be

relevant in the field setting. Selection in a controlled environment for a controlled environment

makes sense, yet most of the crops grown in such space actually have been developed for a

completely different environment. What are the horticultural attributes that may be prioritized for

growth in controlled environments? A good example is plant architecture. With a finite vertical

space and a need to optimize vegetative growth with competition between plants for light, plant

height, leaf position, and leaf expansion are critical features of the ideal ideotype. Stem elongation,

whether hypocotyl elongation or internode expansion, is sensitive to light control, as is coleoptile

expansion (Parks et al., 2001; de Wit et al., 2016). Some plant varieties have been shown to respond

to touch, leading to a shorter plant that could possibly be controlled by a mechanical stimulus

(Graham and Wheeler, 2017).

In some cases breeding for controlled environments may be facilitated by analysis of early

traits (Watt et al., 2013), and selection may even be automated using machine vision (Fahlgren et al.,

2015). Models have been devised to predict light interception potential of plants by tracing canopy

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 architecture, leaf area, and proximity to other plants (Kim et al., 2016). New selections may be

identified through these automated analyses.

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Dwarfing Phenotypes

Space may be optimized with implementation of dwarf phenotypes. These may be

specifically bred by analyzing growth in vitro, and identifying short seedlings under light. A subset of

the short plants will be gibberellin deficient or have defects in gibberellin sensing or turnover, leading

to the short internode phenotype. Such observations have been made in many crops, including peas

(Lockhart, 1956; Campell and Bonner, 1986) and barley (Chandler and Robertson, 1999), eliminating

the need for large plantings to identify drawfing varieties. These approaches may be extremely

beneficial when screening for woody perennials that could fit well in the controlled environment. New

methods in gene editing may target gibberellin receptors or synthesis mechanisms, creating custom

dwarfing varieties or rootstocks designed specifically for plant factories.

In addition to genetic control of plant stature, production systems have been devised where

specific pruning regimens stimulate the production of new productive canes, keeping bushes small

while continually productive. Such strategies (e.g. “rejuvenation pruning”) have been applied in

blueberry (Lyrene and Williamson, 1996) and raspberries (Krivorot and Emelianova, 2016). Here

genetics and environment collide with management tactics to produce a potential means to support

indoor production of high value fruits.

Ease of Harvest

Selection of varieties with architecture amenable to hand and mechanical harvest will be

necessary in the next generation of improved varieties. For instance, the JOINTLESS gene in tomato

encodes a transcription factor that controls flower abscission zone development (Mao et al., 2000).

The gene control the force needed to remove the fruit from the plant, and was important in tomato

domestication (Soyk et al., 2017). Because the genes controlling fruit abscission are well understood,

it is possible to breed for those varieties using marker-assisted approaches.

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 Automated pickers are being developed for these applications, and variation in plant

architecture is the enemy of the robot. In the example of sweet pepper, the positions of fruits are not
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uniform from plant to plant, so they are not easily detected using robotic sensory techniques (Bac et

al., 2014). The central challenges are that branches and leaves can block detection or harvest, the

lighting is different from environment to environment, and systems to train vegetative growth can

affect harvester access. Clearly breeding for uniformity in plant stature, limited vegetative structures

near flowers/fruits, and fruits that are uniform for fruit shape, color and placement are reasonable

priorities with respect to mechanical harvesting.

Flowering plants may be selected that produce fruits on longer pedicles, placing the high-

value portions of the plant into unobstructed human or machine vision. Wild species may have

important roles in re-introduction of genes that control inflorescence structure with respect to length,

branching and numbers of flowers (Soyk et al., 2017). This is especially true when controlled

environment plants may be bred to produce more smaller fruits per plant if inflorescence architecture

can be changed with adjustment or selection of specific genes.

Sensory Quality

Breeding for field and industry priorities has led to an erosion of sensory characteristics,

mainly flavor and aroma (Bartoshuk and Klee, 2013; Folta and Klee, 2016). Breeders of most high-

value annual crops specifically selected for rapid growth, resistance to disease, yield and postharvest

performance. While flavor, aroma and texture were always considered to be important, they would not

hold back the deployment of a large, firm fruit that survived shipping. These genetics were carried

forward and used in future variety development, leading to the loss of genes favorably influencing

sensory quality.

But could those qualities be recaptured not by breeding alone, but also by tugging at

metabolic networks with light? The pathways that give rise to the volatile compounds often contain

enzymes that are regulated by light. Such examples include the phenylpropanoid pathway, which is

strongly influenced by blue and UV light, along with the carotenoid derivatives which also

accumulate in response to light signals.

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 Basil plants obtain their unique flavor and aroma from the production of a large class of

volatile compounds (Costa et al., 2016). The major classes of volatiles have been shown to be strongly
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influenced by light quality (Carvalho et al., 2016). Light has also been shown to affect apocarotenoid

production in flowers and vegetative crops, leading to the production of compounds like β-ionone

(Simkin et al., 2004) and 3-hydroxy-β-ionone (Kato-Noguchi, 1996). Narrow-bandwidth red and blue

light have been shown to differentially affect the accumulation of important volatile classes in tea

(Camellia sinensis) leaves (Fu et al., 2015). These are just several examples of how specific

wavebands can change the abundance of particular volatiles that can influence consumer interest.

Nutrients and Neutraceuticals

Just as plants may also be bred to increase the accumulation of specific nutrient compounds

(Newell-McGloughlin, 2008), and these secondary metabolites have been shown to be under control

of light signals (Kopsell et al., 2015). The genes that control the flux through specific pathways are

frequently regulated, at least in part, by environmental variables. Light has been shown to modulate

the accumulation of glucosinolates in broccoli florets (Jin et al., 2015), broccoli sprouts (Kopsell et

al., 2014), kale sprouts (Carvalho and Folta, 2014; Qian et al., 2016) and kale leaves (Lefsrud et al.,

2008), mirroring observations in Arabidopsis (Huseby et al., 2013).

One especially exciting example is the breeding of transgenic tomato lines that express the

miraculin protein, a glycoprotein produced in the fruits of the West African shrub Richadella dulcifica

(Kato et al., 2010). This protein functions as a sweetener under acidic conditions and is proposed as a

potential sugar substitute in some foods. Kato et al., (2010) crossed the variety Moneymaker bearing

the transgenic miraculin construct with MicroTom to produce a hybrid tomato. Subsequent

generations were selected for self pruning, plant size, and high miraculin production, optimizing

production for controlled environment space. The same group later would optimize light conditions

to maximize protein expression and electricity costs (Kato et al., 2011).

Other examples include increasing antioxidant levels in pea sprouts (Wu et al., 2007), lettuce

(Johkan et al., 2010), tomato (Kim et al., 2013), and kales (Carvalho and Folta, 2014). Effects on

ascorbic acid levels were observed in lettuce (Li and Kubota, 2009), strawberry (Kim et al., 2011),

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 kale (Deng et al., 2017) and Chinese cabbage (Li et al., 2012). Changes in polyphenol and

anthocyanin content were observed in many of the above-referenced reports and others (e.g. Craver et
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al., 2017). Even levels of secondary metabolites like “essential oils” can be influenced by light inputs

(Sabzalian et al., 2014). The ability to manipulate nutrient levels has been shown for a wide variety of

compounds in many plants and many conditions in controlled environments (reviewed in Bian et al.,

2015; Dou et al., 2017).

Fruit Without Pollinators

Many high-value fruit crops require pollination to maximize yield and fruit shape. In the

context of a controlled environment this means that insect pollinators must be brought in, which opens

the door to a number of potential hazards, costs, and introduction of fungal and bacterial pathogens.

Techniques have been defined for greenhouses and extra-terrestrial environments where bees are not

an option (Schubert, 2017). In these confines pollination is enhanced with manually vibrating each

plant by hand (Freitas et al., 2015), vibration from a supporting structure (Short and Bauerle, 1973)

through the use of vibrating wands (Massa et al., 2015), vibrating tables or air blast devices that

promote pollination as anthers dehisce. Selection of specific flower types may enhance amenability to

mechanical, non-insect pollination.

In cases of apomictic reproduction an embryo forms from maternal tissue, making vegetative

reproduction possible through seed. Essentially the plant produces a fruit that contains copies of self,

and does not require fertilization. Effects of light on induction of parthenocarpic fruits have been

described for decades, suggesting that the process may be amenable to manipulation (Osborne and

Went, 1953; de Ponti, 1978; Robinson and Reiners, 1999). These studies noted roles for high or low

light environments in the induction of fruit without pollination. More recent work has shown discrete

roles for auxin and gibberellin signaling in the process (Kim et al., 1992; Goetz et al., 2007; Martí et

al., 2007) , and the action of both of these hormones is influenced by light (de Wit et al., 2016).

Future work will examine the relationship between specific light wavebands, hormones, and the

induction of fruit without pollination.

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 Market-Timed Production

The precise timing of production is attractive to growers as they may reach counter-seasonal
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markets where produce may command a higher retail price. Manipulation of the light environment

may provide a means to alter developmental transition to flowering, as light quality has been shown to

affect the process in fruit crops (Rantanen et al., 2014; Yoshida et al., 2016) and flowers (Park et al.,

2015; Tsukamoto et al., 2016). In the case where vegetative plant products are desired, such as herbs,

specific light treatments can be implemented to suppress flowering or increase biomass (Stagnari et

al., 2018). The controlled environment offers an exquisite opportunity to manipulate the transition to

flowering using photoperiod as well as light quality. Breeding and selection efforts around light

sensors and their signaling networks may reveal useful variants for controlled environment

production.

The genetic control of flowering has been well described in the model system (Song et al.,

2015), and many of the fundamental rules translate to crop plants. For instance, elegant experiments

by Valverde et al., (2004) demonstrated that flowering in the model plant Arabidopsis thaliana was

dictated by light input through the plant’s photoreceptors that ultimately controlled the accumulation

of a protein that stimulated the molecular circuits leading to flowering. The report showed that blue

and far-red light, operating through cryptochrome 2 and phytochrome A, induced the accumulation of

CONSTANS, a protein that induced flowering. Conversely red light, sensed by phytochrome B,

caused the turnover of CONSTANS and inhibited flowering. In short, flowering is a process that

could be dictated by light quality once the plant was developmentally competent to integrate and

execute the floral initiation program.

In the parlance of plant breeding, if the rules of the models apply, plants that are insensitive to

red light should flower more robustly. Those more sensitive to blue or far-red would presumably

flower less. Following the model, the breeder would select for herbs and lettuces that would be

sensitive to red light, or blue/far-red insensitive (or both!). Those varieties would be less sensitive to

light induced flowering, potentially leading to more production of the high-value leaves with

signature flavors. A breeder of strawberries or cut flowers might select blue/far-red hypersensitive

plants, or those that are red light insensitive. They would be more likely to flower under permissive

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 conditions. It is exciting to imagine a model where a desirable cut flower variety could be grown

under red/green light and then induced into flowering by switching the program to blue and far-red
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light, followed by days under white light. These examples represent possible avenues for precision

control of the flowering process to match market opportunities.

Prime Time for Gene Editing?

Plant breeding requires significant investment in screening genotypes, either in identifying

optimal parents to cross, or in the analysis of offspring. These activities require access to significant

materials, space, labor, inputs and other resources, and those may not be realistic in selecting plants

specifically for controlled environments. The production of varieties for controlled environments may

be a prime opportunity for the use of gene editing tools. Gene editing is the process of using

specialized enzymes to make precise changes in DNA that affect specific traits. With these

technologies it is possible to make tailored edits that affect a single trait, making changes that may not

be possible by traditional breeding. Evaluation of elite genotypes in controlled environment spaces

could reveal well-suited varieties with a small number of negative traits. A simple gene edited

correction could potentially provide adjustments that change a good genotype with a few defects

augmented by controlled environments into a variety well suited for such conditions.

Conclusions

Controlled environment agriculture will not replace the field in most cases. However, the

ability to control multiple variables that affect plant growth minimizes losses due to abiotic and biotic

stressors, and allows the inherent production genetics to flourish. When the priorities shift from yield,

postharvest quality and disease resistance to novelty, nutrition, and energy savings, a new set of

varieties may enable the sustainable profitability to indoor farming operations in urban areas. Success

will depend on the production of new genotypes that specifically fit the constraints of the controlled

environment, and at the same time exploit its potential opportunities.

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 Figure 1. In plants, the presentation of a trait is orchestrated between genetics and previailing
environmental conditions. (A) Traditional breeding provides varieties that almost always produce
acceptable products under most environmental conditions. (B) Genotypes bred specifically for
Accepted Article
controlled environments may be selected to match static conditions, enabling finer control of
product quality.

Table 1. Priorities and opportunities in breeding specifically for controlled environments.

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 Figure 1.
Accepted Article

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