REVIEW   Open Access    

Progress and challenges in applying CRISPR/Cas techniques to the genome editing of trees

More Information
  • With the advent of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) system, plant genome editing has entered a new era of robust and precise editing for any genes of interest. The development of various CRISPR/Cas toolkits has enabled new genome editing outcomes that not only target indel mutations but also enable base editing and prime editing. The application of the CRISPR/Cas toolkits has rapidly advanced breeding and crop improvement of economically important species. CRISPR/Cas toolkits have also been applied to a wide variety of tree species, including apple, bamboo, Cannabaceae, cassava, citrus, cacao tree, coffee tree, grapevine, kiwifruit, pear, pomegranate, poplar, ratanjoyt, and rubber tree. The application of editing to these species has resulted in significant discoveries related to critical genes associated with growth, secondary metabolism, and stress and disease resistance. However, most studies on tree species have involved only preliminary optimization of editing techniques, and a more in-depth study of editing techniques for CRISPR/Cas-based editing of tree species has the potential to rapidly accelerate tree breeding and trait improvements. Moreover, tree genome editing still relies mostly on Cas9-based indel mutation and Agrobacterium-mediated stable transformation. Transient transformation for transgene-free genome editing is preferred, but it typically has very low efficiency in tree species, substantially limiting its potential utility. In this work, we summarize the current status of tree genome editing practices using the CRISPR/Cas system and discuss limitations that impede the efficient application of CRISPR/Cas toolkits for tree genome editing, as well as future prospects.
  • One of the traditional techniques for increasing value and reducing agricultural produce spoilage is drying. Where more expensive alternative storage methods are used, this is especially crucial[1]. Through the addition of one or more energy sources, moisture from a product is removed throughout the drying process[2,3]. The physicochemical characteristics of the fruit are changed by drying, which can improve the flavor and texture of specific foods like raisins and dates[2]. It lowers the product's water activity (aw), and when the aw value drops to less than 0.6, it inhibits the growth and spread of spoiling bacteria[4]. Drying also reduces product weight, which reduces packing, storage, and shipping costs and ensures off-seasonal production[5,6]. The demand for dried fruit is rising globally as people become more health conscious[7].

    Worldwide pomegranate production is steadily rising, although large post-harvest losses are also common, according to reports[8]. When fruit is unsuitable for standard processing methods due to fruit cracking or sunburn, drying is a great way to reduce post-harvest losses because it extends shelf life and can be utilized to reduce food waste[9]. Numerous products, such as pharmaceuticals, snacks, cereals, quick drinks, and other confectionary items, employ dried pomegranate arils[10]. Dried pomegranate arils, also known as anardana, are utilized both medicinally and culinarily in several regions of the world, including India[11]. Dried arils can therefore be quite useful as value-added items that generate revenue. According to research conducted in the Indian Ramban area, anardana trade accounts for at least 41% of all annual household income[11].

    There are many different drying techniques. The most popular are freeze-drying, hot air drying, vacuum drying, and solar drying. Each technique has pros and cons in terms of the final product's quality and how efficiently it uses energy. Pre-drying procedures are frequently used in conjunction with drying. Pretreatment enhances the drying rate, product quality, and energy efficiency of the drying process. Enzymes that cause enzymatic browning, which lowers the product quality, are rendered inactive by pretreatments[1214]. Sensory qualities like color, texture, taste, scent, microbiological activity, and general acceptability are among the criteria that determine the quality of dried pomegranate arils[15]. These elements are crucial because they can have a big impact on customer preferences and, if not taken into full account, can lead to financial losses[16,17].

    Several studies[12,18,19] have looked at the impact of drying and pretreatment techniques on the general quality of the completed product. However, the combined impact of pretreatment and drying on quality was not sufficiently investigated. Reviews on pomegranate fruit often discuss the fruit's chemistry, nutritive value, and pharmacology. Therefore, by evaluating, highlighting, and reflecting on recent studies on pomegranate aril drying, this review seeks to close these gaps. This review paper compared and contrasted several pretreatment and drying setups with an emphasis on product quality.

    Heat, mass, and momentum exchanges all occur simultaneously during the drying of fruit materials in a sophisticated cellular architecture of biological tissue[20,21]. The characteristics of the material that affect the drying process are intricately dependent on size, shape, porosity, moisture content, and time[22]. For instance, the initial moisture level and the bioactive chemicals in pomegranate arils can vary depending on the cultivar and fruit ripeness. The understanding, engineering, and management of the drying process are further complicated by the intrinsic diversity of biological materials[23,24]. The mass, heat, and momentum transfer events that happen during a typical drying process are shown in Fig. 1[25]. Conduction and convection are the most common heat transfer methods, but radiation is typically only employed for high-end items due to its expensive cost[1,26]. Diffusion, capillary action, and bulk flow are only a few of the processes that might transfer mass. These mass transfer mechanisms must adapt to the ongoing physical changes in the material that take place as it dries out[22,27].

    Figure 1.  A visual representation of the drying processes of solid materials.

    Although it is native to Iran, the pomegranate (Punica granatum L.) is widely distributed worldwide[28]. It belongs to the family Lythraceae and is a deciduous shrub. It is a versatile plant that can be found growing in both semi-arid and subtropical climates. Pomegranates, however, need hot summer temperatures to ripen[29]. Pomegranate fruit has a non-uniform round shape and a range of hues depending on the cultivar and fruit development stage, including yellow, green, pink, deep red, deep purple, and black[30,31]. An outsized calyx crowns the fruit. The leading producers worldwide are Peru, Australia, South Africa, and Chile in the southern hemisphere, and India, China, and Iran in the northern hemisphere[32].

    Pomegranate is a one-of-a-kind fruit with distinct edible seeds (arils) that must be extracted by hand (Fig. 2)[33]. An aril is made up of a seed and fleshy, moist tissue surrounding the seed. Color, sweetness, juice content, and hardness of arils vary depending on cultivar and fruit maturity[30,31]. While the arils can be eaten fresh, they can also be made into jams, jellies, coloring agents, juices, vitamins, and anardana (dried arils). They can also be mixed into yoghurts, biscuits, and cereals[34]. Fresh pomegranate arils can be kept at 7 °C for up to 14 d without losing much quality. Dried pomegranate aril has an extremely low perishability, with a potential shelf life of more than 14 weeks in ambient air[35].

    Figure 2.  A typical breakdown of the material balance throughout the drying process for pomegranate aril.

    As demonstrated in Table 1, pomegranate is high in ellagitannins, gallic acids, ferulic acids, anthocyanins, flavonoids, fiber, and minerals like vitamin C, calcium, and phosphorus. Pomegranates' phenolic components and high vitamin C content (Table 1) have attracted the interest of both researchers and consumers due to their health advantages[3638]. As a result of its strong antioxidant activity and nutritional benefits, pomegranate is considered a superfruit. Pomegranate can also be employed in cosmetics and pharmacology due to its phytochemical and antioxidant qualities[39]. Pomegranate fruit extract (PFE) has bioactive elements that have been found to inhibit or prevent various types and levels of cancer[40]. Punicalagic acid, ellagic acid, urolithin, and luteolin are the most important pomegranate components known to have anticarcinogenic characteristics[40,41]. Pomegranate fruit has also been linked to the prevention of diseases such as Alzheimer's, hypertension, and diabetes[42,43]. Pomegranate supplements may also help during or after exercise because they have the potential to speed up hard exercise recovery[44].

    Table 1.  The nutritional composition of 100 g of pomegranate arils.
    NutrientValueUnit
    Water77.9g
    Energy346kJ
    Protein1.67g
    Total lipid fat1.17g
    Ash0.53g
    Total dietary fiber4g
    Total sugar13.7g
    Calcium10mg
    Phosphorus36mg
    Magnesium12mg
    Iron0.3mg
    Potassium236mg
    Sodium3mg
    Zinc0.35mg
    Vitamin C10.2mg
    Vitamin K16.4µg
    Vitamin E0.6mg
    Vitamin B-60.075mg
    Total choline7.6mg
    Folate38µg
    Adapted from United States Department of Agriculture (Agricultural Research Service), FoodData Central[52].
     | Show Table
    DownLoad: CSV

    Pretreatment procedures are utilized to improve the drying process's effect on product quality characteristics such as color, flavor, appearance, and some physicochemical aspects[45,46]. Figure 3 depicts the most often used pretreatment procedures[46]. A product is immersed in a chemical solution prior to drying in chemical pretreatment. Physical pretreatments, on the other hand, necessitate a physical alteration of the product. When drying with heat, Maillard reactions might occur, resulting in an unpleasant color change[47]. As a result, pretreatment techniques are critical in many drying applications, including the drying of pomegranate arils[45,48,49]. There is evidence that pretreatment reduces the product's exposure to heat by reducing drying time[50,51].

    Figure 3.  A classification of the numerous pretreatment techniques utilized in the drying process for pomegranate aril.

    Soaking in acidic solutions involves immersing the product to be dried in a hot acidic solution for many minutes before drying. Pretreatment with an acidic solution keeps the product's color and speeds up the drying process. The acidic solution suppresses polyphenol oxidase enzyme activity, slowing the rate of enzymatic browning (Fig. 3). Furthermore, numerous investigations[5355] have documented the retention of nutrients such as vitamin C in acidic solution pretreatment samples. Some acid-sensitive components, on the other hand, can be destroyed or leached away. As a result, while employing this strategy, this effect must be considered. In a pomegranate aril drying research, arils prepared with 3% citric acid had the highest sensory acceptance[56]. Vardin & Yilmaz[57] conducted research on the combined effect of acid blanching and subsequent drying temperature. The authors blanched the arils in 0.1% citric solution for 2 min at 80 ± 2 °C followed by drying at 55, 65, or 75 °C and discovered that drying at 55 °C had the maximum antioxidant capacity[46]. Understanding the connection between soaking in acid (balancing in acid) and the subsequent drying temperature is required to carry out the operation correctly.

    This entails immersing products in an alkaline solution. Alkaline solutions act by dissolving the wax covering on the fruit's surface, removing resistance to moisture transfer and increasing drying rate[58]. As a result, this pretreatment accelerates the drying process. However, the usage of alkaline solutions raises food safety concerns because the residue might be harmful to one's health[46,59]. In addition, although acidic solutions retain vitamin C, alkaline solutions leach it out and destroy it[46]. Samples dipped in ethyl oleate for roughly one minute revealed a considerably reduced drying rate: a 26.9, 28.5, and 27.2% decrease in drying time at drying air temperatures of 55, 65, and 75 °C, respectively, than the control[60].

    The fruit is dipped into a hypertonic solution, such as salt or sugar solutions, in this approach (Fig. 3). Because of the osmotic pressure differential, the hypertonic solution causes water to diffuse out of the fruit tissue[61]. When compared to other drying processes, osmotically pretreated dried products have great rehydration capability and little losses in quality parameters such as color, appearance, and nutrients[62]. Madhushree et al.[63] discovered that osmotic pretreatment (in 50oBrix sugar syrup concentrations) dried arils had high color retention. This could be owing to the samples' reduced exposure to oxygen when immersed in the sucrose solution. A separate investigation on the osmotic pretreatment of pomegranate arils with a 65°Brix sucrose solution revealed a decrease in drying rate in hot air drying at 70 °C compared to untreated control samples[64]. The scientists attributed the longer drying time (lower drying rate) to the creation of a dense sucrose layer beneath the fruit's surface, which created an additional barrier to moisture transfer. To that aim, the osmotic solution concentration must be assessed because it can result in prolonged drying times.

    Gaseous or liquid sulphur solutions have been used as a food preservation method and as a pretreatment in food drying procedures. Typically, sulphur solutions are utilized for their browning properties, both enzymatic and non-enzymatic[65]. In addition, sulfur pretreatment is associated with high vitamin C and A retention after drying, as well as inhibition of spoilage-related microbial proliferation[66].

    More et al.[23] compared physical pretreatments to chemical pretreatments with 1% potassium metabisulphide on arils. It was discovered that arils prepared with potassium metabisulphide had superior nutritional quality as well as improved color, flavor, taste, and overall acceptability (Table 2)[23]. As a result, processing of pomegranate arils with sulfur solutions can result in high-quality dried goods. Despite their anti-browning, antibacterial, antifungal, and nutrient retention qualities, sulphites might be harmful to one's health if the recommended dosage or daily intake is exceeded[67,68]. Furthermore, while the sulfur solutions maintain vitamins A and C, they deplete vitamin B1[65].

    Table 2.  Key findings in pomegranate aril pretreatment and drying studies.
    Pretreatment methodPretreatmentDrying techniqueKey findingsReference
    BlanchingWater blanching at 90 and 100 °CHot air oven dryingBlanched samples had a shorter drying time.[24]
    Water blanching at 80 °CHot air oven dryerBlanched samples had higher phytonutrient retention than unblanched samples.[69]
    Blanching using 0.1% citric solution
    at 80 ± 2 °C
    Cabinet tray dryerDrying process was shorter for blanched samples and there was a higher rate of bioactive compounds.[57]
    Sulphuring1% potassium metabisulphideSolar drying
    Cabinet tray dryer
    Freeze dryer
    Fruit of cv. Ganesh 1% potassium metabisulphide was of the highest quality and the highest acceptance.[23]
    Blanching and SulphuringHot water blanching 85 °C and 0.2% potassium metabisulphateMechanical dryer
    Solar dryer
    Keeping quality of mechanically dried arils was higher than the solar-dried arils.[70]
    Steam blanching, potassium metabisulphide and 0.3% Sulphur fumigationCabinet tray dryerThe highest dried aril quality was obtained from the combination of steam blanching and 0.3% Sulphur fumigation.[71]
    Steam blanching, sulphuring at 0.3%Vacuum dryer
    Hot oven dryer
    Sun drying
    Poly-tent house drying
    Room drying
    Sun drying had the highest moisture content reduction and the highest overall acceptance.[72]
    Hot water blanching 85 °C,
    potassium metabisulphite varying
    from 0.25% to 1%
    Hot air oven dryerThe best treatment was blanching in hot water at 85 °C for 1 min and then dipping the arils in 0.25% potassium metabisulphite.[70]
    Steam blanching, sulphuringSun drying
    Cabinet dryer
    Blanching reduced drying time. Cabinet drying of blanched samples without sulphuring was considered optimum for anthocyanins.[73]
    Acidic solution2%, 3% and 4% citric acidCabinet tray dryer

    3% acidic treatment was found to be the most acceptable.[56]
    Microwave100 and 200 W.Hot air oven dryer200 W pretreatment resulted in minimum energy utilization and drying time.[74]
    100 and 200 WHot air oven dryer200 W had the highest drying rate.[75]
    Osmotic treatmentSugar syrup, freezing at minus 18 °COpen sun drying,
    Solar tunnel dryer,
    Cabinet tray dryer
    Osmotic treatment and cabinet tray dryer produced dried arils with better physicochemical and sensory qualities.[63]
    • 100% pomegranate juice
    • 50% pomegranate and 50% chokeberry juice
    • 50% pomegranate and 50% apple
    • 50% apple and 50% chokeberry
    • 75% apple and 25% chokeberry
    Freeze drying
    Convective pre-drying vacuum microwave finish drying
    Vacuum-drying and freeze drying
    Pomegranate and chokeberry concentrated juice improved the quality of the dried arils.[12]
    Sucrose solutionHot air oven dryingPretreatment increased the drying time of the samples.[64]
     | Show Table
    DownLoad: CSV

    The dipping or soaking of a product in an alcoholic solution, usually ethanol, is known as alcoholic pretreatment. Ethanol dissolves the cell wall components, which increases moisture loss and thus the drying rate[76]. Several fruits, including melon (Cucumis melo L.) and apples (Malus domestica), have been pretreated in alcoholic solutions before drying[77,78]. However, no investigations on the pretreatment of pomegranate arils with alcohol were reported. This could be owing to the aril's waxy layer, which could impede permeability and hence the efficacy of the alcohol pretreatment[79].

    In this method, the fruit is dipped, submerged, or sprayed with a liquid solution that forms a thin coating layer on the product's surface and then dried (Fig. 3). According to studies, the use of edible coatings can help to retain the color, texture, and nutrient retention of dried items[80]. It is critical to note that the drying pace and dried product quality are affected by the coating thickness, drying method, and coating solution. Most of the research on edible coverings for pomegranate arils has focused on cold preservation and packing.

    Acoustic cavitation is utilized to rupture cell walls using ultrasound pretreatment[81]. According to one investigation on the effect of sonification on osmotic dehydration and subsequent air drying of pomegranate arils, ultrasonography caused a 2-fold and 2.7-fold increase in water loss[82]. The authors hypothesized that ultrasonic promoted cell wall disintegration and enhanced permeability. While using ultrasonic improved color quality, it also reduced anthocyanin content when compared to osmotically dehydrated samples[82].

    Blanching is a pretreatment technique that involves rapidly heating and then cooling a product that will be dried[45]. Blanching can be used to inactivate enzymes that potentially degrade product quality, such as polyphenol oxidase, peroxidase, and polygalacturonase[4]. Unwanted sensory traits in color, flavor, texture, and nutritional aspects are examples[4,83]. Blanching also improves cell membrane permeability, resulting in a faster drying rate[45]. Furthermore, blanching kills bacteria that might cause product spoiling[45,83]. As indicated in Fig. 3, there are several blanching processes, including hot water blanching and modern technologies such as microwave blanching and infrared blanching.

    Adetoro et al.[18] discovered that blanching pomegranate arils in hot water accelerated drying rates compared to unblanched samples. In a separate investigation, the authors found that blanching arils at 90 °C for 30 s and drying at 60 °C had higher total anthocyanin content and radical scavenging activity than blanching at 100 °C for 60 s and drying at 60 °C. In another work, Karaaslan et al.,[69] blanched arils in water at 80 °C for 2 min to investigate the effects of temperature and pretreatment on the arils. The authors discovered that while 75 °C had the fastest drying time, 55 °C had the maximum anthocyanin concentration, phenolic content, and antioxidant capacity. In other studies, pretreatment procedures are combined to produce high-quality dried fruit products.

    Singh et al.[73] conducted a study to evaluate the drying of pomegranate seeds under various drying conditions. They discovered that blanched samples dried faster and had higher acidity than sulphured samples. Furthermore, the anthocyanin concentration of blanched samples was higher than that of blanched and sulphured samples using the mechanical dryer. The authors hypothesized that the reduced anthocyanin concentration seen after sun drying was caused by the long drying hours in the sun. They also suggested that pomegranate arils be dried using blanching rather than sulphuring to achieve the maximum nutritional quality. Sharma et al.[70] investigated ideal methods for drying pomegranate arils by blanching them in hot water at 85 °C for one minute and then immersing them in a solution of potassium metabisulphite with concentrations ranging from 0.25% to 1% for two minutes (Table 2). The highest potassium metabisulphite content resulted in the lowest acidity.

    Thakur et al.[71] used steam blanching for 30 s and 0.3% sulphur fumigation for one hour to standardize pretreatments for dried arils from wild pomegranate. The authors discovered that cabinet drying outperforms solar drying and open sun drying. The solar dryer ranked second in terms of sensory characteristics like texture, taste, and general acceptability. Sun-dried pomegranate arils, on the other hand, exhibited the highest reduction in moisture content and overall acceptance when compared to vacuum drying, hot air oven drying, polytent drying, and room temperature drying, according to Bakshi et al.[72].

    The effect of pulsed electric field treatment on the behavior of microwave-assisted hot air drying of pomegranate arils was examined by Amiali et al.[84]. When compared to drying at 70 °C, they found that pulsed electric field treatment was only advantageous when the subsequent drying process was done at the lowest temperature (50 °C). The lower the temperature, the higher the overall phenolic concentration. Arils treated with a pulsed electric field had a 21.02% higher total phenolic content than untreated arils.

    Various pretreatment procedures on pomegranate arils have been utilized with the goal of conserving physicochemical, physical, and chemical properties or enhancing drying rates. However, pretreatment standardization is currently restricted and underexplored. Table 2 lists some of the methods for preparing dried pomegranate arils.

    Despite the fact that pomegranate is a fruit with numerous health and nutritional benefits, it is now a modest crop with limited marketability. The difficulty in collecting the interior edible seeds (arils) is the greatest impediment to realizing the full potential of this unusual fruit[29,31]. Only manual extraction of pomegranate arils for laboratory scale testing is described in the literature.

    Pomegranates are first cleaned and sorted for uniformity in color, size, shape, and weight before aril extraction[18,85]. All pomegranates should be washed. To avoid introducing bacteria into the arils when the fruit is sliced open, excess water from the fruit surface is dried before cutting[86]. Following that, the fruit is cut along the ridges and the segments are gently pulled apart to form a flower-like structure. The deconstructed pomegranate is then flipped over a bowl of water and gently tapped with a wooden spoon on the skin side. As a result, the arils will begin to come out without being broken. Once all arils have dropped out, the white membranes are skimmed off the surface of the water as it floats, the water is drained, the arils are separated, and the surplus water is gently patted off with a towel. This method involves cutting the pomegranate with a knife, which results in a loss of more than 30% of the arils owing to mechanical damage[86]. As a result, a better approach was required, such as the machinery developed by Schmilovitch et al.[87], which allows opening the fruit without cutting, extracting the arils with minimal damage, separating the arils from extraneous materials, and delivering clean arils to a packaging machine. This technology could be used to produce dried pomegranate on a greater scale.

    The drying time is determined by the pretreatment process, kind, and technique of dehydration used. The dehydration methods that will be investigated in this study are low-temperature drying and high-temperature drying.

    Low-temperature drying methods employ temperatures ranging from subzero to 50 °C[49,88]. These drying processes are time-consuming and are usually utilized for temperature-sensitive goods like herbs. Furthermore, low-temperature drying procedures reduce the risk of scorching the fruit, protecting heat-sensitive components such as vitamin C[89]. Freeze drying, vacuum drying, and sun drying are all low-temperature drying procedures[90]. Pomegranate arils dried using low-temperature procedures such as freeze drying and vacuum drying have a more acceptable look and nutrient composition than most high-temperature drying methods[12,91].

    Freeze-drying (FD) is a low-temperature technology frequently used for drying food samples for high-quality or heat-sensitive products[92]. It is also recognized as one of the most expensive, time-consuming, and energy-intensive procedures in the food industry[93]. It entails removing moisture from food ingredients under low temperature and high vacuum via ice sublimation[48]. Because the product is frequently frozen, it is also known as sublimation drying.

    Adetoro et al.[94] freeze-dried fresh pomegranate arils at a freezer temperature of −80 °C for 96 h to examine the effect of drying procedures on pomegranate arils. The researchers discovered that color, total phenolic compounds (TPC), total anthocyanin content (TAC), and radical-scavenging activity stability differed significantly from the hot air-drying procedure (Table 3). More et al.[23] investigated the effect of drying procedures on the quality of dried pomegranate arils from three varieties. The authors discovered that FD produced the greatest results in terms of color, flavor, taste, and nutritional factors across all cultivars. However, FD stood out due to its prolonged drying duration, 24−48 h, when compared to solar drying (17 h) and hot air drying (10 h). A study on the influence of freeze-drying on the color attributes of 'Assiuty' pomegranate arils revealed that FD had the best color attributes (L* value of 46.50 ± 4.4 and a* value of 13.97 ± 1.23)[95]. Gölükcü[91] discovered that the FD had the maximum phenolic matter content (5580 mg/kg), followed by vacuum, convective, and sun-dried pomegranate arils (Table 3). Caln-Sánchez et al.[96] investigated the chemical composition, antioxidant capability, and sensory quality of pomegranate arils and rind after exposure to FD. The investigators found that FD pomegranate arils retained the most sensory characteristics and punicalagin content. Similarly, Cano-Lamadrid et al.[12] discovered the best sensory profile and sweetness in FD pomegranate arils at 65 Pa for 24 h at −60 °C. The drying kinetics, total bioactive content, in-vitro bio accessibility of bioactive compounds, and color and microstructural features of pomegranate arils were also studied[97]. When compared to alternative drying methods, the FD was shown to be the best approach in terms of final product quality and has been highly recommended by multiple reviewers[48]. FD arils have been demonstrated to have a higher bioactive chemical content, less shrinking, and excellent color quality. The FD for pomegranate arils has a disadvantage in terms of bioactive chemical recovery when compared to other methods, as well as extensive drying times[97]. Furthermore, FD is costly due to high energy consumption and initial investment expenses[98].

    Table 3.  A summary of the many techniques for drying pomegranate arils.
    CultivarDrying methodDrying
    time (h)
    Drying conditionInitial moisture
    content (%)
    Final moisture
    content (%)
    Key findingsReference
    WonderfulFreeze dryer96−80 °C
    5,999.1 Pa
    74.7 (w.b.)FD showed a higher color shift (19.6% ± 2,77%) at week 4 compared to hot air drying at week 0.[94]
    Ganesh, Bhagwa and AraktaFreeze dryer24−48−45 °C79.9 (w.b.)
    80.5 (w.b.)
    78.9 (w.b.)
    9.65−9.9 (w.b.)
    9.8−10.2 (w.b.)
    9.8−9.9 (w.b.)
    Arakta pre-treated with 1% potassium metabisulphide had the highest ascorbic acid concentration (6.81 ± 0.07 mg 100 g−1).[23]
    AssiutyFreeze dryer36−70 °CTA (18.80, 2.80 mg 100 g−1), TP (608.09a, 41.26 mg 100 g−1), DPPH (68.91, 0.72%), and ABTS (2,956.59c, 120 mol trolox
    100 g−1) were all higher in frozen pomegranate arils than in freeze-dried arils.
    [95]
    Mollar de Elche24−60 °C, 65 Pa,81.5 (w.b.)FD showed higher anthocyanin content (646 mg kg−1) compared to osmotic drying and conventional drying.[12]
    Hicaznar36−20 °C, 100 Pa for
    12 h
    −70 °C, 0.26 Pa
    76.96 (w.b.)10 (w.b.)Arils dried using FD had the highest magnesium content (96.17 ± 6.95 mg kg−1), manganese content (0.96 ± 0.05 mg kg−1) and zinc content (3.93 ± 0.07 mg kg−1) compared to sun drying, hot air drying and vacuum drying.[91]
    KebenFreeze dryer57−55 °C77.6 ± 1 (d.b.)20 ± 1 (d.b.)FD had lower bioactive recovery during in-vitro gastrointestinal digestion (TPC of 2.92%, ABTS of 6.12% and CUPRAC of 38.85%) compared to vacuum drying, hot air drying and ultrasound-assisted vacuum drying.[97]
    KebenVacuum dryer10.855 °C77.6 ± 1 (d.b.)20 ± 1 (d.b.)Vacuum drying had the highest bio accessibility recovery of bioactive compounds at 10.32% compared to HAD, FD and ultrasound-assisted vacuum drying.[97]
    HicaznarVacuum dryer3.7
    4.6
    7.8
    75 °C
    65 °C
    55 °C
    85,000 Pa
    78.1 ± 0.2 (w.b.)16 (w.b.)Drying temperatures of 75°C resulted in higher degradation of anthocyanins, phenolic compounds and antioxidant capacity (20.0%, 51.0%, 29.7% ± 0.28% respectively).[99]
    HicaznarVacuum dryer2455 °C
    3 500 Pa
    76.96 (w.b.)10 (w.b.)FD had the highest quality attributes such as TAC-1288.73 mg/kg) compared to VD and HAD however, due to physical changes that were undesirable physical changes, VD and HAD are recommended for pomegranate aril drying.[91]
    Wild pomegranates (cultivar- unspecified)Vacuum dryer1342 ± 2 °CVD had a higher sensorial overall acceptance (17.1) compared to sun drying (16.2) and room temperature (12.6).[72]
    BasseinSun drying1715.73
    (unspecified)
    Drying rate of pomegranate arils is affected by tray load and the recommended tray load is 1.25 kg m−2[73]
    Wild pomegranates (cv. Unspecified)Solar poly-tunnel14014.9−28.4 °C
    48.5%−74% -RH
    0.639−0.944 -wind speed
    Arils dried in the solar poly-tunnel had higher ascorbic acid, anthocyanins, and phenol content, 12.7 mg 100 g−2, 28.12 mg 100 g−2, and 108.60 mg 100 g−2 respectively than open sun drying.[100]
    SefriIndirect solar dryer75
    10
    6
    4
    40 °C
    50 °C
    60 °C
    75 °C
    78 ± 0.1(w.b.)The optimal water activity for drying and storing arils is 0.3684 ± 0.03.[101]
    Wild pomegranates
    (cv. Unspecified)
    Solar tunnel30−45 °CArils from the Karsog location had the highest TSS, sugars, anthocyanin, total phenols and antioxidant activity[102]
    Microwave2.3
    1.3
    0.7
    270 W
    450 W
    630 W
    70.25 ± 0.5(w.b.)10(d.b.)Color changes increased from 6.77−13.11 with an increase in microwave power from 270−630 W and were lower compared to arils dried using HAD.[85]
    HicazMicrowave1.2
    0.6
    0.4
    210 W
    350 W
    490 W
    23.93 ± 1.4 (unspecified)22.2
    (unspecified)
    Based on quality parameters, a microwave drying power of 350 W was recommended for drying pomegranate arils.
    Sweet acid
    (cv. Unspecified)
    Infrared4.3
    2.2
    1.6
    50 °C
    60 °C
    70 °C
    78 ± 0.2 (w.b.)9 ± 0.2 (d.b.)
    22.2
    (unspecified)
    Drying time for infrared drying was less than for HAD.[103]
    HicazHAD2450, 60, 70 °C at
    1.0 m/s air velocity
    To obtain better dried aril quality, 60 °C was recommended for drying pomegranate arils.[104]
    Wild pomegranates
    (cv. Unspecified)
    HAD16.542 ± 2 °CSun drying resulted in a maximum loss of moisture compared to VD, HAD, poly-tent house drying and room drying.[72]
    Wild pomegranates
    (cv. Unspecified)
    HAD1062 ± 2 °CHAD achieved the highest total soluble solids (39.6°Brix) and drying rate compared to solar drying and open sun drying.[105]
    KebenHAD555 °C; with 1.3 m s−1 constant air velocity77.6 ± 1 (d.b.)20 ± 1 (d.b.)In comparison to hot air oven drying, ultrasound-assisted vacuum drying and freeze-drying have higher quality characteristics.[97]
    Bassein seedlessHAD5−660 ± 5 °C. Airflow in
    the dryer was 1.2−1.8 m s−1.
    8.98 ± 0.091For the finest preparation of anardana, blanched samples (with sulphur) should be dried in a cabinet.[73]
    Mollar de ElcheVacuum-
    microwave
    240, 360, 480 W and pressure ranging
    from 4,000−6,000 Pa
    80.4 (w.b.)Arils dried using vacuum microwave drying at 240 W had the highest sensorial scores for odour and aroma at 3.1 and 5.6 respectively.[106]
     | Show Table
    DownLoad: CSV

    Vacuum drying (VD) is the process of subjecting items to low pressure in a vacuum. Because of the low pressure, water has a lower boiling point, allowing samples to be dried at low temperatures. As a result, VD is appropriate for heat and/or oxygen-sensitive items. During VD, heat transmission can occur by conduction, radiation, or microwave energy. VD is distinguished by faster drying times when compared to FD, and the products are not initially frozen as necessary for FD[107]. This low-temperature operation, combined with the elimination of oxygen during vacuum drying, allows nutrients and bioactive components such as phenolic compounds and vitamins to be retained[108,109].

    Ozay-Arancioglu et al.[97] investigated the influence of drying methods on dried pomegranate arils by comparing four distinct drying techniques: FD, VD, ultra-assisted vacuum drying, and hot air drying. They discovered that VD had better antioxidant capacity values than the samples tested for ABTS following FD. According to Gölükcü[91], VD is second only to FD as the finest choice for producing dried pomegranate (Hicazar) arils. Another study found that arils dried at 55 °C had higher phytonutrient levels than those dried at 65 and 75 °C under vacuum conditions[69]. When compared to other drying procedures, vacuum drying produces products with higher levels of phytochemical components. However, drying times range from 7.8 to 24 h at 55 °C, contributing to high costs, and products can only be dried in batches[91,99,110].

    Sun drying is one of the oldest and most used methods of drying. Sun drying is a low-cost, renewable energy-based drying process. In a nutshell, products are laid out on a flat area where they can be fully exposed to the sun for as long as possible. Because the drying process is dependent on solar radiation, the temperature is low and the drying process can be lengthy, taking approximately 15 d for pomegranate arils[60]. Furthermore, exposure to light and oxygen can lead to decreased preservation of substances like vitamin C. Furthermore, solar drying is an uncontrolled process with substantial risks of pest contamination, dust exposure, and product remoistening at night. To increase safety, solar dryers and solar tunnels are proposed to reduce pest and dust contamination[111]. Solar dryers use a contained environment comprised of a transparent or opaque cover, resulting in either direct or indirect drying[112]. The indirect drier system captures solar heat and transfers it to the product drying chamber via a second solar collector. A solar tunnel dryer is typically large in size and has a clear cover (Fig. 4). To regulate drying conditions such as temperature and relative humidity within the tunnel, solar tunnels often require a forced convection facility. A solar tunnel dryer may also include a solar air heater[111]. Solar dryers have the potential to boost drying temperatures, resulting in a quicker drying time[113].

    Figure 4.  This image depicts a sample of wild pomegranate arils being dried in a solar tunnel drier. Reprinted from Thakur et al.[102].

    In a comparison of hot air drying (60 °C), solar tunnel drying, and sun drying by Madushree et al.[63], hot air-dried arils were shown to have the highest quality. However, of all the drying techniques, solar drying had the greatest L* values (lightness), a desired quality. This was due to the comparatively low temperature of sun drying. Additionally, Bakshi et al.[72] discovered that when compared to vacuum drying, oven drying (42 ± 2 °C), and room drying (23 ± 2 °C), sun dried arils had the highest sensory overall acceptance and the lowest moisture content. In their comparative analysis of drying techniques, Singh et al.[73] discovered that hot air-dried pomegranate arils had the greatest anthocyanin and acidity contents. But in hot-air oven-dried samples, undesirable non-enzymatic browning was most pronounced. Sharma & Thakur[100] demonstrated that the quality of arils dried in solar polytunnels was superior to that of arils dried in the open sun (Fig. 4). The ascorbic acid, anthocyanins, and phenols were found to be significantly greater in the sun polytunnel dried arils, according to the authors. They also received superior sensory ratings for color, texture, taste, and acceptability.

    Temperatures above 50 °C are used in high-temperature drying processes[88]. These drying processes are energy intensive, have large operating expenses, and so are costly. These technologies rely on fossil fuels, which pollute the environment where they are generated and utilized, and their continued usage is seriously harming our environment[114]. The drying mechanism is designed such that there is a controlled direct or indirect heat transmission to the product, leading in moisture elimination. These drying procedures may not be suited for some foods because they may induce nutritional breakdown[115]. Furthermore, high temperatures might cause product shrinkage and distortion. Hot-air drying ovens, steam drying, heat pump drying, and spray drying are all examples of high-temperature drying processes.

    Using forced convection, hot air oven drying (HAD) eliminates moisture from materials. Objects dry out through evaporation when hot air is forced through and around the substance. As a result, the dried product's flavor, color, nutrients, and ability to rehydrate may alter unintentionally[97,104,106]. The HAD techniques were shown to have a comparatively high total color change by Ozay-Arancioglu et al.[97]. As shown in Fig. 5, hot air-dried arils were darker than freeze-dried and vacuum-dried arils.

    Figure 5.  Illustration of dried pomegranate arils that have been dried using different methods. (a) Freeze drying, (b) vacuum drying, and (c) hot air drying. Adapted from Ozay-Arancioglu et al.[97].

    Başlar et al.[99] prepared dried aril samples using the hot air-drying process and subjected them to various quality assessments. Fresh aril samples were dried at three different temperatures (55, 65, and 75 °C). According to the authors' findings, high temperatures and short drying times are optimal for retaining valuable food biocomponents. However, whereas bioactive chemical losses increased over time, they degraded faster at higher temperatures. The antioxidant activity, on the other hand, decreased with drying time and was unaffected by drying temperatures. Horuz & Maskan[104] investigated the effect of hot air drying on pomegranate aril cv. Hicaz at three different drying temperatures and compared quality metrics such color, shrinkage, rehydration capacity, and drying time (Table 3). The authors suggested 60 °C for pomegranate aril HAD. The authors also discovered that shrinkage was greater in HAD than in microwave drying. In a second study, researchers discovered that the optimal drying temperature for retaining bioactive chemicals when drying pomegranate arils (cv. Hicaznar) in a hot air dryer was 65 °C[116]. When compared to the sun drying method for anardana made from wild pomegranate, Bhat et al.[105] discovered HAD dried arils with maximum acidity of 13.72%, phenols of 110.7 mg per 100 g, total sugars (24.2%), and reducing sugars (21.2%).

    However, Bakshi et al.[72] carried out a study with lower temperatures in which they studied the influence of different drying processes on the moisture content of dried pomegranate aril (cv. Wild). Lower temperatures were employed to gain insight into the quality of the dried product when compared to the low temperature drying methods used in the study, such as sun drying, poly tent house drying, room drying, and VD. When compared to alternative drying methods, the authors discovered that HAD (42 ± 2 °C ) for 16.5 h and drying in room at normal air (23 ± 2 °C ) for 10−12 d produced in the greatest loss of moisture from fresh arils of wild pomegranate (75.12%).

    Singh et al.[73] evaluated the influence of different drying conditions on the quality of dried pomegranate arils (Bassien Seedless) samples (Table 3). The scientists discovered that sun-drying preserved more MC while drying was faster with a HAD dryer and generally recommended it as a better strategy for preparing dried pomegranate arils.

    HAD drying of pomegranate arils is a standard drying procedure that can be utilized in commercial settings. Although HAD does not generate high-quality goods like FD, it does provide better TSS, TA, and antioxidant capacity stability. Furthermore, although having a higher rate of bioactive component degradation, higher temperatures may result in higher retention compared to approaches such as solar drying due to the short drying times.

    Electrical current is passed through the pomegranate aril during electric drying techniques including ohmic heating. The intrinsic resistance of the aril induces internal heating as the electrical current flows through it[117,118]. Ohmic heating is typically employed for liquid, viscous, and particle-containing foods[119]. Regardless of the meal's densities, food products prepared using this approach are heated quickly and uniformly[120].

    Dielectric techniques, on the other hand, use electromagnetic waves to directly produce heat inside the product, such as microwave, radio frequency drying, and infrared radiation[121]. Dielectric heating results from the conversion of electromagnetic energy to kinetic energy by dipolar molecules oscillating in accordance with the rapidly oscillating electric field[122,123]. Compared to traditional methods like hot air drying, dielectric technologies dry materials more quickly[124]. Additionally, the items are of a higher caliber than those produced by traditional drying techniques.

    Microwave drying (MD) is one of the emerging drying technologies. Unlike other techniques, MD utilizes volumetric heating to rapidly dehydrate the sample material[104]. Some studies[85,104] have indicated that arils desiccated at 150 W microwave power and 58 bar (abs) pressure produced the highest quality arils. In another study, microwave power of 80 W and vacuum pressure of 60 mm Hg provided the highest drying efficiency and qualitative attributes, including color and texture[125]. Horuz & Maskan[104] observed that microwave-dried pomegranate samples had lower levels of shrinkage and bulk density than hot air-dried samples. The authors also noted that microwave drying caused a greater loss of color in terms of total color difference (E) compared to air drying. It was observed that microwave-dried samples had a brownish hue.

    Drying with MD reduces drying time, but essential quality parameters, such as color, are sacrificed. Since the product is directly heated, the lack of heating uniformity during MD, which is difficult to control and could contribute to product burning has been cited as a disadvantage[126].

    Infrared drying is an effective technique of drying in which the product is heated directly without the use of air as the drying medium. In a comparative study of drying methods (hot air drying and infrared drying) to dry pomegranate arils, the authors discovered that infrared drying effectively dried pomegranate arils and that the polyphenol content in arils dried using infrared drying was higher at 50 and 60 °C than in arils dried using hot air drying at similar temperatures[103]. Therefore, pomegranate arils can be infrared-dried at 50 °C for optimal nutrient retention[103]. In contrast, a distinct study dried pomegranate arils under near-infrared vacuum conditions and found that drying at 60 °C and 20 kPa air pressure resulted in optimal colour retention and shrinkage[127].

    Although infrared drying is a rapid drying method, it is challenging to control due to parameters such as infrared intensity and radiation distance, and its energy consumption is unpredictable[26].

    Drying kinetics is the study of how factors that influence the removal of moisture from products during a drying process interact[110]. The drying kinetics of a substance is dependent on its thermal and mass transport properties. Understanding drying kinetics relates to process variables, and therefore aids in identifying suitable drying methods and controlling drying processes[57,96,116]. For optimal operating conditions, drying kinetics can be used to estimate drying time, energy requirements, and drying efficiency[2]. Due to the complexity of the drying phenomenon, however, mathematical models describing the drying kinetic of biological tissues are devised based on the time history of the moisture ratio from a controlled drying experiment[128]. There are numerous mathematical models, but Table 4 provides a summary of the most used models.

    Table 4.  A summary of the mathematical equations that are most commonly used to model the drying kinetics of pomegranate arils is shown here.
    Model nameModel expressionReference
    PageMR = exp(-ktn)[129]
    NewtonMR = exp(-kt)[130]
    Henderson and PabisMR = aexp(-kt)[131]
    Midili et alMR = aexp(-ktn) + bt[132]
    Wang and SinghMR = 1 + at + btn[133]
    Two TermMR = (aexp(-k0 t) + bexp(-k1 t))[134]
    LogarithmicMR = aexp(-kt) + c[135]
     | Show Table
    DownLoad: CSV

    The most common models that best describe the hot air drying of pomegranate arils include the Logarithmic, Midili and Page models[24,99]. Baslar et al.[99] found the Logarithmic model as the best in describing hot air drying of arils at 55, 65 and 75 °C. In another study, it was found the Sigmoid model describing the kinetics of hot air drying of pomegranate arils at similar drying temperatures[116].

    In their study on the infrared drying of pomegranate arils, Briki et al.[103] discovered that the Midili model was the most accurate representation of the drying kinetics. In a similar manner, it was discovered that the Midili model provided the best fit to the experimental data for drying using a combination of infrared and hot air[136]. Another investigation indicated that the Aghbashlo model provided the greatest fit for the data obtained from near-infrared vacuum drying at a temperature of 60 °C[127].

    Based on measurement data from three pomegranate cultivars (cvs. 'Acco', 'Herkaswitz', and 'Wonderful') at 60 °C, Adetoro et al. demonstrated cultivar as another influencing factor in selecting an optimal model. While the drying data of the blanched samples of all the cultivars in this investigation were best fit by the Logarithmic model, the unblanched samples of 'Acco' and 'Herkaswitz' and 'Wonderful' were best fitted by the Page and Midili models, respectively[24].

    The bioactive chemicals retained and drying periods may be affected by the pretreatment process, although frequently the drying kinetics of both untreated and pretreated samples may be described by the same model. The Page and Modified Page were determined to be the best models to fit the drying data of both blanched and unblanched pomegranate arils under vacuum air drying by Karaslaan et al.[69]. In a different investigation, the Page and Modified Page were shown to be the model that best suited the drying data of pomegranate arils that had been bathed in citric acid and dried by hot air[57]. Although the drying rate of pre-treated samples is higher than that of untreated samples, the scientists noted that the same models were found to best reflect the drying kinetics. The Page, Logarithmic, and Midili drying models are the most popular and effective drying models for pomegranate arils employing HAD, MD, and VD. The mathematical models that were utilized to explain the drying kinetics of pomegranate arils are summarized in Table 5.

    Table 5.  A synopsis of the results of mathematical modeling of the kinetics of drying pomegranate arils.
    CultivarDrying methodDrying parametersPretreatmentSuitable drying modelReference
    cv. HicazHAD55, 65, 75 °C0.1% citric acidPage and Modified Page[57]
    cv. HicaznarHAD55, 65, 75 °CSigmoid[116]
    HAD55, 55, 60 °CPage[137]
    HAD50, 60, 70 °CPage[85]
    MD270, 450, and 630 WPage[85]
    cv. HicaznarVD55, 65, 75 °CHot water blanchingPage and Modified page[69]
    HAD45, 50, 55, 60, 65, and 70 °CMicrowaveMidili[75]
    cvs. Acco, Herskawitz and WonderfulHAD60 °CHot water blanching (at 90 and 100 °C, each for 30 s
    and 60 s)
    Logarithmic, Page,
    Midili for unblanched arils
    Midili and Page for blanched
    [24]
     | Show Table
    DownLoad: CSV

    The drying procedure aids in reducing bacterial growth, which can result in reducing spoilage. However, while food is being dried, other changes may occur that degrade its quality. To determine the product's expiration life, chemical, physical, physicochemical, and microbiological changes are monitored[138,139]. These modifications are affected by stowage, environment, and packaging methods. The most significant factor affecting the integrity of stored food products is temperature[140]. Consequently, most shelf-life experiments are designed to evaluate the temperature-time history in relation to changes in product quality[138,141]. To accurately evaluate quality changes and safety, shelf-life evaluations should ideally simulate actual storage conditions[142]. In the case of desiccated goods, the actual storage period is lengthy, and the evaluation of shelf-life can become time-consuming and expensive. When the actual storage time is lengthy for practical reasons, an accelerated shelf-life test or analysis of the worst-case scenario is employed[142]. Ordinarily, the end of shelf life is determined by relevant food legislation, guidelines issued by enforcement authorities or agencies, guidelines issued by independent professional organizations, current industrial best practices, self-imposed end-point assessment, and market data[142].

    Appropriate packaging material can help to reduce quality losses. The packaging and shelf-life tests on dried pomegranate arils are summarized in Table 6. Sharma et al.[70] examined the packaging of dried pomegranate arils with high-density polyethylene (HDPE), low-density polyethylene (LDPE), and polypropylene (PP) films. For 12 months, samples were held at 7 °C and ambient (14−39 °C). They found that HDPE retained the most color, total tannins, and acidity while gaining the least moisture. The authors proposed a safe storage time of 6 and 9 months for HDPE packed dried pomegranate arils under ambient and refrigerated conditions, respectively.

    Table 6.  A list of the several types of containers used to store dried pomegranate arils.
    Drying methodDrying temperaturePackaging materialStorage period (months)Shelf-life performanceReference
    MC drier
    Solar cabinet drier
    Open sun
    62−64 °C
    50−55 °C
    18−24 °C
    Aluminum laminated polyethylene pouch, polyethylene pouches and thermoform trays.6Aluminum laminated polyethylene pouches were best for packaging.[105]
    Microwave-vacuum drying38 °CHigh-density polypropylene (HDPP) and aluminum laminated polyethylene (ALP).3−6Pomegranate arils stored showed that ALP is more protective than HDPP.[35]
    Solar tunnel30−45 °CGunny bags, aluminum laminated polyethylene pouches (ALP) and vacuum-sealed aluminum laminated polyethylene pouches (ALPV).12Both refrigerated and ambient storage can securely preserve dried pomegranate samples for 12 months. Best performance was ALP with vacuum and cold storage.[144]
    Hot air dryer60 °CAluminum laminated polyethylene pouch (ALP), polyethylene pouch (PEP), and thermofoam tray (TT) covered in shrinkable polypropylene transparent sheet.6Moisture absorbers aid in the preservation of samples.[100]
     | Show Table
    DownLoad: CSV

    Bhat et al.[105] compared aluminum-laminated polyethylene (ALP, 99.8 g m−2) and polyethylene pouches (93.9 g m−2) each storing 100 g dried pomegranate arils and stored at ambient (15−25 °C). The authors discovered that aluminum laminated polyethylene pouches performed best after a 6-month storage period. Dak et al. [35] compared HDPP and ALP under accelerated shelf-life conditions (38 ± 1 °C and 90% ± 1% relative humidity) and evaluated the correlation between packaging material, storage period, and anthocyanin, phenolics, TSS, TA, and microbial count. The authors estimated that HDPP and ALP have shelf lives of 96 and 187 d, respectively. The above two research confirmed that ALP had the best performance features. This could be owing to the pouches' thickness and the opaque barrier of the aluminum lamination. The use of opaque packaging material may extend the shelf life of pomegranate arils by minimizing photodegradation of components such as carotenoids, flavonoids, and lipids, which can alter qualitative qualities such as aroma, texture, and color[143]. Based on safe consumption criteria, Mokapane et al.[19] proposed a shelf life of 5 months for citric acid pretreatment and dried arils wrapped in kraft paper pouches.

    In a second investigation, Thakur et al.[144] examined the effectiveness of gunny bags, ALP, and ALP combined with vacuum for storing dried pomegranate arils for a period of one year. According to the authors' findings, ALP performed best when performed under vacuum. The various types of containers that are used to store dried pomegranate arils are broken down into categories and shown in Fig. 6.

    Figure 6.  Different types of storage bags for dried pomegranate arils. (a) Aluminum-laminated polyethylene pouches, (b) vacuum-sealed aluminum-laminated polyethylene pouches, (c) gunny bags and (d) transparent polyethylene pouch. From Thakur et al.[144], modified.

    Sharma & Thakur[100] investigated the effect of active packaging on the quality features of dried wild pomegranate arils over a 6-month storage period. Salt or sugar sachets were inserted in ALP pouches or Thermofoam trays that had been wrapped in shrinkable polypropylene transparent film or polyethylene pouches. The researchers reported that for arils dried in a mechanical drier, ALP pouches had the best quality retention of criteria such as ascorbic acid, anthocyanins, total phenols, color, and texture. Furthermore, the inclusion of salt or sugar in active packing aids in the production of high-quality dried arils. However, salt-based active packaging had somewhat higher TA, ascorbic acid content, total sugars, anthocyanin content, and total phenols than sugar-based active packaging.

    The shelf life of dried pomegranate aril can range anywhere from three months to a year depending on the pretreatment, drying procedures and packaging that were used. There is, however, no definitive guideline about the influence that pretreatment and drying procedures have on the quality characteristics of the product when it is being stored. Many studies on the shelf life of dried pomegranate arils focus on examining the influence that different types of packaging material have on the storage life. These studies pay less attention to the physical and microbiological changes that accompany quality alterations. Additionally, a specialized shelf-life testing process and quality standard for dried pomegranate arils can be difficult to locate in the literature.

    While high temperatures have a positive influence on the drying rate, it has a negative effect on the product's texture, color, and nutritional content. Because of this, lower temperatures are often ideal for retaining the pomegranate arils' nutritional value and maintaining their consistency. Freeze dryers offer the best result in this regard. Freeze-drying, on the other hand, is a time- and money-consuming process. When paired with other types of pretreatment, inexpensive procedures such as sun dryers can be adjusted to produce high retention on chemicals that are virtually identical to those obtained in freeze dryers. However, before implementation, it is necessary to examine the intended outcome of the pretreated arils. This is because pretreatments affect both the drying rate and the retention of nutrients. Therefore, in order to completely optimize the process, it is necessary to have an awareness of the interaction that occurs between the pretreatments and the subsequent drying procedure. It is proposed that recommendations be formulated to assist in the manufacture and marketing of dried pomegranate arils that are consistent, nutritious, and hygienically safe.

    The authors confirm contribution to the paper as follows: study conception and design: Ambaw A, Opara UL; project administration and supervision: Ambaw A, Opara UL; draft manuscript preparation: Maphosa B; manuscript review and editing: Ambaw A. all authors reviewed the results and approved the final version of the manuscript.

    Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.

    This work is based on the research supported wholly/in part by the National Research Foundation of South Africa (Grant No. 64813). The opinions, findings and conclusions or recommendations expressed are those of the author(s) alone, and the NRF accepts no liability whatsoever in this regard. Research reported in this publication was supported in part by the Foundation for Food and Agriculture Research under award number 434—grant ID: DFs-18- 0000000008.

  • The authors declare that they have no conflict of interest.

  • Supplemental Table S1 Current availability of tree genome data in sgRNA design tools.
  • [1]

    Jiang F, Doudna JA. 2017. CRISPR-Cas9 structures and mechanisms. Annual Review of Biophysics 46:505−29

    doi: 10.1146/annurev-biophys-062215-010822

    CrossRef   Google Scholar

    [2]

    Mojica FJM, Montoliu L. 2016. On the origin of CRISPR-Cas technology: from prokaryotes to mammals. Trends in Microbiology 24:811−20

    doi: 10.1016/j.tim.2016.06.005

    CrossRef   Google Scholar

    [3]

    Wu S, Li Q, Yin C, Xue W, Song C. 2020. Advances in CRISPR/Cas-based gene therapy in human genetic diseases. Theranostics 10:4374−82

    doi: 10.7150/thno.43360

    CrossRef   Google Scholar

    [4]

    Li J, Norville JE, Aach J, McCormack M, Zhang D, et al. 2013. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nature Biotechnology 31:688−91

    doi: 10.1038/nbt.2654

    CrossRef   Google Scholar

    [5]

    Shan S, Soltis PS, Soltis DE, Yang B. 2020. Considerations in adapting CRISPR/Cas9 in nongenetic model plant systems. Applications in Plant Sciences 8:e11314

    doi: 10.1002/aps3.11314

    CrossRef   Google Scholar

    [6]

    Mao Y, Botella JR, Liu Y, Zhu J. 2019. Gene editing in plants: progress and challenges. National Science Review 6:421−37

    doi: 10.1093/nsr/nwz005

    CrossRef   Google Scholar

    [7]

    Wolter F, Puchta H. 2018. The CRISPR/Cas revolution reaches the RNA world: Cas13, a new Swiss Army knife for plant biologists. The Plant Journal 94:767−75

    doi: 10.1111/tpj.13899

    CrossRef   Google Scholar

    [8]

    Khan MZ, Haider S, Mansoor S, Amin I. 2019. Targeting plant ssDNA viruses with engineered miniature CRISPR-Cas14a. Trends in Biotechnology 37:800−804

    doi: 10.1016/j.tibtech.2019.03.015

    CrossRef   Google Scholar

    [9]

    Collias D, Beisel CL. 2021. CRISPR technologies and the search for the PAM-free nuclease. Nature Communications 12:555

    doi: 10.1038/s41467-020-20633-y

    CrossRef   Google Scholar

    [10]

    Jia H, Wang N, Prasad M. 2014. Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS One 9:e93806

    doi: 10.1371/journal.pone.0093806

    CrossRef   Google Scholar

    [11]

    Charrier A, Vergne E, Dousset N, Richer A, Petiteau A, et al. 2019. Efficient targeted mutagenesis in apple and first time edition of pear using the CRISPR-Cas9 system. Frontiers in Plant Science 10:40

    doi: 10.3389/fpls.2019.00040

    CrossRef   Google Scholar

    [12]

    Malnoy M, Viola R, Jung MH, Koo OJ, Kim S, et al. 2016. DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Frontiers in Plant Science 7:1904

    doi: 10.3389/fpls.2016.01904

    CrossRef   Google Scholar

    [13]

    Nishitani C, Hirai N, Komori S, Wada M, Okada K, et al. 2016. Efficient genome editing in apple using a CRISPR/Cas9 system. Scientific Reports 6:31481

    doi: 10.1038/srep31481

    CrossRef   Google Scholar

    [14]

    Lin CS, Hsu CT, Yang LH, Lee L, Fu J, et al. 2018. Application of protoplast technology to CRISPR/Cas9 mutagenesis: from single-cell mutation detection to mutant plant regeneration. Plant Biotechnology Journal 16:1295−310

    doi: 10.1111/pbi.12870

    CrossRef   Google Scholar

    [15]

    Ye S, Chen G, Kohnen MV, Wang W, Cai C, et al. 2020. Robust CRISPR/Cas9 mediated genome editing and its application in manipulating plant height in the first generation of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro). Plant Biotechnology Journal 18:1501−3

    doi: 10.1111/pbi.13320

    CrossRef   Google Scholar

    [16]

    van Zeijl A, Wardhani TAK, Seifi Kalhor M, Rutten L, Bu F, et al. 2018. CRISPR/Cas9-mediated mutagenesis of four putative symbiosis genes of the tropical tree Parasponia andersonii reveals novel phenotypes. Frontiers in Plant Science 9:284

    doi: 10.3389/fpls.2018.00284

    CrossRef   Google Scholar

    [17]

    Odipio J, Alicai T, Ingelbrecht I, Nusinow DA, Bart R, et al. 2017. Efficient CRISPR/Cas9 genome editing of Phytoene desaturase in cassava. Frontiers in Plant Science 8:1780

    doi: 10.3389/fpls.2017.01780

    CrossRef   Google Scholar

    [18]

    Gomez MA, Lin ZD, Moll T, Chauhan RD, Hayden L, et al. 2019. Simultaneous CRISPR/Cas9-mediated editing of cassava eIF4E isoforms nCBP-1 and nCBP-2 reduces cassava brown streak disease symptom severity and incidence. Plant Biotechnology Journal 17:421−34

    doi: 10.1111/pbi.12987

    CrossRef   Google Scholar

    [19]

    Mehta D, Stürchler A, Anjanappa RB, Zaidi SS, Hirsch-Hoffmann M, et al. 2019. Linking CRISPR-Cas9 interference in cassava to the evolution of editing-resistant geminiviruses. Genome Biology 20:80

    doi: 10.1186/s13059-019-1678-3

    CrossRef   Google Scholar

    [20]

    Peng A, Chen S, Lei T, Xu L, He Y, et al. 2017. Engineering canker-resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus. Plant Biotechnology Journal 15:1509−19

    doi: 10.1111/pbi.12733

    CrossRef   Google Scholar

    [21]

    Jia H, Orbovic V, Jones JB, Wang N. 2016. Modification of the PthA4 effector binding elements in Type I CsLOB1 promoter using Cas9/sgRNA to produce transgenic Duncan grapefruit alleviating XccΔpthA4: dCsLOB1.3 infection. Plant Biotechnology Journal 14:1291−301

    doi: 10.1111/pbi.12495

    CrossRef   Google Scholar

    [22]

    Jia H, Zhang Y, Orbović V, Xu J, White FF, et al. 2017. Genome editing of the disease susceptibility gene CsLOB1 in citrus confers resistance to citrus canker. Plant Biotechnology Journal 15:817−23

    doi: 10.1111/pbi.12677

    CrossRef   Google Scholar

    [23]

    Jia H, Orbović V, Wang N. 2019. CRISPR-LbCas12a-mediated modification of citrus. Plant Biotechnology Journal 17:1928−37

    doi: 10.1111/pbi.13109

    CrossRef   Google Scholar

    [24]

    Zhang F, LeBlanc C, Irish VF, Jacob Y. 2017. Rapid and efficient CRISPR/Cas9 gene editing in Citrus using the YAO promoter. Plant Cell Reports 36:1883−87

    doi: 10.1007/s00299-017-2202-4

    CrossRef   Google Scholar

    [25]

    Jia H, Xu J, Orbović V, Zhang Y, Wang N. 2017. Editing citrus genome via SaCas9/sgRNA system. Frontiers in Plant Science 8:2135

    doi: 10.3389/fpls.2017.02135

    CrossRef   Google Scholar

    [26]

    Fister AS, Landherr L, Maximova SN, Guiltinan MJ. 2018. Transient expression of CRISPR/Cas9 machinery targeting TcNPR3 enhances defense response in Theobroma cacao. Frontiers in Plant Science 9:268

    doi: 10.3389/fpls.2018.00268

    CrossRef   Google Scholar

    [27]

    Breitler JC, Dechamp E, Campa C, Zebral Rodrigues LA, Guyot R, et al. 2018. CRISPR/Cas9-mediated efficient targeted mutagenesis has the potential to accelerate the domestication of Coffea canephora. Plant Cell, Tissue and Organ Culture 134:383−94

    doi: 10.1007/s11240-018-1429-2

    CrossRef   Google Scholar

    [28]

    Ren C, Liu X, Zhang Z, Wang Y, Duan W, et al. 2016. CRISPR/Cas9-mediated efficient targeted mutagenesis in Chardonnay (Vitis vinifera L.). Scientific Reports 6:32289

    doi: 10.1038/srep32289

    CrossRef   Google Scholar

    [29]

    Wang X, Tu M, Wang D, Liu J, Li Y, et al. 2018. CRISPR/Cas9-mediated efficient targeted mutagenesis in grape in the first generation. Plant Biotechnology Journal 16:844−55

    doi: 10.1111/pbi.12832

    CrossRef   Google Scholar

    [30]

    Nakajima I, Ban Y, Azuma A, Onoue N, Moriguchi T, et al. 2017. CRISPR/Cas9-mediated targeted mutagenesis in grape. PLoS One 12:e0177966

    doi: 10.1371/journal.pone.0177966

    CrossRef   Google Scholar

    [31]

    Ren C, Guo Y, Kong J, Lecourieux F, Dai Z, et al. 2020. Knockout of VvCCD8 gene in grapevine affects shoot branching. BMC Plant Biology 20:47

    doi: 10.1186/s12870-020-2263-3

    CrossRef   Google Scholar

    [32]

    Wang Z, Wang S, Li D, Zhang Q, Li L, et al. 2018. Optimized paired-sgRNA/Cas9 cloning and expression cassette triggers high-efficiency multiplex genome editing in kiwifruit. Plant Biotechnology Journal 16:1424−33

    doi: 10.1111/pbi.12884

    CrossRef   Google Scholar

    [33]

    Varkonyi-Gasic E, Wang T, Voogd C, Jeon S, Drummond RSM, et al. 2019. Mutagenesis of kiwifruit CENTRORADIALIS-like genes transforms a climbing woody perennial with long juvenility and axillary flowering into a compact plant with rapid terminal flowering. Plant Biotechnology Journal 17:869−80

    doi: 10.1111/pbi.13021

    CrossRef   Google Scholar

    [34]

    Chang L, Wu S, Tian L. 2019. Effective genome editing and identification of a regiospecific gallic acid 4-O-glycosyltransferase in pomegranate (Punica granatum L.). Horticulture Research 6:123

    doi: 10.1038/s41438-019-0206-7

    CrossRef   Google Scholar

    [35]

    Ma J, Wan D, Duan B, Bai X, Bai Q, et al. 2019. Genome sequence and genetic transformation of a widely distributed and cultivated poplar. Plant Biotechnology Journal 17:451−60

    doi: 10.1111/pbi.12989

    CrossRef   Google Scholar

    [36]

    Zhou Y, Zhang Y, Wang X, Han X, An Y, et al. 2020. Root-specific NF-Y family transcription factor, PdNF-YB21, positively regulates root growth and drought resistance by abscisic acid-mediated indoylacetic acid transport in Populus. New Phytologist 227:407−26

    doi: 10.1111/nph.16524

    CrossRef   Google Scholar

    [37]

    Fan D, Liu T, Li C, Jiao B, Li S, et al. 2015. Efficient CRISPR/Cas9-mediated targeted mutagenesis in Populus in the first generation. Scientific Reports 5:12217

    doi: 10.1038/srep12217

    CrossRef   Google Scholar

    [38]

    Wang L, Ran L, Hou Y, Tian Q, Li C, et al. 2017. The transcription factor MYB115 contributes to the regulation of proanthocyanidin biosynthesis and enhances fungal resistance in poplar. New Phytologist 215:351−67

    doi: 10.1111/nph.14569

    CrossRef   Google Scholar

    [39]

    Yang L, Zhao X, Ran L, Li C, Fan D, et al. 2017. PtoMYB156 is involved in negative regulation of phenylpropanoid metabolism and secondary cell wall biosynthesis during wood formation in poplar. Scientific Reports 7:41209

    doi: 10.1038/srep41209

    CrossRef   Google Scholar

    [40]

    Xu C, Fu X, Liu R, Guo L, Ran L, et al. 2017. PtoMYB170 positively regulates lignin deposition during wood formation in poplar and confers drought tolerance in transgenic Arabidopsis. Tree Physiology 37:1713−26

    doi: 10.1093/treephys/tpx093

    CrossRef   Google Scholar

    [41]

    Fan D, Wang X, Tang X, Ye X, Ren S, et al. 2018. Histone H3K9 demethylase JMJ25 epigenetically modulates anthocyanin biosynthesis in poplar. The Plant Journal 96:1121−36

    doi: 10.1111/tpj.14092

    CrossRef   Google Scholar

    [42]

    Jiang Y, Guo L, Ma X, Zhao X, Jiao B, et al. 2017. The WRKY transcription factors PtrWRKY18 and PtrWRKY35 promote Melampsora resistance in Populus. Tree Physiology 37:665−75

    doi: 10.1093/treephys/tpx008

    CrossRef   Google Scholar

    [43]

    Elorriaga E, Klocko AL, Ma C, Strauss SH. 2018. Variation in mutation spectra among CRISPR/Cas9 mutagenized Poplars. Frontiers in Plant Science 9:594

    doi: 10.3389/fpls.2018.00594

    CrossRef   Google Scholar

    [44]

    Zhou X, Jacobs TB, Xue LJ, Harding SA, Tsai CJ. 2015. Exploiting SNPs for biallelic CRISPR mutations in the outcrossing woody perennial Populus reveals 4-coumarate: CoA ligase specificity and redundancy. New Phytologist 208:298−301

    doi: 10.1111/nph.13470

    CrossRef   Google Scholar

    [45]

    An Y, Zhou Y, Han X, Shen C, Wang S, et al. 2020. The GATA transcription factor GNC plays an important role in photosynthesis and growth in poplar. Journal of Experimental Botany 71:1969−84

    doi: 10.1093/jxb/erz564

    CrossRef   Google Scholar

    [46]

    Ramos-Sánchez JM, Triozzi PM, Alique D, Geng F, Gao M, et al. 2019. LHY2 integrates night-length information to determine timing of poplar photoperiodic growth. Current Biology 29:2402−2406.E4

    doi: 10.1016/j.cub.2019.06.003

    CrossRef   Google Scholar

    [47]

    Fellenberg C, Corea O, Yan LH, Archinuk F, Piirtola EM, et al. 2020. Discovery of salicyl benzoate UDP-glycosyltransferase, a central enzyme in poplar salicinoid phenolic glycoside biosynthesis. The Plant Journal 102:99−115

    doi: 10.1111/tpj.14615

    CrossRef   Google Scholar

    [48]

    Triozzi PM, Schmidt HW, Dervinis C, Kirst M, Conde D. 2021. Simple, efficient and open-source CRISPR/Cas9 strategy for multi-site genome editing in Populus tremula × alba. Tree Physiology 41:2216−27

    doi: 10.1093/treephys/tpab066

    CrossRef   Google Scholar

    [49]

    Maurya JP, Singh RK, Miskolczi PC, Prasad AN, Jonsson K, et al. 2020. Branching regulator BRC1 mediates photoperiodic control of seasonal growth in hybrid aspen. Current Biology 30:122−126.E2

    doi: 10.1016/j.cub.2019.11.001

    CrossRef   Google Scholar

    [50]

    Li S, Lin YCJ, Wang P, Zhang B, Li M, et al. 2019. The AREB1 transcription factor influences histone acetylation to regulate drought responses and tolerance in Populus trichocarpa. The Plant Cell 31:663−86

    doi: 10.1105/tpc.18.00437

    CrossRef   Google Scholar

    [51]

    Cao S, Wang C, Ji H, Guo M, Cheng J, et al. 2021. Functional characterisation of the poplar atypical aspartic protease gene PtAP66 in wood secondary cell wall deposition. Forests 12:1002

    doi: 10.3390/f12081002

    CrossRef   Google Scholar

    [52]

    Xu W, Cheng H, Zhu S, Cheng J, Ji H, et al. 2021. Functional understanding of secondary cell wall cellulose synthases in Populus trichocarpa via the Cas9/gRNA-induced gene knockouts. New Phytologist 231:1478−95

    doi: 10.1111/nph.17338

    CrossRef   Google Scholar

    [53]

    An Y, Geng Y, Yao J, Fu C, Lu M, et al. 2020. Efficient genome editing in Populus using CRISPR/Cas12a. Frontiers in Plant Science 11:593938

    doi: 10.3389/fpls.2020.593938

    CrossRef   Google Scholar

    [54]

    Cai L, Zhang L, Fu Q, Xu Z. 2018. Identification and expression analysis of cytokinin metabolic genes IPTs, CYP735A and CKXs in the biofuel plant Jatropha curcas. PeerJ 6:e4812

    doi: 10.7717/peerj.4812

    CrossRef   Google Scholar

    [55]

    Fan Y, Xin S, Dai X, Yang X, Huang H, et al. 2020. Efficient genome editing of rubber tree (Hevea brasiliensis) protoplasts using CRISPR/Cas9 ribonucleoproteins. Industrial Crops and Products 146:112146

    doi: 10.1016/j.indcrop.2020.112146

    CrossRef   Google Scholar

    [56]

    Cui Y, Xu J, Cheng M, Liao X, Peng S. 2018. Review of CRISPR/Cas9 sgRNA design tools. Interdisciplinary Sciences: Computational Life Sciences 10:455−65

    doi: 10.1007/s12539-018-0298-z

    CrossRef   Google Scholar

    [57]

    Wang Z, He Z, Qu M, Liu Z, Wang C, et al. 2021. A method for determining the cutting efficiency of the CRISPR/Cas system in birch and poplar. Forestry Research 1:16

    doi: 10.48130/fr-2021-0016

    CrossRef   Google Scholar

    [58]

    Gelvin SB. 2017. Integration of Agrobacterium T-DNA into the plant genome. Annual Review of Genetics 51:195−217

    doi: 10.1146/annurev-genet-120215-035320

    CrossRef   Google Scholar

    [59]

    Cook A, Bono F, Jinek M, Conti E. 2007. Structural biology of nucleocytoplasmic transport. Annual Review of Biochemistry 76:647−71

    doi: 10.1146/annurev.biochem.76.052705.161529

    CrossRef   Google Scholar

    [60]

    Merkle T. 2010. Nucleo-cytoplasmic transport of proteins and RNA in plants. Plant Cell Reports 30:153−76

    doi: 10.1007/s00299-010-0928-3

    CrossRef   Google Scholar

    [61]

    Meier I, Richards EJ, Evans DE. 2017. Cell biology of the plant nucleus. Annual Review of Plant Biology 68:139−72

    doi: 10.1146/annurev-arplant-042916-041115

    CrossRef   Google Scholar

    [62]

    Sikorska N, Zuber H, Gobert A, Lange H, Gagliardi D. 2017. RNA degradation by the plant RNA exosome involves both phosphorolytic and hydrolytic activities. Nature Communications 8:2162

    doi: 10.1038/s41467-017-02066-2

    CrossRef   Google Scholar

    [63]

    Sharma B, Joshi D, Yadav PK, Gupta AK, Bhatt TK. 2016. Role of ubiquitin-mediated degradation system in plant biology. Frontiers in Plant Science 7:806

    doi: 10.3389/fpls.2016.00806

    CrossRef   Google Scholar

    [64]

    Ellison EE, Nagalakshmi U, Gamo ME, Huang P, Dinesh-Kumar S, et al. 2020. Multiplexed heritable gene editing using RNA viruses and mobile single guide RNAs. Nature Plants 6:620−24

    doi: 10.1038/s41477-020-0670-y

    CrossRef   Google Scholar

    [65]

    Ji X, Yang B, Wang D. 2020. Achieving plant genome editing while bypassing tissue culture. Trends in Plant Science 25:427−29

    doi: 10.1016/j.tplants.2020.02.011

    CrossRef   Google Scholar

    [66]

    Maher MF, Nasti RA, Vollbrecht M, Starker CG, Clark MD, et al. 2020. Plant gene editing through de novo induction of meristems. Nature Biotechnology 38:84−89

    doi: 10.1038/s41587-019-0337-2

    CrossRef   Google Scholar

    [67]

    Liao T, Liu G, Guo L, Wang Y, Yao Y, et al. 2021. Bud initiation, microsporogenesis, megasporogenesis, and cone development in Platycladus orientalis. HortScience 56:85−93

    doi: 10.21273/hortsci15479-20

    CrossRef   Google Scholar

    [68]

    Watson A, Ghosh S, Williams MJ, Cuddy WS, Simmonds J, et al. 2018. Speed breeding is a powerful tool to accelerate crop research and breeding. Nature Plants 4:23−29

    doi: 10.1038/s41477-017-0083-8

    CrossRef   Google Scholar

    [69]

    Kapiel TY. 2018. Speed breeding: a powerful innovative tool in agriculture. Innovative Techniques in Agriculture 2:413−15

    Google Scholar

    [70]

    Ochatt SJ, Sangwan RS. 2008. In vitro shortening of generation time in Arabidopsis thaliana. Plant Cell, Tissue and Organ Culture 93:133−37

    doi: 10.1007/s11240-008-9351-7

    CrossRef   Google Scholar

    [71]

    Samineni S, Sen M, Sajja SB, Gaur PM. 2020. Rapid generation advance (RGA) in chickpea to produce up to seven generations per year and enable speed breeding. The Crop Journal 8:164−69

    doi: 10.1016/j.cj.2019.08.003

    CrossRef   Google Scholar

    [72]

    Collard BCY, Beredo JC, Lenaerts B, Mendoza R, Santelices R, et al. 2017. Revisiting rice breeding methods - evaluating the use of rapid generation advance (RGA) for routine rice breeding. Plant Production Science 20:337−52

    doi: 10.1080/1343943X.2017.1391705

    CrossRef   Google Scholar

    [73]

    Jähne F, Hahn V, Würschum T, Leiser WL. 2020. Speed breeding short-day crops by LED-controlled light schemes. Theoretical and Applied Genetics 133:2335−42

    doi: 10.1007/s00122-020-03601-4

    CrossRef   Google Scholar

    [74]

    Zheng Z, Wang HB, Chen GD, Yan GJ, Liu CJ. 2013. A procedure allowing up to eight generations of wheat and nine generations of barley per annum. Euphytica 191:311−16

    doi: 10.1007/s10681-013-0909-z

    CrossRef   Google Scholar

    [75]

    Kong J, Martin-Ortigosa S, Finer J, Orchard N, Gunadi A, et al. 2020. Overexpression of the transcription factor GROWTH-REGULATING FACTOR5 improves transformation of dicot and monocot species. Frontiers in Plant Science 11:572319

    doi: 10.3389/fpls.2020.572319

    CrossRef   Google Scholar

    [76]

    Debernardi JM, Tricoli DM, Ercoli MF, Hayta S, Ronald P, et al. 2020. A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants. Nature Biotechnology 38:1274−79

    doi: 10.1038/s41587-020-0703-0

    CrossRef   Google Scholar

    [77]

    Lowe K, Wu E, Wang N, Hoerster G, Hastings C, et al. 2016. Morphogenic regulators Baby boom and Wuschel improve monocot transformation. The Plant Cell 28:1998−2015

    doi: 10.1105/tpc.16.00124

    CrossRef   Google Scholar

    [78]

    Mianné J, Codner GF, Caulder A, Fell R, Hutchison M, et al. 2017. Analysing the outcome of CRISPR-aided genome editing in embryos: screening, genotyping and quality control. Methods 121−122:68−76

    doi: 10.1016/j.ymeth.2017.03.016

    CrossRef   Google Scholar

    [79]

    van Overbeek M, Capurso D, Carter MM, Thompson MS, Frias E, et al. 2016. DNA repair profiling reveals nonrandom outcomes at Cas9-mediated breaks. Molecular Cell 63:633−46

    doi: 10.1016/j.molcel.2016.06.037

    CrossRef   Google Scholar

    [80]

    Shen MW, Arbab M, Hsu JY, Worstell D, Culbertson SJ, et al. 2018. Predictable and precise template-free CRISPR editing of pathogenic variants. Nature 563:646−51

    doi: 10.1038/s41586-018-0686-x

    CrossRef   Google Scholar

    [81]

    Allen F, Crepaldi L, Alsinet C, Strong AJ, Kleshchevnikov V, et al. 2019. Predicting the mutations generated by repair of Cas9-induced double-strand breaks. Nature Biotechnology 37:64−72

    doi: 10.1038/nbt.4317

    CrossRef   Google Scholar

    [82]

    Leenay RT, Aghazadeh A, Hiatt J, Tse D, Roth TL, et al. 2019. Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells. Nature Biotechnology 37:1034−37

    doi: 10.1038/s41587-019-0203-2

    CrossRef   Google Scholar

    [83]

    Li VR, Zhang Z, Troyanskaya OG. 2021. CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes. Bioinformatics 37:i342−i348

    doi: 10.1093/bioinformatics/btab268

    CrossRef   Google Scholar

    [84]

    Pickar-Oliver A, Gersbach CA. 2019. The next generation of CRISPR-Cas technologies and applications. Nature Reviews Molecular Cell Biology 20:490−507

    doi: 10.1038/s41580-019-0131-5

    CrossRef   Google Scholar

    [85]

    Adli M. 2018. The CRISPR tool kit for genome editing and beyond. Nature Communications 9:1911

    doi: 10.1038/s41467-018-04252-2

    CrossRef   Google Scholar

    [86]

    Thakore PI, Black JB, Hilton IB, Gersbach CA. 2016. Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nature Methods 13:127−37

    doi: 10.1038/nmeth.3733

    CrossRef   Google Scholar

    [87]

    Dominguez AA, Lim WA, Qi LS. 2016. Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nature Reviews Molecular Cell Biology 17:5−15

    doi: 10.1038/nrm.2015.2

    CrossRef   Google Scholar

    [88]

    Shalem O, Sanjana NE, Zhang F. 2015. High-throughput functional genomics using CRISPR-Cas9. Nature Reviews Genetics 16:299−311

    doi: 10.1038/nrg3899

    CrossRef   Google Scholar

    [89]

    Singh V. 2020. An introduction to genome editing CRISPR-Cas systems. In Genome Engineering via CRISPR-Cas9 System, eds. Singh V, Dhar PK. Academic Press, Elsevier. pp. 1−13 https://doi.org/10.1016/B978-0-12-818140-9.00001-5

    [90]

    Goell JH, Hilton IB. 2021. CRISPR/Cas-based epigenome editing: advances, applications, and clinical utility. Trends in Biotechnology 39:678−91

    doi: 10.1016/j.tibtech.2020.10.012

    CrossRef   Google Scholar

    [91]

    Moradpour M, Abdulah SNA. 2020. CRISPR/dCas9 platforms in plants: strategies and applications beyond genome editing. Plant Biotechnology Journal 18:32−44

    doi: 10.1111/pbi.13232

    CrossRef   Google Scholar

    [92]

    Karlson CKS, Mohd-Noor SN, Nolte N, Tan BC. 2021. CRISPR/dCas9-based systems: mechanisms and applications in plant sciences. Plants 10:2055

    doi: 10.3390/plants10102055

    CrossRef   Google Scholar

    [93]

    Atkins PA, Voytas DF. 2020. Overcoming bottlenecks in plant gene editing. Current Opinion in Plant Biology 54:79−84

    doi: 10.1016/j.pbi.2020.01.002

    CrossRef   Google Scholar

    [94]

    Huang TK, Puchta H. 2019. CRISPR/Cas-mediated gene targeting in plants: finally a turn for the better for homologous recombination. Plant Cell Reports 38:443−53

    doi: 10.1007/s00299-019-02379-0

    CrossRef   Google Scholar

    [95]

    Yang B, Yang L, Chen J. 2019. Development and application of base editors. The CRISPR Journal 2:91−104

    doi: 10.1089/crispr.2019.0001

    CrossRef   Google Scholar

    [96]

    Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, et al. 2019. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576:149−57

    doi: 10.1038/s41586-019-1711-4

    CrossRef   Google Scholar

    [97]

    Matsoukas IG. 2020. Prime editing: genome editing for rare genetic diseases without double-strand breaks or donor DNA. Frontiers in Genetics 11:528

    doi: 10.3389/fgene.2020.00528

    CrossRef   Google Scholar

    [98]

    Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. 2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:420−24

    doi: 10.1038/nature17946

    CrossRef   Google Scholar

    [99]

    Marzec M, Hensel G. 2018. Targeted base editing systems are available for plants. Trends in Plant Science 23:955−57

    doi: 10.1016/j.tplants.2018.08.011

    CrossRef   Google Scholar

    [100]

    Marzec M, Hensel G. 2020. Prime editing: game changer for modifying plant genomes. Trends in Plant Science 25:722−24

    doi: 10.1016/j.tplants.2020.05.008

    CrossRef   Google Scholar

  • Cite this article

    Pak S, Li C. 2022. Progress and challenges in applying CRISPR/Cas techniques to the genome editing of trees. Forestry Research 2:6 doi: 10.48130/FR-2022-0006
    Pak S, Li C. 2022. Progress and challenges in applying CRISPR/Cas techniques to the genome editing of trees. Forestry Research 2:6 doi: 10.48130/FR-2022-0006

Figures(3)  /  Tables(1)

Article Metrics

Article views(7379) PDF downloads(1321)

Other Articles By Authors

REVIEW   Open Access    

Progress and challenges in applying CRISPR/Cas techniques to the genome editing of trees

Forestry Research  2 Article number: 6  (2022)  |  Cite this article

Abstract: With the advent of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) system, plant genome editing has entered a new era of robust and precise editing for any genes of interest. The development of various CRISPR/Cas toolkits has enabled new genome editing outcomes that not only target indel mutations but also enable base editing and prime editing. The application of the CRISPR/Cas toolkits has rapidly advanced breeding and crop improvement of economically important species. CRISPR/Cas toolkits have also been applied to a wide variety of tree species, including apple, bamboo, Cannabaceae, cassava, citrus, cacao tree, coffee tree, grapevine, kiwifruit, pear, pomegranate, poplar, ratanjoyt, and rubber tree. The application of editing to these species has resulted in significant discoveries related to critical genes associated with growth, secondary metabolism, and stress and disease resistance. However, most studies on tree species have involved only preliminary optimization of editing techniques, and a more in-depth study of editing techniques for CRISPR/Cas-based editing of tree species has the potential to rapidly accelerate tree breeding and trait improvements. Moreover, tree genome editing still relies mostly on Cas9-based indel mutation and Agrobacterium-mediated stable transformation. Transient transformation for transgene-free genome editing is preferred, but it typically has very low efficiency in tree species, substantially limiting its potential utility. In this work, we summarize the current status of tree genome editing practices using the CRISPR/Cas system and discuss limitations that impede the efficient application of CRISPR/Cas toolkits for tree genome editing, as well as future prospects.

    • Trees are essential components of most ecosystems that play significant roles in lowering the atmospheric level of CO2, protecting biodiversity, and providing food and materials for human consumption. Ever-increasing demands for forest products, as well as concerns about global warming due to elevated CO2 levels, have increased the need for more efficient improvement of tree varieties. In the past, researchers and breeders have employed traditional approaches, including hybrid breeding, mutagenesis, and polyploid breeding, to achieve a variety of trait improvements and gain a better understanding of gene function. Traditional breeding approaches require tremendous time, and mutation screening is dramatically hindered by tree species' long generation time and complex genome polyploidy and heterozygosity. The advent of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) genome editing technology has significantly accelerated plant breeding and functional genomics with high speed and precision.

      The CRISPR/Cas approach involves an adaptive phage immunity system from archaea and bacteria. This system relies on a single RNA called "single guide RNA" (sgRNA) to guide DNA–RNA recognition and binding for sequence-specific nucleic acid cleavage and can be readily programmed to introduce DNA double-strand breaks (DSBs) at any desired target site at minimal cost[1]. For more than two decades, CRISPR/Cas systems were of interest mainly to microbiologists who investigated the unique mechanisms underlying the CRISPR/Cas adaptive immunity systems of prokaryotes. The potential for CRISPR/Cas systems to serve as genome editing tools was initially recognized in 2012; thereafter, they began to be applied to mammals and were developed into crucial tools for research and clinical applications such as gene therapy[2,3]. CRISPR/Cas systems have also been widely used in plants. CRISPR/Cas was first applied to plants in 2013[4] and has subsequently been used in 45 plant genera from 24 different families, demonstrating the high efficiency, simplicity, and versatility of this system[5]. Various Cas9 variant proteins such as Cas12a (Cpf1), Cas13, and Cas14, as well as nuclease-deactivated Cas proteins (dCas9 or dCas12) fused with a base editor, prime editor, or other epigenomic modifier proteins, have been developed to enhance the versatility of CRISPR toolkits in mammals and plants[3,68]. Moreover, the requirement for a protospacer adjacent motif (PAM), which is a natural constraint on the flexibility of CRISPR toolkits, has recently been overcome. PAM-free nucleases such as SpRY have been generated through natural ortholog mining and protein engineering, enabling the targeting of virtually any site in genomic DNA[9].

      The application of CRISPR/Cas for gene function studies and trait improvement has been comparatively slow in tree species. In 2014, tree genome editing by the Cas9/sgRNA system was first reported in a citrus genome[10], in which rapid and precise mutation of target genes was demonstrated within a short period (4 days) at a low efficiency (3.2%–3.9%). Significant effort has been made to improve the efficiency and stability of targeted mutagenesis in various tree species, such as apple[1113], bamboo[14,15], Cannabaceae[16], cassava[1719], citrus[10,2025], cacao tree[26], coffee tree[27], grapevine[12,2831], kiwifruit[32,33], pear[11], pomegranate[34], poplar[3553], ratanjoyt[54], and rubber tree[55]. These efforts have not only contributed to the establishment of CRISPR/Cas based-genome editing systems in trees[1014,17,2325,2730,32,35,37,43,48,53,55] but also promoted functional studies on tree trait genes that are crucial for tree breeding. Table 1 shows recent applications of CRISPR/Cas toolkits to tree genome editing. These practices all involve the sequential procedures of target gene selection, sgRNA design, and nuclease/sgRNA DNA vector construction or ribonucleoprotein preparation. These initial steps are followed by transformation, regeneration, screening of transformants, and mutation detection. Most practices have used the Cas9 nuclease, but there have been a few reported uses of the Cas12a nuclease[23,53]. Agrobacterium-mediated stable transformation has been the dominant transformation protocol, but despite its high efficiency, it is impractical owing to the current GMO (genetically modified organism) regulations in application. Transient transformation protocols such as the delivery of ribonucleo-protein (RNP) complexes can achieve transgene-free (non-GMO) genome editing and are therefore preferred. However, these approaches have much lower efficiency[12,55], limiting their wide application. Overall, significant progress will be required to increase the utility of the CRISPR/Cas system in tree species. In this review, we summarize current progress in CRISPR/Cas-based tree genome editing and discuss limitations that affect the efficiency of this system, as well as future prospects.

      Table 1.  Application of the CRISPR/Cas system to tree genome editing.

      Tree speciessgRNA design
      tool
      Cas delivery enhancerPromoter
      (sgRNA)
      Promoter
      (Cas)
      Multiplex targetingTransformation protocol/explantRegeneration protocol/timeMutagenesis efficiency; mutation; mutantsPotential off-targets (Number; activity)Reference
      Actinidia chinensis
      cv. Hongyang
      Cas-DesignerNLSAtU635SPTGAgrobacterium/
      leaf disc
      CI-S; —7.14%–91.67%; indel; biallelic, chimeric4; N[32]
      A. chinensis
      cv. Hort16A
      GeneiousNLSAtU3, AtU6Ubi, 35SPTGAgrobacterium/
      leaf strip
      CI-S-R; —30%–75%; indel; biallelic, heterozygous[33]
      Bambusa oldhamiiNLSOsU32× 35SPEG (DNA)/protoplastCI-S; 3 mon12.5% (5/40); del&subs; —[14]
      Citrus sinensis cv. ValenciaNLS35S35SAgroinfiltration/leaf3.2%–3.9%; del; —46; N[10]
      C. sinensis OsbeckAtU635SAgrobacterium/epicotylS-G; —34.5% (38/110); del; biallelic, homozygous, heterozygous11; 1-bp point mutations (5–10%)[20]
      C. paradisiNLS35S35SAgrobacterium/epicotylS-G; ——; indel; —85; N[21]
      35SAgrobacterium/leaf & epicotylS-G; —23.8%–89.36%; indel; —7; N[22]
      Yao, 35SAgrobacterium/epicotylS-G; —42.8% (3/7); del; —0[23]
      Dendrocalamus latiflorus MunroOsU6UbiPEG (DNA)/protoplastCI-S-R; —83.3%–100%; indel; homozygous, biallelic, heterozygous, chimeric[15]
      Hevea brasiliensisPEG (RNP)/protoplast3.74%–20.11%; indel; —[55]
      Malus × domestica Bork.CRISPORNLSMdU3, MdU6PcUbi4-2Gateway cloningAgrobacterium/young leavesB; 6 mon90% (27/30); indel&subs; biallelic chimeric4; N[11]
      Malus prunifolia cv. Golden DeliciousCRISPR RGENNLSPEG (RNP)/protoplast6.9%; indel; —[12]
      M. prunifolia Borkh. 'Seishi'× M.NLSAtU62× 35SAgrobacterium/leaf discS-R; 8 mon10.9% (18/164); indel; homozygous, heterozygous, chimeric0[13]
      Coffea canephora
      clone 197
      NLSAtU635SRestriction enzyme ligationAgrobacterium/
      embryonic calli
      SE; 18 mon30.4% (28/92); indel; homozygous, heterozygous0[27]
      Manihot esculenta cv. 60444; cv. TME 204CRISPR-PNLSAtU635SAgrobacterium/
      embryonic calli
      SE; —19.1%–46.6%; indel&subs; homozygous, biallelic, heterozygous[17]
      M. esculenta
      cv. 60444
      CRISPR-PAtU62× 35SGibson assemblyAgrobacterium/
      embryonic calli
      SE; —91%; indel; homozygous, biallelic, heterozygous, chimeric5; single mutation for one off-target was detected[18]
      Jatropha curcasCRISPR-PNLSAtU335SAgrobacterium/cotyledonCI-S; 4 mon—; indel; homozygous[54]
      Parasponia
      andersonii
      GPP sgRNA designerNLSAtU635SAgrobacterium/
      stem, petiole
      CI-S-R; 4 mon37.9%–88.9%; indel; biallelic, heterozygous[16]
      Poncirus. trifoliata L. Raf. × C. sinensis L.
      Osb
      NLSAtU6YaoAgrobacterium/epicotylS; 4 mon85% (17/20); indel&subs; homozygous, monoallelic heterozygous2; N[24]
      35S, AtU635SAgrobacterium/epicotylS-G; —15.55%–79.67%; indel; homozygous3; N[25]
      Populus albaZiFiTNLSAtU3, AtU635SGolden Gate cloningAgrobacterium/young leavesCI-S-R; 3 mon89%; del; —[35]
      84K poplar (P. alba ×
      P. glandulosa)
      CRISPR-P 2.0NLSAtU6PcUbi4-2Agrobacterium/leaf disc—; indel; —[36]
      NLSAtU62× 35SAgrobacterium/leaf discCI-S-R; —6.7%–70%; del; biallelic, homozygous, heterozygous[53]
      Populus tomentosa Carr. clone 741NLSAtU3, AtU635SGolden Gate cloningAgrobacterium/leaf discCI-S-R; 3 mon51.7% (30/59); indel&invers; biallelic homozygous, heterozygous[37]
      Golden Gate cloningAgrobacterium/leaf discCI-S-R; —93.33%–100%; indel; —[38]
      35SGolden Gate cloningAgrobacterium/leaf discCI-S-R; —48% (12/25); indel; —[39]
      35SGolden Gate cloningAgrobacterium/leaf discCI-S-R; ——; indel; —[40]
      35SAgrobacterium/leaf discCI-S-R; ——; indel; —[41]
      35SGolden Gate cloningAgrobacterium/leaf discCI-S-R; ——; indel; —[42]
      Populus tremula × P. alba clone 717ZiFiTNLSAtU62× 35SRestriction enzyme ligationAgrobacterium/leaf, petiole, stemCI-S-R; 18 wk81.8% (479/585); indel&subs&invers; homozygous, biallelic, heterozygous, chimeric5; N[43]
      GeneiousNLSMtU62× 35SAgrobacterium/
      leaf, stem
      CI-S-R; —100%; indel; biallelic[44]
      GeneiousNLSAtU6PcUbi4-2Agrobacterium/leaf discCI-S-R; 4–8 mon—; indel; —[45]
      Populus tremula × P. alba INRA clone 717-1B4MtU635SAgrobacterium/ —CI; —[46]
      GeneiousNLSMtU62× 35SAgrobacterium/
      hairy root
      HR; —40%; indel; —5; N[47]
      CRISPR-P 2.0NLSAtU6Atact2Golden Gate MoClo system assemblyAgrobacterium/leafHR; —87.5% (14/16); indel; homozygous, biallelic, heterozygous[48]
      Populus tremula × tremuloides clone 353ZiFiTNLSAtU62× 35SRestriction enzyme ligationAgrobacterium/leaf, petiole, stemCI-S-R; 18 wk88.8% (88/99); indel&subs&invers; homozygous, biallelic, heterozygous, chimeric5; N[43]
      Populus tremula × tremuloides clone T89CRISPR-P 2.0NLS35SGolden Gate cloningAgrobacterium/ —[49]
      Populus trichocarpa Nisqually-1CRISPR-P 2.03x NLSAtU62× 35S, PUbi4Golden Gate cloningAgrobacterium/leaf discCI-S; ——; indel; —[50]
      AtU62× 35SAgrobacterium/stemS-R; 17 wk—; indel; —[51]
      CRISPRdirectAtU62× 35SGolden Gate cloningAgrobacterium/stemS-R; 14 wk75%–100%; indel; homozygous, biallelic, heterozygous, chimeric8; N[52]
      Punica granatum L.Cas-DesignerNLSAtU6AtUbiRestriction enzyme ligationAgrobacterium/
      hairy root
      HR; ——; indel&subs; homozygous, biallelic, chimeric[34]
      Pyrus communis L. cv. ConferenceCRISPORNLSMdU3, MdU6PcUbi4-2Gateway cloningAgrobacterium/young leavesB; 7 mon9% (5/54); indel&subs; biallelic chimerism4; N[11]
      Theobroma cacaoGeneiousAtU635SGolden Gate cloningAgrobacterium/leaf, primary SE cotyledonSE; —27%; indel; —9; 0.29–1.9% (off-target rate)[26]
      Vitis vinifera L. cv. ChardonnayCRISPR-PNLSAtU635SGolden Gate cloningAgrobacterium/callusS; —100% (3/3); indel; heterozygous, chimeric4; N[28]
      CRISPR RGENNLSPEG (RNP)/protoplast0.1%; indel; —[12]
      V. vinifera cv. ThompsonCRISPR-P, CRISPR RGENNLSAtU3, AtU62× 35SGolden Gate cloningAgrobacterium/
      embryonic callus
      SE; 12 mon31% (22/72); large del; biallelic, monoallelic6; N[29]
      V. vinifera L. cv. Neo MuscatNLSAtU6PcUbiAgrobacterium/
      embryonic callus
      CI-SE; 19–21 mon2.7%–72.2%; indel; biallelic3; N[30]
      V. vinifera cv. Chasselas × V. berlandieriCRISPR-PAtU635SAgrobacterium/
      embryonic cell
      SE; —66.6% (4/6); indel; biallelic, heterozygous, chimeric2; N[31]
      Abbreviations: NLS, nuclear localization signal; AtU3/AtU6, Arabidopsis promoters for small nuclear RNA transcription; MtU3/MtU6, Medicago truncatula U3/6 promoters; MdU3/MdU6, Malus domestica U3/6 promoters; Cas, Cas nucleases; 35S, cauliflower mosaic virus (CaMV) 35S promoter; Ubi, ubiquitin promoter; PcUbi, Petroselinum crispum ubiquitin promoter; PTG, Polycistronic tRNA process system; GFP, green fluorescent protein; Agrobacterium, Agrobacterium-mediated T-DNA transfer; PEG (DNA), Polyethylene glycol–mediated DNA transfection; PEG (RNP), Polyethylene glycol–mediated ribonucleoprotein transfection; mon, month; wk, week; B, budding; CI, callus induction; S, shooting; R, rooting; G, grafting; SE, somatic embryogenesis; indel, insertion and deletion mutations; del, deletion mutation; subs, substitution mutation; invers, sequence inversion mutation; N, no activity detected; —, not mentioned.
    • The CRISPR/Cas system is a major reverse genetics tool in functional genomics, and its application to trees has greatly promoted tree functional genomics. Various tree trait genes associated with early flowering[33,46,49], growth[15,31,36,45,54], symbiosis[16], lignin biosynthesis associated with secondary growth for wood formation[39,40,51,52], secondary metabolism[34], and resistance to abiotic stresses[36,40,50], diseases[1822,26,38,41,42], and herbivores[47] have been functionally characterized by CRISPR/Cas techniques.

      Since the application of CRISPR/Cas techniques to trees, tree breeding and trait improvement have been accelerated in parallel with rapid progress in tree functional genomics. In poplars, important woody species with high economic and ecological value, CRISPR/Cas9-mediated targeted mutagenesis has been used together with other genetic approaches to characterize the roles of important wood formation-related genes such as PtoMYB156[39], PtoMYB170[40], Atypical aspartic protease (PtAP66)[51], and cellulose synthase (PtrCesA)[52], highlighting their potential utility for enhancing the productivity and quality of wood. Functional characterization of PdNF-YB21[36], PdGNC[45], LHY2[46], and BRC1[49] by CRISPR/Cas9 and other genetic tools suggested that these genes have crucial roles in the regulation of root growth, photosynthesis, and seasonal growth cessation and therefore showed great potential for the breeding of fast-growing poplars. Transcription factors such as PtrABRE1[50], PtoMYB170[40], and PdNF-YB21[36] have been demonstrated to regulate the response of poplar to drought stress, suggesting that they may be useful for breeding drought-resistant poplars. CRISPR/Cas9-mediated loss-of-function mutation has also contributed to the characterization of the MYB115 transcription factor[38], the histone H3K9 demethylase gene JMJ25[41], the PtrWRKY18 and PtrWRKY35 transcription factors[42], and salicyl benzoate UDP-glycosyltransferase[47], which are anti-fungal and anti-herbivore factors that are important for breeding fungal disease-resistant or herbivore-resistant poplars. In citrus, a widely cultivated fruit tree, the CRISPR/Cas system has been used to engineer canker disease-resistant varieties by targeting the promoter region of the disease susceptibility gene CsLOB1[2022]. In cassava, a woody shrub extensively cultivated for its edible starchy tuberous root, two different approaches have been used to improve resistance to viral diseases. One involved knockout of the host eIF4E gene, which is crucial for interaction with viral genome-linked protein (VPg)[18], and the other used CRISPRi (CRISPR interference) to target viral ACMV (African cassava mosaic virus) DNA A[19]. In cacao tree, the source of cocoa, CRISPR/Cas9 demonstrated its potential to enable the development of pathogen-resistant cacao varieties through editing of the Non-Expressor of Pathogenesis-Related 3 (TcNPR3) gene[26]. In kiwifruit, a recently domesticated fruit tree species, the wild-type traits of perennial growth, non-compactness, long juvenility, and axillary flowering have hampered fruit development and productivity. CRISPR/Cas9-mediated mutation of the kiwifruit CEN-like gene AcCEN4 or AcCEN transformed the wild-type plant into a compact plant with rapid terminal flowering, and the engineered kiwifruit plants were amenable to indoor farming and cultivation as annuals[33]. In grapevine, the source of grapes for direct consumption and fermentation into wine, CRISPR/Cas9-mediated knockout of the strigolactone (SL) biosynthesis genes CCD7/8 enhanced shoot branching, showing the potential to increase grape productivity[31].

    • The initial step of CRISPR/Cas genome editing is the design of sgRNAs against selected target genes, and well-designed sgRNAs are critical to editing success. Ideally, an sgRNA targeting sequence will have perfect homology to the target DNA, with no homology elsewhere in the genome. Online bioinformatic tools such as Cas-Designer[32,34], CRISPOR[11], CRISPR-P[17,18,28,29,31,36,4850,54], CRISPR RGEN[12,29,52], and ZiFiT[35,3743], as well as the offline software tool Geneious[33,44,45,47], have been used to design target-specific sgRNAs. However, the low availability of complete genome data for tree species has typically caused issues when attempting to assess on-target efficiency and potential off-targeting.

      Recent efforts to sequence the genomes of trees have dramatically improved the design of sgRNAs. The TreeGenes database (https://treegenesdb.org) is a comprehensive resource for forest tree genomics that now includes complete genome sequences of 38 species and 3,920,817 transcriptome sequences from 263 tree species. Using these tree genomic resources and sgRNA design tools, it is now easy to design sgRNAs that are highly specific to any target DNA sequence and to predict on-target efficiency as well as off-target sites. Many of these tree genomic resources have already been uploaded to sgRNA design tools. Among the sgRNA design tools[56], Cas-OFFinder, CCTop, CHOPCHOP, CRISPOR, CRISPRdirect, CRISPR-P v2.0, and E-CRISP now incorporate genome data from several tree species, enabling the genome-wide design of sgRNAs (see Supplemental Table S1). The genome data of 28 tree species are now available, including Actinidia chinensis, Actinidia eriantha, Carica papaya, Citrus clementina, Citrus sinensis, Coffea canephora, Diospyros kaki, Eucalyptus grandis, Juglans macrocarpa, Juglans regia, Malus domestica, Manihot esculenta, Musa acuminata, 717 hybrid poplar, Populus alba (sPta717 v2), Populus alba × Populus tremula var. glandulosa, Populus deltoides, Populus tremula, Populus tremula × alba, Populus tremula × tremuloides, Populus tremuloides, Populus trichocarpa, Prunus avium, Prunus persica, Pyrus × bretschneideri, Ricinus communis, Theobroma cacao, and Vitis vinifera. Cas-OFFinder, CCTop, CHOPCHOP, CRISPOR, and CRISPRdirect users can now also send requests for the addition of new genome data specific to their research, as long as the genome data are present in TreeGenes or other genome databases, including Ensembl, NCBI, and Phytozome. For tree species without sequenced genomes, the use of CRISPR still relies on gene cloning to obtain the target gene sequence (typically only exons), and off-target sites cannot be reliably predicted.

      The sgRNA design tools also support the identification of sgRNAs without a genome sequence, although only cleavage efficiency is scored.

      Several studies have shown that large genome size, high polyploidy and heterozygosity, and abundant single nucleotide polymorphisms (SNPs) in tree genomes cause significant problems in the design of highly target-specific sgRNAs. The frequent occurrence of SNPs in tree genomes (as many as 1 per 100 bp) can completely abolish cleavage of the target gene when they exist in the target sequence or the PAM sequence[44]. Recent efforts to sequence more tree genomes will undoubtedly remove these limitations and ensure more precise genome editing of tree species.

    • Once sgRNAs are designed against target genes, they are inserted into plasmid vectors that contain the DNA sequence encoding a nuclease, such as Cas9, or directly mixed with the nuclease protein prior to transformation into tree explants. Target-specific nuclease tools such as Cas9/sgRNAs can be delivered via plasmid binary vectors or RNP complexes.

      The most widely used form of CRISPR/Cas reagent is the Agrobacterium Ti plasmid binary vector, which harbors sequences of the Cas9 nuclease gene and designed sgRNAs in the T-DNA portion. During the construction of T-DNA vectors containing the Cas nuclease/sgRNAs expression cassette, the nuclear localization signal (NLS) has typically been fused to the Cas nuclease to enhance proper transport of Cas nuclease into the nucleus. Because the Cas9 nuclease is bacterial in origin, its codons are typically optimized for eukaryotic translation[3547,49,50]. Promoters such as CaMV 35S, ubiquitin, and U3/6 small nuclear RNA (snRNA) have been used to drive the transcription of Cas nuclease genes and sgRNAs. The CaMV 35S promoter and ubiquitin promoter are strong constitutive promoters that drive Cas9 gene expression broadly. This promoter is often used as a form of dual promoter to enhance Cas9 gene transcription. Some studies have also used the meristem-specific Yao promoter to improve Cas nuclease expression efficiency[23,24]. For sgRNA transcription, U3/6 snRNA promoters have typically been employed. These promoters require A/G to be the first nucleotide at the transcription start site, which limits their utility[10,2123,25]. Targeting of multiple genes or multiple sites in a gene has been performed using a multiple sgRNA cassette in a single CRISPR/Cas construct[11,18,2629,3235,3740,42,43,4850,52], and the efficiency of multiplex gene editing has been improved by the use of a polycistronic tRNA-sgRNA cassette (PTG)[32,33].

      The use of a ribonucleoprotein complex with Cas nuclease protein and sgRNAs has been reported in some studies[12,55]. RNPs work transiently and then disappear, limiting potential off-targeting that can occur during prolonged Cas9 activity and enabling transgene-free genome editing that can avoid GMO regulation. The use of RNPs can also reduce the time required for Cas9 to be transcribed and translated in the Ti plasmid vector. Moreover, unlike plasmid vectors, RNP construction does not require codon optimization and species- and tissue-specific promoters.

      The delivery of CRISPR/Cas reagents has mainly been achieved by Agrobacterium-mediated T-DNA integration into the genome. This stable transformation approach has been shown to result in highly efficient mutagenesis, but prolonged expression of the Cas9 nuclease has the potential to create off-target effects. In addition, delivery and further integration of the transgene is not favorable in the current regulations in application. Alternatively, transient expression approaches such as RNP transfection have been used to reduce off-targeting and achieve transgene-free genome editing, but they typically result in much lower editing efficiency[12]. The explants used for transformation include mostly the juvenile leaf, stem, petiole, embryogenic callus, and occasionally protoplasts. As the cell wall–free protoplast can easily take up exogenous transformation materials such as DNA or RNP, it is regarded as the "ideal" explant tissue for direct transformation approaches, including PEG (polyethylene glycol)-mediated transfer, electroporation, liposome-mediated transfer, biolistic bombardment, and others. However, it has only been reported in a few tree species[12,14,15,55].

    • In general, transformation is immediately followed by sequential tissue culture phases such as callus induction, shooting, and rooting. With the aid of tissue culture techniques, mutant cells can be readily cloned and then regenerated into whole plants. Stable inheritance of T-DNA containing CRISPR/Cas constructs within cells is critical for successful targeted mutagenesis, but could be subjected to the GMO regulations. RNP transfection has therefore been used as an alternative to avoid these issues and potentially reduce off-target effects[12,55]. Because all cells of the explant undergo regeneration under tissue culture conditions, selection markers such as antibiotic resistance genes (NPTII or HPTII) or reporter genes (GUS or GFP) have been used to identify transformants among regenerated plants. Mutations in the site of target genes and potential off-targets can then be detected by PCR and direct sequencing of the target gene amplicons. In most studies, no off-targeting has been detected even after stable transformation, despite the presence of potential off-targets (Table 1). Various kinds of on-target mutagenesis have been found, including biallelic, homozygous, heterozygous, and chimeric mutations.

    • As shown in Table 1, targeted mutagenesis using the CRISPR/Cas system in trees still relies on the laborious and tedious processes of conventional protocols for the transformation of CRISPR/Cas reagents and the regeneration of transformants. Among conventional transformation protocols, Agrobacterium mediated transformation protocols are most efficient and have been most widely employed, but they have still been restricted to a few types of explants such as the juvenile leaf, petiole, cotyledon, or embryogenic cell masses within only a small percentage of tree species because many economically important tree species such as citrus trees are generally recalcitrant to Agrobacterium infection. Moreover, tissue culture systems have only been established for a limited number of tree species, with several species, such as Theobroma cacao, shown to be recalcitrant to this approach. Even for tree species with no tissue culture problems, transformation efficiency is far below 100%, resulting in significant regeneration of non-transgenic plantlets as well as transgenic plantlets that lack the desired edits (Fig. 1).

      Figure 1. 

      Schematic diagram for the wet-lab workflow of CRISPR/Cas-based genome editing, showing the limitations of current transformation and regeneration protocols. After CRISPR/Cas reagents, such as a plasmid DNA vector or RNP for the genes of interest, are transformed into explant cells, these cells must then be regenerated into mutant transgenic plants. Each step of the tissue culture process reduces its efficiency owing to the regeneration of non-transformed plants and the regeneration of transformed plants that lack the desired edit. Antibiotics are typically added to the culture medium to increase the proportion of transformed cells by inhibiting the growth of non-transformed cells (only in the Agrobacterium T-DNA transfer method). The transformation efficiency, regeneration rate, and in vivo activity of CRISPR/Cas reagents all impact the total genome editing efficiency during this process. However, genome editing efficiency in most tree genome editing practices (Table 1) has not been accurately measured. Efficiency is typically calculated as A/(A+B+C), where A indicates the number of mutant transgenic plants, and B and C indicate the numbers of non-mutant transgenic plants obtained from transformed and non-transformed cells. This does not account for the number of explant cells that were transformed but not regenerated. Most tree genome editing studies have focused more on whether the CRISPR/Cas reagents function than on their efficiency. Conventional protocols for transformation and regeneration are laborious and time-consuming, and their low efficiencies are major obstacles to tree genome editing using the CRISPR/Cas system. Possible solutions to these problems are discussed in Section 4.

      A selection process is required during the regeneration of transformants to ensure that non-transformed plants are not carried forward into subsequent steps. The primary selection method for Agrobacterium-mediated T-DNA transformation is antibiotic resistance-based selection, which works by inhibiting the growth of non-transformed cells. Culture media with antibiotics should only allow the growth of the transformants that possess antibiotic resistance genes present in the transformed T-DNA. However, the antibiotic resistance gene products of the transformed cells are secreted into the culture medium and degrade the antibiotics in their vicinity, allowing the growth of neighboring non-transformed cells, reducing selection efficiency. Reporter gene (GUS or GFP)-based selection cannot inhibit the growth of non-transformants and is therefore not ideal for the process. In transient transformation such as T-DNA-free RNP transfection, the selection to screen out mutant plantlets depends on PCR and sequencing of randomly chosen samples, resulting in much lower efficiency. Recently, a novel approach called transient CRISPR/Cas editing in plants (TCEP) has been developed to quantitatively determine the in vivo activity of CRISPR/Cas reagents during transient transformation[57]. Precise assessment of transient activity of CRISPR/Cas reagents by this approach will help to guide improvements in the process, enabling easier selection of genome-edited cells. Unfortunately, this process still depends on the extraction of DNA or RNA, which means that the tested cells cannot survive after the DNA or RNA extraction. Therefore, even if very high activity of Cas/sgRNAs is determined by the TCEP method, it is impossible to culture those cells and regenerate mutant plantlets from them. Overall, significant progress has been made in editing tree genomes, but efficiency is still low.

    • Transformation systems deliver in vitro manufactured CRISPR/Cas reagents, such as plasmids or RNPs, into cells. After transformation, the CRISPR/Cas system is converted into an RNP complex of Cas nuclease and sgRNAs, which then edits the target loci. It should be noted that delivery of CRISPR/Cas reagents into the plant cell does not guarantee delivery into the nucleus owing to the compartmentalized nature of eukaryotic cell structures. All eukaryotic organelles, including the nucleus, are enclosed within membrane structures that can prevent movement of the complex. Because Cas nuclease editing requires entry into the nucleus, the presence of a nuclear envelope can significantly affect editing efficiency.

      Delivery and integration of T-DNA into the genome of host plant cells by Agrobacterium has been the predominant transformation protocol, and its underlying mechanisms are well understood[58]. The transgenes (Cas nuclease gene and sgRNAs) in the T-DNA region that are integrated into the genome can be stably expressed in the nucleus. In transient transformation, non-integrated T-DNA strands duplicated by DNA polymerase θ are transiently expressed in the nucleus[58], but the non-integrated T-DNA cannot be inherited by progeny cells. Cas nuclease mRNAs and sgRNAs are transcribed in the nucleus, and the mRNAs are then transferred to the cytoplasmic matrix to be expressed. Because the Cas9 nuclease protein must enter the nucleus to edit the genome, the NLS peptide is attached to it in order to allow its entry. This system therefore bypasses the barrier posed by the nuclear envelope during Agrobacterium-mediated transformation.

      Other transient transformation protocols, such as biolistic bombardment or PEG-mediated delivery of CRISPR/Cas reagents through plasmids or RNPs, have also been employed in genome editing practices (Fig. 2). These protocols are regarded as more direct and straightforward than Agrobacterium-mediated transformation, but their efficiency in genome editing is lower (Table 1). This low efficiency may be due to the fact that such direct transformation systems can stall upon cell entry due to additional barriers, such as the nuclear envelope. Delivery of CRISPR/Cas reagents from the cytoplasm to the nucleus where the target genes are accessible is required, but the delivery mechanism of transient systems is still unclear, making their success unpredictable. Efficient transgene-free genome editing by direct delivery of plasmids or RNPs relies on effective nucleocytoplasmic transfer of the plasmid or RNP into the nucleus via pores in the nuclear envelope. Relatively low efficiency of genome editing in transient transformation using direct delivery of plasmids or RNPs implies that the nucleocytoplasmic transfer of CRISPR/Cas reagents into the nucleus may be a major limiting factor to efficient editing. Although the components and functions of nuclear envelope structures are well known[59,60], the mechanism by which they affect the transfer of CRISPR/Cas reagents into the nucleus is still poorly understood. Mitosis during cell division may allow the import of CRISPR/Cas reagents into the nucleus[61] because nuclear envelope breakdown and reorganization events occur during this time. This would present an opportunity for the import of CRISPR/Cas reagent into the nucleus, although it is unclear whether or not the CRISPR/Cas reagent would be compartmentalized inside the reorganized nucleus. The low efficiency of RNP transfer may also be due to other mechanisms, such as protein or RNA decay mediated by endogenous degradation systems[62,63]. Thus far, no reports are available on the stability of sgRNAs in the cytoplasm or the nucleus, hindering improvements in sgRNA stability. Only fusion of the NLS peptide into Cas nuclease to promote the delivery of CRISPR/Cas reagents into the nucleus (Table 1) and high concentrations of RNP complexes have been attempted to increase editing efficiency in tree genomes. Further research is required to understand the mechanisms of nucleocytoplasmic transfer and intracellular degradation of the plasmid DNA, small sgRNA, and Cas nuclease protein during transient transformation to stabilize CRISPR/Cas reagents and improve their delivery through the nuclear envelope.

      Figure 2. 

      Direct delivery of CRISPR/Cas reagents (plasmid or RNP) and potential barriers affecting their delivery efficiency and intranuclear genome editing activities. The active form of CRISPR/Cas reagents is the RNP, which is generated from transcription and translation of the CRISPR/Cas and sgRNA sequences. Because transcription only takes place in the nucleus, these plasmids must therefore gain entry to this cellular compartment. In the nucleus, Cas+NLS and sgRNAs are transcribed into RNAs, and the Cas + NLS mRNA must be exported into the cytoplasm to be translated into the Cas + NLS protein, which then re-enters the nucleus to form the RNP complex with sgRNAs. Therefore, the plasmid delivery process involves a total of three passes through the nuclear envelope. Although this process has been studied extensively, it still remains unclear how the nuclear envelope regulates the import of plasmid DNA, RNA, or RNP complexes into the nucleus, and the low efficiency of direct delivery systems may be due to the negative regulatory role of the nuclear envelope during the nucleocytoplasmic transfer of CRISPR/Cas reagents into the nucleus. Furthermore, intracellular protein and RNA degradation systems, such as the Ubiquitin-Proteosome and RNA exosome, may be potential obstacles for the RNP complex. These “degradosomes” may render the activity of RNPs more transient, resulting in a much lower editing efficiency.

    • Tissue culture techniques, such as somatic embryogenesis, callus induction, and shoot and root organogenesis, have been used to clone mutant cells and regenerate mutant plantlets. However, these processes can take six months or longer to regenerate T0 or T1 transgenic mutant plants, during which extensive work must be carried out in order to continually select for positive transgenic plants using antibiotic resistance genes or reporter genes (Fig. 3a). Thus far, no work has been conducted to attempt to overcome these challenges in genome engineering of tree species (Table 1). In non-trees, such as herbs and crops, novel protocols have already been applied to establish time-saving strategies for genome editing. These protocols involve both tissue culture–dependent and tissue culture–independent strategies.

      Figure 3. 

      Faster and easier regeneration of genome-edited plants by tissue culture–independent protocols. (a) Conventional tissue culture is both tedious and laborious. This process normally takes anywhere from six to eighteen months and requires a sterile environment and a large amount of tissue culture medium, dishes, bottles, and chemical reagents. Its regeneration efficiency is relatively low, and recalcitrancy limits its utility. (b) Recently, novel technologies, such as mobilization of sgRNAs by FT mRNA fusion and de novo meristem induction, have been developed, enabling researchers to overcome some of the problems of conventional tissue culture. In the FT mRNA/sgRNAs protocol, FT mRNA encodes the mobile florigen essential for induction of flowering, which is fused to sgRNAs to facilitate their movement from the leaf to the shoot apical meristem. This causes genome editing of the floral meristem, which results in genome-edited seed production. In the de novo meristem induction protocol, genome editing and meristem induction are performed simultaneously to generate genome-edited seeds. These in planta transformation protocols require only one or two months to generate genome-edited plants. In addition, these protocols do not require laborious processes of sterilization and sterile tissue culture.

      Among the tissue culture–independent methods, one protocol involves mobile sgRNAs that can move from the leaf to the shoot apical meristem (SAM) for tobacco genome editing[64]. In this process, sgRNA was fused with a Flowering Locus T (FT) mRNA encoding the mobile florigen essential for induction of flowering, and the result was termed "mobile sgRNA". This sgRNA was then transformed using tobacco rattle virus (TRV) into the leaf of a tobacco plant overexpressing the Cas9 nuclease. Transformed mobile sgRNA then moved from the leaf to the SAM and edited the target gene with high efficiency, while FT induced flowering and seed formation from the edited SAM, finally generating genome-edited seeds. This protocol relies on in planta transformation that exploits the natural developmental process from the SAM to flowers and then seeds. It also bypasses the time-consuming process of tissue culture but still achieves high efficiency. In addition, FT induces precocious flowering, thereby shortening the time for seed development and reducing the entire process to only one or two months. Another protocol utilizing in planta transformation through Agrobacterium has also achieved rapid and efficient genome editing of tobacco plants[65]. In this study, de novo reprogramming of somatic tissues into plant meristems (mainly SAMs) and genome editing were concurrently induced by Agrobacterium-mediated transformation of co-expression vectors containing both developmental regulators (DRs) and sgRNA cassettes into pruned sites of tobacco plants overexpressing Cas9 nuclease[66]. CRISPR/Cas then edited the genome of somatic cells, and DRs induced de novo reprogramming of genome-edited somatic cells into meristems, finally leading to fertile plants and genome-edited seed production. This in planta protocol enabled both rapid and efficient genome editing by omitting tissue culture. Although both of these novel approaches (Fig. 3b) are just the beginning of tissue culture–free genome editing and have some limitations[64,65], they represent a significant step towards the simplification of CRISPR/Cas-mediated genome editing in plants. Because these protocols rely on the natural developmental process that proceeds from the SAM to flowers and then seeds, they can be applied to angiosperms such as poplars. Gymnosperms have different reproductive mechanisms[67] and may therefore require some additional modification to enable the successful in planta transformation of CRISPR/Cas.

      Other attempts to save time during crop improvement and research have shown that tissue culture–based regeneration can be boosted with the aid of speed breeding. The concept of speed breeding was first proposed by Watson et al. in 2018[68] and is now regarded as a promising technique for accelerating crop breeding and improvement. In speed breeding, techniques for the regulation of multiple factors, including photoperiod, light intensity, temperature, moisture, high cultivation density, and plant hormones, have been harnessed to shorten the time to reproduction[68,69]. Harvesting and germinating immature seeds are also crucial for reducing the generation time[68]. Speed breeding greatly reduces generation time, thereby allowing the production of 3 to 9 generations per year in various plant species including Arabidopsis, barley, chickpea, rice, soybean, and wheat[7074]. These experiences from speed breeding practices can be exploited for tissue culture practices to save time in tree regeneration. In addition to speed breeding, genetic manipulations can also boost regeneration speed. Recently, GROWTH-REGULATING FACTOR (GRF) and its cofactor GRF-INTERACTING FACTOR (GIF), as well as GRF-GIF chimera, have been shown to improve regeneration efficiency in plant transformation and genome editing practices[75,76]. The GRF-GIF chimera has several advantages. First, its mode of action is different from the aforementioned de novo SAM induction by DRs such as BBM and WUS transcription factors, and it can therefore be used to avoid the side-effects of those systems[66,77]. In addition, the GRF-GIF chimera can act as a reporter gene, eliminating the need for an antibiotic resistance marker. For example, its transformation into callus generates new green embryos, enabling easy identification of transformed tissues[76]. Finally, GRF-GIF chimera solves issues related to callus regeneration and have been shown to enable the regeneration of recalcitrant callus in wheat[76]. Results suggest that the GRF-GIF chimera enables the successful transformation of CRISPR/Cas reagents and the subsequent regeneration of even recalcitrant plants, making it especially useful for tree genome editing.

      As described above, several innovative protocols have emerged to achieve efficient regeneration of genome-edited seeds or plantlets via tissue culture–independent or tissue culture–dependent pathways. Their application has thus far been restricted to Arabidopsis, tobacco, and a few crop species, and some additional improvements are needed before their widespread deployment. Despite these limitations, they represent a significant step forward and could potentially be used to overcome the unique challenges of editing tree species.

    • Current studies on tree genome editing focus primarily on the induction of target-specific DSBs. After the transformation of Cas9/sgRNA constructs into cells, the sgRNAs guide the nuclease toward the target locus of the genome to induce the DSBs. DNA repair pathways then result in several different mutagenesis outcomes. Most tree genome editing studies have only assessed the induction of DSBs and subsequent mutagenesis, and more data are needed to understand the mechanism by which Cas9/sgRNA-induced DSBs generate biallelic, homozygous, heterozygous, or chimeric mutations in tree genome editing.

      Although DSBs induced at the target loci initiate the editing process, they are not directly responsible for differences in the resulting mutants. The DSBs are recognized as genotoxic lesions, and consequently, intrinsic DNA repair pathways, such as homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ), and single-strand annealing (SSA), are activated to repair the DSBs. Among these pathways, only the template-dependent HR is error-free, and others, including template-independent cNHEJ, MMEJ, and SSA, are error-prone. Therefore, the accuracy and efficiency of targeted mutagenesis are greatly influenced by which DNA repair pathway is activated. However, the underlying causes of repair mechanism selection are not clear, making it impossible to predict which one will be activated after Cas9 cleavage[78].

      Emerging evidence indicates that Cas9 nuclease–induced DSB repair results in the human genome are not random[7981]. Based on the nonrandom nature of DSB repair, machine learning algorithms and abundant experimental data of repair outcomes have been combined to predict outcomes[8082]. Three machine learning (ML) models, inDelphi, FORECasT, and SPROUT, are typically employed for predicting Cas9-induced DSB repair results. ML models have continued to develop, and a new method called CROTON is highly automated and simplified by an end-to-end framework with better results than earlier algorithms[83]. These ML models enable precise prediction of mutagenesis outcomes without the need to conduct wet-lab experiments, thereby saving large amounts of time, effort, and reagents. However, none of these models has yet been trained on tree cells, and model training requires abundant data on DSB-induced DNA repair outcomes obtained from wet-lab experiments of tree genome editing using diverse sgRNAs.

    • To date, various Cas nucleases such as Cas12a (Cpf1), Cas13, and Cas14 have been developed and applied to genome editing in mammals and plants[68]. In trees, genome editing practices have used mostly Cas9 (Table 1). Cas12a, Cas13, and Cas14 have several advantages over standard Cas9, such as additional RNA cleavage activity and diverse PAM profiles; they enable RNA editing as well as single stranded RNA/DNA targeting, expanding genome editing toolkits and their applicability. Also, they are smaller than Cas9, promoting their entry into the nucleus and broadening the range of selectable vectors. Wild-type Cas nucleases have also been modified into nuclease-deactivated Cas proteins (dCas nucleases such as dCas9 or dCas12), which are then tethered to various effector proteins and harnessed to achieve a broad range of applications, such as CRISPR interference (CRISPRi), CRISPR activation (CRISPRa), and epigenome editing[8488]. Recent progress in their mechanisms and applications in human and plants have been the subject of several reviews[8992]. Thus far, only a few studies have reported the use of Cas12a[23,53] and CRISPRi[19] in trees, and further application of the various Cas nucleases and dCas/effector complexes will undoubtedly expand the versatility and efficiency of CRISPR/Cas genome editing toolkits in trees.

      In addition, the dCas nucleases have been tethered to effector proteins like base editors and prime editors, thereby enabling base editing or prime editing while overcoming the limitations of classical CRISPR/Cas systems[3]. Classical CRISPR/Cas systems have successfully achieved precise targeting, and the resulting outcomes mainly reflect indel mutagenesis (Table 1) by DSBs and subsequent error-prone DNA repair pathways such as nonhomologous end joining (NHEJ). Mutation outcomes from NHEJ repair pathways are now subject to prediction, as mentioned in Section 4.3, but the outcomes typically include a large number of undesired changes, thus reducing the precision of genome editing. Error-free HR pathways and donor DNA-dependent homology directed repair (HDR) offer the potential for precise genome editing. However, in the DSB-induced repair process, the HDR pathway competes with error-prone DNA repair pathways, and the efficiency of precise genome editing is therefore very low, limiting the application of this approach[93,94]. Classical CRISPR/Cas genome editing tools using DSBs have significantly advanced, but they reveal their limitations when dealing with SNPs, which are not only important pathogenic point mutations in human but also agronomically important genetic variations. Novel CRISPR/Cas toolkits such as base editing and prime editing have recently emerged as alternative genome editing tools. They have enabled efficient, versatile, and precise editing by installing or reverting transition/transversion point mutations and even directly copying desired sequences into targets in mammals, plants and bacteria[9597]. They use the nuclease-deactivated dCas9 protein fused with base editors (adenosine deaminase and/or cytidine deaminase fused with uracil DNA glycosylase) or prime editors (reverse transcriptase fused with a prime editing guide RNA; pegRNA), enabling efficient and precise genome editing without the need for DSBs or donor DNA templates[95]. Base editing and prime editing were reported in mammals such as human and mice in 2016[98] and 2019[96], respectively, and then applied to crop plants such as rice and wheat, opening up new possibilities for plant genome editing[99,100]. Although they have not yet been applied to trees, they have great potential for rapidly accelerating tree breeding and trait improvement. For example, trees typically have highly abundant SNPs—as many as one SNP per 100 bp in their genomes. SNPs in genes lead to changes in gene activities, thereby causing phenotypic changes associated with plant growth and development and responses to abiotic and biotic stress. Because of the high abundance of SNPs in tree genomes of different species, identifying functional SNPs and determining their roles through phenotypic validation are urgent tasks for tree breeding and trait improvement and require large numbers of tree SNP models. Novel CRISPR/Cas toolkits such as base editing and prime editing can create tree models that carry desired SNPs precisely and efficiently.

    • The CRISPR/Cas system has been used for targeted genome editing of trees since 2014. Despite natural barriers, including large genome sizes, high polyploidy and heterozygosity, and abundant SNPs, rapidly developing tree genome data and sgRNA design tools have enabled successful targeted genome editing in several tree species. Over the last seven years, the CRISPR/Cas system has been successfully applied to many tree species, including apple, bamboo, Cannabaceae, cassava, citrus, cacao tree, coffee tree, grapevine, kiwifruit, pear, pomegranate, poplar, ratanjoyt, and rubber tree. CRISPR/Cas-based mutagenesis at desired target loci has been demonstrated in these species, contributing to the further development of genome editing in trees and enabling the identification of genes associated with tree growth, secondary metabolism, and resistance to biotic and abiotic stress. However, genome editing still has several limitations, and most practices have relied on high-efficiency Agrobacterium-mediated stable transformation, which is not favorable in the current regulatory environment. Transient transformation protocols, such as the delivery of RNP complexes, can achieve transgene-free (non-GMO) genome editing and are preferred. However, the efficiency of such systems is currently very low, limiting their widespread application[12,55].

      Low transformation efficiency is the main factor limiting the application of transient CRISPR/Cas systems for genome editing in trees. Lack of knowledge about the intracellular stability and nucleocytoplasmic delivery of CRISPR/Cas reagents (plasmid DNA or RNP) hampers efforts made to improve this system. In addition, low regeneration efficiency results in a significant waste of time, effort, and reagents, creating further challenges for CRISPR/Cas-based genome editing in trees. Several innovations have emerged to promote efficient regeneration of genome-edited seeds or plantlets with or without the need for tissue culture. Although these approaches have not yet been applied to tree species, they represent new avenues for improving the efficiency and simplicity of tree genome editing. In addition, the DSBs created by Cas9 cleavage are known to result in the activation of different repair pathways that generate different outcomes. Machine learning models are now being used for effective prediction of mutagenesis outcomes, but they still require the input of large amounts of empirical data, which are currently unavailable for trees.

      CRISPR/Cas genome editing practices in trees have thus far relied mainly on the classical wild-type Cas9 nuclease. Other wild-type Cas nucleases such as Cas12a (Cpf1), Cas13, and Cas14 and dCas nucleases tethered to various effectors, including transcriptional regulators and epigenetic modifiers, are newly emerging CRISPR/Cas toolkits that can be used for a broad range of applications beyond basic genome editing, including CRISPRi, CRISPRa, and epigenome editing. dCas nucleases tethered to base editors or prime editors can also be harnessed to improve the precision of genome editing practices, an approach that shows great potential for the generation of tree SNP models.

      CRISRP/Cas system-based tree genome editing is still evolving and requires innovations in conventional transformation and regeneration protocols, as well as machine learning model-based simulation of mutagenesis to achieve more efficient and rapid outcomes. In planta transformation and tissue culture–free or modified tissue culture protocols, which have been developed recently, show great potential to improve the efficiency of CRISPR/Cas toolkits. Together with these novel strategies for transformation and regeneration, newly emerging CRISPR/Cas toolkits show great versatility, and their application to trees will expedite tree breeding and trait improvement.

      • This work was supported by the National Natural Science Foundation of China (31971671) and the Fundamental Research Funds for the Central Universities of China (2572018CL04).

      • The authors declare that they have no conflict of interest.

      • Copyright: © 2022 by the author(s). Published by Maximum Academic Press, Fayetteville, GA. This article is an open access article distributed under Creative Commons Attribution License (CC BY 4.0), visit https://creativecommons.org/licenses/by/4.0/.
    Figure (3)  Table (1) References (100)
  • About this article
    Cite this article
    Pak S, Li C. 2022. Progress and challenges in applying CRISPR/Cas techniques to the genome editing of trees. Forestry Research 2:6 doi: 10.48130/FR-2022-0006
    Pak S, Li C. 2022. Progress and challenges in applying CRISPR/Cas techniques to the genome editing of trees. Forestry Research 2:6 doi: 10.48130/FR-2022-0006

Catalog

  • About this article

/

DownLoad:  Full-Size Img  PowerPoint
Return
Return