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OBM Genetics

(ISSN 2577-5790)

OBM Genetics is an international Open Access journal published quarterly online by LIDSEN Publishing Inc. It accepts papers addressing basic and medical aspects of genetics and epigenetics and also ethical, legal and social issues. Coverage includes clinical, developmental, diagnostic, evolutionary, genomic, mitochondrial, molecular, oncological, population and reproductive aspects. It publishes a variety of article types (Original Research, Review, Communication, Opinion, Comment, Conference Report, Technical Note, Book Review, etc.). There is no restriction on the length of the papers and we encourage scientists to publish their results in as much detail as possible.

Publication Speed (median values for papers published in 2024): Submission to First Decision: 6.4 weeks; Submission to Acceptance: 12.2 weeks; Acceptance to Publication: 7 days (1-2 days of FREE language polishing included)

Current Issue: 2025  Archive: 2024 2023 2022 2021 2020 2019 2018 2017
Open Access Review

Agrobacterium-Mediated Genome Modification for Improvement of Oil Palm Planting Materials

Ayub Nor Hanin 1, Mat Yunus Abdul Masani 1,*, Ong-Abdullah Janna 2, Omar Abdul Rasid 1, Ghulam Kadir Ahmad Parveez 1

  1. Malaysian Palm Oil Board (MPOB), No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia

  2. Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Malaysia

* Correspondence: Mat Yunus Abdul Masani

Academic Editor: Vishnu D Rajput

Special Issue: Genome Editing for Crop Improvement

Received: December 18, 2024 | Accepted: March 30, 2025 | Published: April 15, 2025

OBM Genetics 2025, Volume 9, Issue 2, doi:10.21926/obm.genet.2502292

Recommended citation: Hanin AN, Masani MYA, Janna O, Rasid OA, Parveez GKA. Agrobacterium-Mediated Genome Modification for Improvement of Oil Palm Planting Materials. OBM Genetics 2025; 9(2): 292; doi:10.21926/obm.genet.2502292.

© 2025 by the authors. This is an open access article distributed under the conditions of the Creative Commons by Attribution License, which permits unrestricted use, distribution, and reproduction in any medium or format, provided the original work is correctly cited.

Abstract

Oil palm is the most productive vegetable oil crop compared to other oil-bearing crops because it produces the highest oil yield per hectare. Palm oil is very versatile since it is used for producing food and beverages, personal care and cosmetics, cleaning products, biofuel, and bioenergy. To cater to the increasing demand in the global palm oil market, much research has been done to improve the oil's yield and modify its quality in addition to the oil palm height through breeding. Due to its long breeding cycle, oil palm planting materials have been improved using biotechnological approaches such as genetic engineering and genome editing. The ability to transform oil palm with high efficiency is the key to effect genome modification of the palm. The current oil palm transformation efficiency for Agrobacterium-mediated transformation is very low compared to other monocots such as rice, maize, and wheat. Over the last few decades, numerous studies have been conducted to enhance the transformation efficiency, providing a more reliable landscape for CRISPR/Cas9 genome editing. In this review, we discussed the progress made in oil palm genetic transformation, focusing on the Agrobacterium-mediated transformation, and outline possible strategies to enhance transformation and regeneration efficiencies. The progress and prospect of Agrobacterium-mediated CRISPR/Cas9 genome editing for improving oil palms agronomic traits, such as oil yield, plant height, fruit color, and resistance to resist biotic and abiotic stresses, were also discussed.

Keywords

Agrobacterium-mediated transformation; CRISPR/Cas9; transgenic oil palm; oil palm genome editing

1. Introduction

Oil palm (Elaeis guineensis Jacq.) is a highly productive vegetable oil crop compared to other crops. The oil yield is about 3-6 tons per hectare, depending on the type of plantations [1]. In 2023, Malaysia's oil palm cultivation area covered 5.65 million hectares [2]. Malaysia ranked second place as the palm oil producer after Indonesia. Other palm oil-producing countries are Thailand, Colombia, Nigeria, and others [3]. In 2022, palm oil contributed to 60% of the global vegetable oil trade as compared with soybean (14%), sunflower (10%), coconut (2%) and olive (1%) [4]. In 2023, Malaysia produced about 18.55 million tons of palm oil, supplying 24% of global palm oil production as compared to 47 million tons (59%) from Indonesia [3]. Malaysia exported 15.13 million tons of palm oil, worth RM 62.58 billion in 2023 [2]. India remains the major importer of Malaysia's palm oil, followed by China, the EU, Kenya, Turkiye, Japan, and Pakistan, with a total export of 8.23 million tons [2].

Palm oil is versatile since it is used in manufacturing food and drinks, personal care and cosmetics, cleaning products, biofuel, and bioenergy. In addition, oil palm biomasses can be used to make furniture, car components, feed formulation, and natural fertilizer. The Organization for Economic Cooperation and Development (OECD) and the Food and Agricultural Organization (FAO) predicted that by the year 2032, the food use of global vegetable oil will hit 57% of total consumption due to increased population growth and increased use per capita especially in the lower- and middle-income countries [5]. For 2024, the United States Department of Agriculture (USDA) predicted that worldwide palm oil consumption might rise by 4.9% to reach 77.2 million metric tons [6]. In order to support the increasing need for palm oil, conventional breeding and biotechnology are employed to improve the oil's yield and quality.

The oil palm is a long-lived tree species with a productive lifespan ranging from 20 to 25 years, and it took nearly 50 years to introduce a new trait into this palm, considering crossing and backcrossing [7]. Significant achievements have been made in improving oil quality and yield as well as other planting material attributes such as height and disease resistance [8]. The Malaysian Palm Oil Board (MPOB) has introduced 14 planting series with traits such as dwarf, high carotene content, high vitamin E, high bunch index, and high oleic acid using germplasm collection [9]. Other target traits that can only be produced through genetic engineering, such as high ricinoleic acid content and biodegradable plastic [10], were also explored. Genetic engineering is beneficial in oil palm breeding since this technique could reduce time and cost, increase the precision of trait introgression, and widen the genetic background of oil palm [7]. MPOB has embarked on an oil palm genetic engineering program since 1987, focusing on a high oleic acid trait that increases palm oil's marketability for liquid and salad oil consumption [11,12].

Transgenic oil palms were successfully produced using the biolistic delivery method, Agrobacterium-mediated transformation, and DNA microinjection [12]. Nevertheless, the efficiency of transformation was notably low, ranging from 0.7% to 1.5% [13] in comparison with other monocots, such as rice at 14 to 26.4% [14] and sorghum at 14 to 33% [15]. The success of oil palm genome sequencing [16] opens up new opportunities. It paves the way for the oil palm genome editing program using CRISPR/Cas9 technology. In 2021, Yeap and co-workers [17] published the first victory of oil palm genome editing, followed by Bahariah et al. [18], Jamaludin et al. [19], and Norfaezah et al. [20]. Therefore, this review discusses the progress of Agrobacterium-mediated transformation and its application in oil palm genetic engineering and genome editing, aiming for a sustainable future of the oil palm industry.

2. Agrobacterium-Mediated Plant Transformation

Agrobacterium-mediated transformation is widely utilized as a tool for crop improvement. This system utilizes Agrobacterium, a gram-negative soil bacteria, to integrate foreign DNA into the plant genome. The most commonly used Agrobacterium is A. tumefaciens, which triggers crown gall disease, and A. rhizogenes, which triggers hairy root disease naturally in infected plants [21]. The discovery of Agrobacterium was announced in 1907 by plant pathologists Erwin Smith and Charles Townsend, who studied the contributing factors to crown gall disease in ornamentals [22]. The history of Agrobacterium discovery and the subsequent breakthrough technologies have been extensively reviewed by Nester [22]. For instance, in 1974, Zaenen and co-workers discovered an enormous plasmid during the crown gall formation, and six years later, Zambryski and colleagues demonstrated that the plasmid's fragment was arbitrarily incorporated into the plant's genome [22]. Besides plant cells, this remarkable bacterium was also capable of transferring its T-DNA (transferred DNA) into fungi, algae, and human cells [23].

In dicotyledons, Agrobacterium-mediated transformation has always been the method of choice because they are the natural host of the bacteria. Since the elucidation of the basic mechanism of tumorigenesis in crown gall disease, methods to produce tumor-free transgenic plants were established for tobacco (Nicotiana tabacum L.) and petunia (Petunia × hybrida) [24], soybean (Glycine max L.) [25] and other dicotyledons by the middle of 1980s. The first commercialized transgenic dicotyledon crop developed by Agrobacterium-mediated transformation was the Flavr Savr™ tomato [26]. Agrobacterium-mediated transformation for monocotyledonous plants was initially considered impossible because they are not the natural hosts for Agrobacterium and, thus, are not prone to crown gall disease. This paradigm revolutionized in 1987 when Bytebier and co-workers demonstrated that Agrobacterium T-DNA could be incorporated into the genome of asparagus (Asparagus officinalis), a monocotyledon plant [27]. The first reported successful transformation of monocot commercial crops was rice (Oryza sativa) using the mature embryos and maize (Zea mays) using the shoot apex [24]. Subsequently, genetic engineering via Agrobacterium has been successfully employed to modify cereal crops such as sorghum (Sorghum bicolor L.), barley (Hordeum vulgare L.), as well as wheat (Triticum aestivum L.) [24]. However, herbicide-tolerant and insect-resistant maize were the only transgenic cereals that were planted for commercialization on 57.4 million acres globally [24]. In addition to cereal crops, Agrobacterium-mediated transformation was also utilized to enhance the quality of woody fruits and nuts [28]. The virus-resistant "Honey Sweet" plum has been granted for planting in the USA, while the non-browning apple has already been marketed for consumption [28]. Besides, Agrobacterium-mediated transformation was also employed to improve prominent oil-bearing crops such as oil palm [27,29,30,31,32], soybean (Glycine max L.) [25], sunflower (Helianthus annuus L.) [33], and rapeseed (Brassica rapa and B. napus) [34]. The progress made in Agrobacterium-mediated transformation for oil palm improvement is listed in Table 1.

Table 1 Application of Agrobacterium-mediated oil palm transformation.

Agrobacterium-mediated transformation is a more favored transformation method compared to other methods because it is easy, economical, has less incidence of transgene re-arrangement, is capable of delivering large DNA fragments, and is excellent in the integration of transgene into transcriptionally potent domain, which will lead to successful transgene expression in the plant cells [43]. The Agrobacterium transfers gene(s) into the plant cells in five crucial stages: (a) Stimulation of Agrobacterium virulence mechanism, (b) Formation of T-DNA complex, (c) Movement of T-DNA from Agrobacterium to the plant cell nucleus, (d) Integration of T-DNA into the plant genome and (e) Expression of the T-DNA in the plant cells [21]. The fruitful transformation of plants was accomplished by optimizing parameters and developing an efficient protocol where the selected parameters act synergistically during transformation [44]. In many Agrobacterium-mediated transformation studies, the transfer of T-DNA and its integration into the plant genome is affected by the plant's genotype, type of explant, transformation vector, Agrobacterium strain, composition of the culture medium, co-cultivation temperature, co-cultivation duration, Agrobacterium density, selectable markers, chemicals, and surfactant [45,46,47]. If these factors are sufficiently optimized, it will facilitate the integration of T-DNA into the plant genome, as it impedes successful Agrobacterium-mediated transformation in numerous plant species [45].

3. Strategy to Improve Agrobacterium-Mediated Transformation Efficiency

Although stable transgene integration in the oil palm genome via Agrobacterium-mediated transformation has been demonstrated [27,31], efforts to improve the transformation efficiency are still being carried out. Compared to other monocots, the oil palm's transformation efficiency is still relatively low. The transformation efficiency was only 0.7% when the bialaphos resistance or bar gene was utilized as the selectable marker [27]. Later, the transformation efficiency increased to 1.0% when the 2-deoxyglucose-6-phosphate phosphatase (DOGR1) gene was used as the selectable marker for oil palm transformation [31]. Currently, the oil palm embryogenic calli [27,31,35] and immature embryos [29,36] are the most widely used explants for Agrobacterium-mediated oil palm transformation.

Optimization of other critical parameters for Agrobacterium-mediated transformation of oil palm was also carried out. Among the parameters are Agrobacterium strains [35], Agrobacterium density, inoculation and co-cultivation periods [30], and transformation vectors [32,36]. Sonication treatment was also evaluated as the wounding method, but the study was done on oil palm somatic embryos rather than embryogenic calli and immature embryos [37].

However, a systematic comparison of other Agrobacterium-mediated oil palm transformation parameters, such as explant type and age, acetosyringone concentration, and physical injury methods, has not been reported. Systematic optimization of all critical parameters involved in Agrobacterium-mediated transformation could significantly enhance transformation efficiency and regeneration frequency as observed in other plants [13], whether the plant is readily transformable or previously described as recalcitrant to transformation and regeneration via tissue culture.

According to Ziemienowicz [46], Agrobacterium concentration, age of callus, wounding methods, preculture periods, co-cultivation periods, and acetosyringone concentrations are among the crucial parameters that require optimization to establish an effective Agrobacterium-mediated transformation procedure for any given species. Other factors can also influence Agrobacterium-mediated plant transformation, including inoculation time [48], vector plasmid, bacterial strain [49], and resting periods [50]. According to Li et al. [47], the overall transformation efficiency is influenced by the efficaciousness of Agrobacterium infection and explant regeneration. To establish an effective transformation protocol, researchers must determine the precise ratio of many elements that interact during the transformation process [44]. An efficient transformation and regeneration protocol will enable the execution of CRISPR/Cas9 genome editing technology to regenerate transgene-free, stably edited plants with economically important traits, thereby supporting their sustainability in the current bioeconomy era. Studies related to optimizing critical parameters for Agrobacterium-mediated transformation are discussed in the following subtopics.

3.1 Agrobacterium Strains and Transformation Vectors

One of the most critical factors in Agrobacterium-mediated transformation is the infecting ability of the Agrobacterium strain, as each strain has a distinct capacity to transform plant tissues [44]. In general, the nopaline strains have a better potential to infect woody species than the octopine strain [51]. The combination of Agrobacterium strains and vectors was known to affect the transformation efficiency of plants [45]. For japonica rice transformation, LBA4404 carrying a super-binary vector pTOK233 was more effective than super virulent strain EHA101 carrying the same super-binary vector in transforming Tshukinohikari and Koshihikari cultivars [24]. The EHA105 strain was superior to LBA4404 in maize transformation [52].

Boonyaves et al. [53] showed that EHA105 gave the highest transient expression of the β-glucuronidase (gus) gene compared to AGL-1 in oil palm suspension culture. Promchan and Te-chato [35] reported that EHA101 was more efficient than AGL-1 in infecting oil palm suspension culture. In Jatropha curcas, EHA105 was superior to LBA4404, GV3101, and AGL-1 in infecting J. curcas cotyledon and was able to transfer a single copy of the transgene [54]. These studies were consistent with the survey in Micro-Tom tomato, which defined that Agrobacterium strain EHA105 was the most efficient compared to AGL-1 and GV3101 and was able to produce transgenic plants carrying a single copy of transgene [55]. Besides the host strain, Hanin et al. [32] demonstrated that a vector carrying the bar and green fluorescent protein (gfp) genes controlled by the CaMV35S promoter in the pBINPLUS/ARS backbone was more efficient than vectors in pCAMBIA0380 backbone based on transient GFP signals. The aforementioned work highlights the importance of evaluating the bacterial host strain and vector components to enhance the success of a transformation event.

3.2 Explant Types and Pre-Treatments

Studies in other crops have shown that Agrobacterium infection exhibits a varying affinity for different plant tissues, organs, and cells. Ribas et al. [56] evaluated three types of somatic embryogenic tissues, namely embryogenic calli, established embryogenic calli suspension, and embryogenic callus culture, and concluded that the established embryogenic calli gave the highest transformation efficiency (17%). Agrobacterium-mediated transformation was performed for oil palm using immature embryos (IEs) as the explant in the early research due to their abundance [29]. A bunch of oil palm fruits yielded about 300 to 500 IEs. Nevertheless, the genetic composition of IEs is not homogenous since they are the result of cross-pollination [29]. Thereafter, somatic embryogenic suspension cultures (ECs) were chosen as the preferred explant [13]. The oil palm ECs were proposed as the ideal explant for oil palm transformation via Agrobacterium owing to their unicellular nature [35]. The use of a single cell could prevent chimerism in the transformed tissue, thus leading to the regeneration of actual transgenic plants, as reported by Huang et al. [57]. Immature embryogenic calli were also utilized for oil palm transformation [58]. In addition, evaluation of oil palm immature leaves as an explant has also been suggested [59].

In an Agrobacterium-mediated transformation system, the explants were wounded to increase transformation efficacy [27]. Wounding triggers the production of phenolic compounds by the injured cells, which are required to activate virulence functions within Agrobacterium [27]. Wounding by bombardment was reported to increase transformation efficiency in carnation (Dianthus caryophyllus L.) [27]. In addition, sonication treatment, which is more cost-effective than bombardment, was proven to enhance the transformation efficiency of chickpeas, soybeans, and flax [60]. Furthermore, a combination of vacuum infiltration and sonication was proven to increase the transformation efficiency of banana cv. Rasthali [61] and Whitania somnifera (L.) Dunal [62]. Therefore, sonication and vacuum infiltration can be potential alternatives to bombardment to increase transformation efficiency in oil palm.

Besides wounding, osmoticum or plasmolysis treatment was used to increase transformation efficiency. Plasmolysis treatment with 10% sucrose prior to Agrobacterium increased transient GUS expression in rice calli [27] and citrus [63]. A combination of plasmolysis treatment with 6% sucrose and bombardment prior to Agrobacterium infection in oil palm embryogenic calli was demonstrated by Masli et al. [27] and Izawati et al. [31]. However, since the protocol utilizes only one treatment parameter, a combination of 6% sucrose and bombardment, it is essential to reevaluate the necessity of the plasmolysis treatment.

3.3 Transformation Conditions

A review by Pérez-Piñeiro et al. [64] on Agrobacterium-mediated transformation summarized the efficient transformation condition into three stages: preculture, inoculation, and co-cultivation. The preculture stage was done to increase the transformation efficiency. Preculture is reported to induce cell division in the explant, thereby enhancing its sensitivity to Agrobacterium, which is highly dependent on the duration of preculture [45]. In the wheat cultivar "Bobwhite", the highest T-DNA transfer frequency was achieved when the immature embryos were precultured for ten days based on transient GUS assay [65]. However, Sivanandhan et al. [62] reported that transient GUS expression in Withania somnifera (L.) Dunal decreased with a long preculture period, suggesting the importance of determining the optimum preculture duration. To date, no report on pre-culture conditions for oil palm transformation has been available.

The second stage is explant inoculation in an Agrobacterium suspension. Yenchon and Te-chato [30] demonstrated that inoculation at an optical density of 0.8 at 600 nm for 6 hours generated the highest number of hygromycin-resistant oil palm embryogenic calli (63.89%) and were able to form somatic embryos after eight weeks of culture. However, no report on transgenic plant regeneration was demonstrated in the paper. Besides cell density, the optimal growth stage of the bacterial culture is also crucial for successful transformation, as infection time also influences transformation efficiencies [21]. The length of contact with Agrobacterium suspension cells is a critical step, as the transfer and integration of T-DNA are completed during this period [66]. The highest frequencies of GUS expression and shoot regeneration were observed when leaf segments of Valencia sweet oranges were inoculated with Agrobacterium suspension cells for 10 min. However, longer infection duration reduced the transformation frequencies [66]. Likewise, Thiruvengadam et al. [67] stated that 30 min infection was the optimum for gherkin transformation, and prolonged duration led to overgrowth of Agrobacterium and tissue browning. Besides the optimum duration and bacterial density, most researchers have also reported that Agrobacterium at the log phase of growth is more efficient than at the lag and stationary phases [49].

The co-cultivation stage in the transformation process has been extensively studied in many crops and plants. In this stage, duration, and temperature of co-cultivation are crucial factors influencing Agrobacterium-mediated crop improvement for barley, citrus, and Withania somnifera L. [62]. Throughout the co-cultivation period, the addition of acetosyringone as a virulence inducer, sugars as carbon sources, plant growth hormones, and osmoprotectants are crucial to enhance the T-DNA transfer efficiency [64].

3.4 Antioxidants

The inoculation of explants with Agrobacterium cells produces reactive oxygen species (ROS) as a response similar to that of a pathogen attack [68]. The ROS causes tissue necrosis, growth inhibition, and altered plant metabolic pathways, resulting in reduced regeneration of transgenic plants [69]. The ROS also induced the expression of pathogenesis-related (PR) proteins, thereby hindering the colonization of Agrobacterium and preventing the integration of T-DNA into the plant's genome [70]. The adverse effects of ROS during Agrobacterium-mediated transformation and regeneration of transgenic plants can be mitigated by antioxidants. Some of the tested antioxidants are dithiothreitol (DTT) and L-cysteine in maize [71], silver nitrate and sodium thiosulfate in grapevines [70], polyvinylpyrrolidone (PVP) in sorghum [72], tocopherol, ascorbic acid and glutathione in banana [73] and α-lipoic acid in soybean, tomato, Carrizo citrange and lentil [23,74,75]. Some studies have shown that using surfactants, such as Silweet L-77, can improve T-DNA transfer frequency, as indicated by the number of GUS blue spots in the tested explant [76].

3.5 Regulation of Plant Signaling Molecules

Whilst considerable research has focused on the role of bacterial proteins in plant transformation mediated by Agrobacterium, limited investigations have explored the plant-based factors that affect the efficiency of this process [43]. Among these host factors, the phytohormone ethylene, gamma-aminobutyric acid (GABA), and salicylic acid (SA) have been identified as potential targets for improving transformation efficiency [77]. It has been demonstrated that the phytohormone ethylene suppresses T-DNA transfer as well as its incorporation into the host genome, hence impairing Agrobacterium-mediated transformation [77,78]. Similarly, GABA could interfere with the Agrobacterium infection process, leading to reduced transformation efficiency [77,79]. Additionally, SA, which is involved in plant defense responses, may also hinder Agrobacterium's ability to transfer its T-DNA into the plant cell [80]. This was due to the suppression of all virulence (vir) genes and repABC operon expression in Agrobacterium, which are needed to facilitate T-DNA transfer [81]. Moreover, SA is capable of increasing the ROS levels produced during pathogen infection as well as other environmental stresses like temperature, dehydration, and salinity [82]. The regulatory effects of ethylene, GABA, SA, and ROS on Agrobacterium-mediated transformation are summarized in Figure 1.

Click to view original image

Figure 1 Regulatory effect of reactive oxygen species (ROS), ethylene, GABA, and salicylic acid (SA) on Agrobacterium-mediated transformation. Wounding prior to Agrobacterium inoculation triggers plant cells to elicit neutral and acidic sugars as well as phenolic compounds to repair the damaged tissues. These molecules attract Agrobacterium to infect the plant cells and induce Agrobacterium virulence. ROS produced at the infection site increases the infected cells' stress-related plant signaling molecules such as ethylene, GABA, and SA. Ethylene, GABA, and SA suppress Agrobacterium virulence (vir) gene expression, thus inhibiting the transfer of T-DNA from Agrobacterium into the plant cell and consequently reducing transformation efficiency.

Inhibiting the production of these host factors may become a promising scheme to improve the efficacy of Agrobacterium-mediated plant transformation. One promising approach involves the utilization of microbial enzymes to modulate key plant metabolites that can influence the transformation process. For example, an Agrobacterium strain engineered with 1-Aminocyclopropane-1-carboxylate (ACC) deaminase (AcdS) and GABA transaminase (GabT) enzymes enhanced the efficiency of melon and tomato transformation [79,83]. The AcdS enzyme will degrade ACC, the ethylene precursor, while the GabT enzyme will degrade GABA [83]. Several studies using transgenic plants expressing the salicylic acid hydroxylase (NahG), an SA metabolizing enzyme, were conducted to investigate the contribution of SA during pathogen attack. The nahG gene was transformed into tobacco, Arabidopsis, and tomato [84] via Agrobacterium-mediated transformation. These NahG transgenic plants were defective in SA due to over-expression of the salicylic acid hydroxylase and were more susceptible to pathogens than the wild-type counterparts. It was observed that the NahG Arabidopsis exhibited more intense GUS staining than the untransformed Arabidopsis [84]. Recently, Liu et al. [85] demonstrated that Arabidopsis plants carrying the nahG gene produced more tumors compared to untransformed Arabidopsis plants when infected with the tumorigenic strain A. tumefaciens A208, indicating a more profound infection in the mutant. Incorporating these metabolic engineering strategies into Agrobacterium strains or the host plants themselves could lead to significant improvements in the success and utility of Agrobacterium-mediated transformation for various agricultural and biotechnological applications, such as the development of stress-tolerant plants, production of biopharmaceuticals, and phytoremediation [46].

3.6 Selection Agent

In addition to the transformation procedure, the use of a reliable selection agent is also crucial to producing a stable transgenic plant [46]. The efficacy of geneticin G-418, Basta®, kanamycin, hygromycin, and neomycin has been investigated for oil palm genetic engineering [12]. They concluded that Basta® and hygromycin are suitable for selecting transformants from oil palm embryogenic calli [12]. Later, the Basta® herbicide was used as the selection agent to regenerate Basta-resistant shoots from oil palm embryogenic calli that were transformed using Agrobacterium strain LBA4404 [27]. In addition, Parveez et al. [86] and Abdullah et al. [29] reported the suitability of hygromycin in selecting transformed oil palm IEs. The hygromycin gene was effective in selecting transformants in various dicot and monocot plants [87]. Recently, the successful regeneration of Agrobacterium-mediated CRISPR/Cas9 edited oil palm using hygromycin selection was reported by Bahariah et al. [18].

3.7 Use of Development Regulator

The ability to regenerate fertile transgenic plants is vital in any plant transformation. Gordon-Kamm et al. [88] stated that the production of transgenic plants involves two stages. The first stage is the incorporation and activation of foreign genes within the host plant (transformation), followed by the development of the modified explant into a fertile transgenic plant through regeneration. Genotype dependency remains a bottleneck in transformation for monocots, particularly in recalcitrant species such as oil palm, maize, rice, sugarcane, cotton, sorghum, wheat, and date palm. One of the most promising tools to overcome this bottleneck is the exploitation of developmental regulator genes such as Wuschel (WUS) and Baby Boom (BBM). The BBM gene was discovered by Boutilier et al. [89] (2002) in Brassica napus during their attempt to identify genes that were upregulated during embryo formation from immature pollen in an in vitro environment. Later, studies in tobacco demonstrated that expression of the BBM gene produced sterile transgenic tobacco lines [90]. In Capsicum annuum, the BBM gene was able to enhance the regeneration of stable transgenic sweet pepper varieties. The transformation efficiencies for the Fiesta and Ferrari sweet pepper varieties were 0.6% and 1.1%, respectively [91].

The utilization of the BBM gene in Agrobacterium-mediated transformation of monocots was initiated in maize [92]. The findings showed that the BBM gene escalated the transformation frequency of two maize inbreds, PHN46 and PH581. The callus transformation frequency of inbred PHN46 increased from 1.7% to 34.9%, while that for inbred PH581 rose from 0.4% to 16.9%. The transformation frequency for both inbreds increased further when the BBM gene was combined with the WUS gene. Discovery of the WUS gene in Arabidopsis was reported by Laux et al. [93]. They concluded that the WUS gene is required for leaf and flower formation, as the wus mutant exhibited premature leaf and flower organization. The combination of BBM and WUS also increased the transformation efficiency of recalcitrant upland switchgrass cultivar Summer to 6% [94]. In palm species such as date, the palm BBM (PdBBM) improved transformation efficiency to 11% in the Ajwa variety, a variety that had previously failed to develop embryos by promoting embryogenesis and the generation of viable seedlings [95]. However, the use of BBM and WUS genes resulted in the regeneration of a sterile transgenic plant; therefore, the removal of these genes is essential [92,96]. The removal of the BBM/WUS combination using the Cre-Lox method was demonstrated to enhance leaf base Agrobacterium-mediated transformation of maize and sorghum and subsequently enable genome editing [97].

Besides BBM and WUS genes, transcription factors, such as Growth Regulating Factors (GRFs), have also been proven to increase the transformation efficiency of monocot species [98]. GRF is involved in various plant development processes, including cell proliferation, overall growth, and maturation, as well as the plant's ability to respond to environmental stress [96]. The activation of the GRF gene is modulated by micro RNA miR396. The interaction of GRF with GRF-interacting factors (GIF), known as its cofactor, enhances its function in development regulation [96]. For maize transformation, Kong et al. [98] reported that the maize GRF5 (ZmGRF5) gene enhanced callus proliferation, improved transformation efficiency, and resulted in the production of normal, mature maize plants with viable seeds. The study also showed that the inserted gene was successfully transmitted to the T1 generation. The variety of wheat genotypes that can be transformed and the transformation efficiency were both increased by the co-expression of the GIF1 and TaGRF4 genes in wheat [99,100].

Moreover, the regenerated transgenic GRF-GIF wheat was productive and exhibited a normal phenotype. Due to wheat's efficient regeneration without cytokinins, this approach also makes transgenic wheat selectable without the need for a selection agent [99]. The efficacy of the TaGRF4-GIF complex in wheat transformation was further improved by altering the miRNA396 target region in the TaGRF4 gene. Hence, the mutated TaGRF4 (mTaGRF4) enhanced regeneration and genome editing frequency in various wheat [101]. Similarly, the utilization of the mTaGRF4-GIF1 complex increased the regeneration of shoots and improved the transformation efficiency of the medicinal orchid Dendrobium catenatum [102]. Incorporating the TaGRF4-GIF1 complex into a CRISPR/Cas9 construct for genome editing of wheat enhanced transformation efficiency in numerous wheat varieties and facilitated the production of stably inherited genome-edited wheat [100]. In addition to the abovementioned development regulator genes, recent studies have demonstrated that the Wuschel-related homeobox 5 (WOX5) also significantly improved the development of transgenic plants and subsequently increased the transformation efficiency of numerous monocots, including recalcitrant genotypes [96].

4. Agrobacterium-Mediated Trait Improvement via Genome Editing for Sustainability

The oil palm (E. guineensis Jacq.) is a crucial crop that provides a significant proportion of the world's edible oil. However, improving the sustainability of oil palm cultivation remains a challenge, as the crop faces issues such as environmental impact, disease susceptibility, and limited genetic diversity. The CRISPR/Cas9 genome editing system has evolved as a cutting-edge technology to address these challenges, allowing for precise modifications to the oil palm genome. CRISPR/Cas9 genome editing has been effectively utilized to enhance nutritional quality, stress tolerance, and disease resistance in a wide range of fruits, vegetables, and ornamentals [103]. This technology holds great potential for enhancing oil palm sustainability through targeted improvements to oil quality, environmental resilience, and resistance to diseases and pests [104,105].

4.1 Improving Palm Oil Quality

The global demand for vegetable oils has been steadily increasing, with palm oil being one of the most widely consumed and versatile oils. However, consumer perception and acceptance of palm oil have been hindered by concerns over its potential environmental impacts and health implications. One potential solution to address these concerns is to genetically modify palm oil to enhance its nutritional profile, particularly by increasing the oleic acid content. Oleic acid, a monounsaturated fatty acid, is widely recognized for its health benefits. Oleic acid has been shown to reduce the possibility of cardiovascular disease and improve cholesterol levels [106]. Furthermore, oleic acid has been found to possess superior lubricating properties compared to other fatty acids, making it a desirable additive for biobased lubricants [107].

Crude palm oil naturally contains 40% monounsaturated oleic acid, 10% polyunsaturated, and 50% saturated fatty acids. Polyunsaturated fatty acids consist of linolenic acid, while saturated fatty acids comprise 44% palmitic acid and 5% stearic acid [12]. Increasing oleic acid content in palm oil is the primary target of the oil palm biotechnology program [11]. According to the biochemical study, manipulating the expression of β-ketoacyl-ACP synthase II (KASII) and palmitoyl-ACP thioesterase (PAT) is expected to upsurge the level of oleic acid in palm oil [108]. To achieve this target, transformation vectors were constructed to downregulate the PAT and upregulate the KASII genes, and these were delivered into the oil palm ECs [11]. Recently, Bahariah et al. [18] demonstrated the first attempt to target candidate genes for increasing oleic acid in palm oil using CRISPR/Cas9 technology. Regeneration of oil palm plants containing the edited EgPAT and oil palm fatty acid desaturase 2 (EgFAD2) genes was successful.

Agrobacterium-mediated CRISPR/Cas9 genome editing was successfully employed to upsurge oleic acid levels in soybeans by editing the soybean FAD2 gene (GmFAD2) [109]. In pennycress, the oleic acid level in the seed oil was elevated by CRISPR/Cas9 knockout of the FAD2 and reduced oleate desaturation 1 (ROD1) genes, in combination with a knockout mutation of the fatty acid elongation 1 (FAE1) gene [110]. The level of oleic acid in fad2-fae1 mutants increased to 90%, while that of rod-fae1 mutants increased to 60% compared with the wild-type pennycress, which contains only 12% of oleic acid [110]. Likewise, improving the levels of stearic, palmitoleic, and ricinoleic acids in palm oil is also important to meet the diverse requirements of the oil palm sector [11,12].

4.2 Improving Oil Palm Height

The ability of CRISPR/Cas9 to generate dwarf and semidwarf plants such as rice [111,112], rapeseed [113], maize [114], and cucumber [115] by manipulating height and gibberellic acid (GA) related genes has been reported. In the context of oil palm, the development of dwarf oil palms through targeted gene editing can provide several benefits for sustainable cultivation. Shorter palm heights can facilitate a more straightforward harvesting process and reduce the risk of mechanical damage during operations [116]. Additionally, the reduced stature can lead to more efficient use of land and resources, ultimately enhancing the overall economic performance and viability of oil palm cultivation areas [104,116].

Genes and transcription factors associated with oil palm height were successfully identified [117,118]. Among the genes are brassinosteroid insensitive 1-associated receptor kinase 1 precursor (BRI1), gibberellin receptor (GID1), late elongated hypocotyl protein (LHY), E3 ubiquitin-protein ligase (E3Ub) and 24-methyltransferase 1 (SMT1). These genes regulate different steps in gibberellins (GA) and brassinosteroids (BR) biosynthesis, as well as signaling pathways for plant development [117,119]. Functional studies for three oil palm GA-related genes, EgGA20ox, EgGA2ox, and EgGAI, have been done using Arabidopsis thaliana as the model plant. The results revealed that downregulation of the EgGA20ox gene decreased the height of A. thaliana as well as the length of the root, leaves, and silique [120].

In the indica rice cultivar, modification of OsGA20ox2 via CRISPR/Cas9 resulted in semidwarf rice with decreased stature, lower GA levels, and a smaller flag leaf dimension. Additionally, the yield per plant increased to up to 6% [111]. Likewise, gene editing of the semidwarf 1 (SD1) gene, which encodes the gibberellin 20-oxidase 2 (GA20ox2) enzyme, using CRISPR/Cas9 technology reduced the height of Xiangdaowan rice [112]. Another gene targeted to produce a dwarf phenotype was CsERECTA, which encodes an LRR receptor-like serine/threonine-protein kinase that controls the extension of the stem in cucumber (Cucumis sativus) [115]. Knockout mutants of this gene produced dwarf cucumber plants with reduced expression of GA-related genes, resulting in decreased GA levels. Other than GA-related genes, BR-related genes were also targeted for genome editing using CRISPR/Cas9. For instance, a single mutation in the soybean (Glycine max) GmDWF1a and GmDWF1b genes, which are essential for BR synthesis, produced moderate dwarfism. In contrast, a double mutant of both genes produced a higher degree of dwarfism. Moreover, the single mutant of GmDWF1a yielded more soybean pods than its wild-type counterpart in the field test [121]. This information leads to a more comprehensive understanding of the genes controlling plant height and may be used in CRISPR/Cas9-mediated production of dwarf palms. For example, Yeap et al. [17] targeted brassinosteroid-insensitive 1 (EgBRI1) genes in an attempt to generate dwarf palm. However, no data on the regeneration of dwarf palm was reported.

4.3 Improving Commercial Oil Palm Fruit Color

Breeding for the virescens oil palm trait has gained interest in oil palm breeders due to its prominent color changes as compared to the common nigrescens palm [122]. The color of the fruit serves as a crucial cue for bunch ripeness to obtain maximum oil yield. The nigrescens palm fruits have deep-violet apex, and the color changes to red with a taint of violet when they ripen. Meanwhile, the unripe virescens palm fruits are fully green, and the color changes to bright orange with some residual green at the apical region [123]. These distinct color changes help a harvester to easily spot the ripe bunches, especially for tall palms [124]. The virescens palms typically exhibit delayed fruit ripening, which can extend the harvest window and reduce waste due to overripening [116]. This trait can also be introduced into non-abscising oil palms to facilitate the harvesting of ripe fruit bunches, as the loose fruit standard is not applicable to bunches that do not shed fruits [124].

The oil palm virescens (EgVIR) gene responsible for controlling oil palm fruit color was identified by Singh et al. [123]. This gene encodes the R2R3-MYB transcription factor, which controls oil palm fruit color by regulating the expression of genes associated with anthocyanin biosynthesis. The EgVIR gene shares homology with Lilium (lily) LhMYB12. The EgVIR gene is also similar to the Production of Anthocyanin Pigment 1 (PAP1) and AtMYB113 of Arabidopsis. Further analysis of the EgVIR gene has identified five independent mutations in exon 3 that are responsible for the virescens fruit color [123]. These mutations resulted in the production of truncated proteins of the R2R3-MYB transcription factor. Notably, these mutations were not observed in the nigrescens palm. Hence, this information could assist in the development of CRISPR/Cas9 vectors to produce virescens oil palm. In 2019, Aprilyanto and colleagues successfully constructed a CRISPR/Cas9 vector carrying a gRNA targeting the EgVIR gene; however, no further results were reported [125].

In other fruits, alteration of the color-related gene sequences produced fruits with colors different from the usual wild type. For example, in tomato (Solanum lycopersicum) cv Ailsa Craig, the use of Agrobacterium-mediated CRISPR/Cas9 to eliminate genes involved in the carotenoid biosynthesis pathway altered levels of different carotenoids depending on which gene was targeted [126]. For instance, the knockout of the stay-green 1 (SGR1) gene increased the lycopene content five-fold compared to the wild type and enhanced the color of the tomato fruit [126]. Besides carotenoid biosynthesis, genes associated with flavonoid biosynthesis were also targeted to modify fruit color. In particular, knockout mutation of the tomato R2R3-MYB transcription factor (MYB12) gene inhibited the accumulation of naringenin chalcone (NarCh), one of the flavonoids that contributed to the red color of ripe tomato fruit. This mutation resulted in a pink tomato fruit [127]. Recently, genome editing via multiplex CRISPR/Cas9 of the tomato phytoene synthase 1 (PSY1), SGR1, and MYB1 genes produced light green tomato fruit due to decreased levels of lycopene, β-carotene and NarCh and increased chlorophyll content. However, despite the changes in fruit color, the agronomic traits such as plant growth, flowering time, ripening time, and tomato yield were similar to those of the wild type [128].

4.4 Improving Oil Palm Resilience to Environmental Stress

Globally, the agricultural sector faces significant challenges in ensuring food security due to the detrimental effects of changing weather patterns. The oil palm industry is not immune to these challenges, as it is susceptible to the effects of drought and other environmental stresses [116]. The unfavorable conditions for oil palm growth exposed the palm to abiotic stress, affecting its productivity [129]. The oil palm industry's capacity to develop climate-resilient varieties has been hindered by the narrow genetic base of the commonly grown Deli dura and AVROS pisifera populations [130]. Genes that exhibit varying levels of expression under different abiotic stress conditions have been isolated and characterized, as reported by Wei et al. [129]. Briefly, the oil palm MYB (EgMYB), some members of the EgARF family, and bZIP genes were upregulated during cold, drought, and salinity stresses [130]. The EgLEA4 gene also has the ability to increase drought resistance [131].

CRISPR/Cas9 technology has been utilized to investigate genes linked to abiotic stress tolerance in various crops, including maize, tomato, rice, potato, and cotton [132,133]. Knockout mutants may have increased resistance or tolerance to the abiotic stress conditions depending on which gene was edited. As an example, enhancing rice's cold stress tolerance was achieved by utilizing Agrobacterium-mediated CRISPR/Cas9 to eliminate the cold-responsive R2R3-type MYB transcription factor, which is encoded by the OsMYB30 gene [134]. In wheat, CRISPR/Cas9 knockout of the TaSal1 gene improved wheat tolerance to drought [135]. Furthermore, CRISPR/Cas9 knockout of the maize abscisic acid-, stress-, and ripening-induced (ASR) gene (ZmASR1) enhanced maize tolerance to drought [136].

4.5 Improving Oil Palm Resistance to Disease

The oil palm sector faces significant challenges in addressing diseases that pose a substantial threat to productivity and sustainability. One such disease is the Basal Stem Rot (BSR), which is triggered by Ganoderma boninense, a fungal pathogen that can cause yield losses of 50%-80% [116]. In Malaysia, the BSR disease affects young palms and seedlings, as well as mature palms [137]. In addition to BSR, oil palms are also susceptible to infection by Phytophthora palmivora, an oomycete that triggered the bud rot disease [138]. This pathogen can attack various monocots and dicots, including vegetables and trees, significantly reducing plant production [139]. In Southeast Asia, among the plants that are affected by P. palmivora are coffee (Coffee arabica), oil palm (E. guineensis), black pepper (Piper nigrum L.), rubber (Hevea brassiliensis) and durian (Durio zibethinus) [140].

To enhance disease resistance in plants, researchers can target the plant susceptibility (S) gene using CRISPR/Cas9 genome editing, thereby affecting the plant-pathogen interaction and preventing infection [141]. Other possible targets for disease resistance are the resistance (R) gene, hormonal pathway, and pathogen virulence factor [142]. This technology has successfully produced a variety of plants with increased resistance to viruses, bacteria, fungi, and oomycetes, as listed in Zaidi et al. [143]. For example, the inactivation of the OsERF922 gene, which encodes an ethylene-responsive factor (ERF) transcription factor, in the japonica rice cultivar Kuiku 131 led to improved resistance against rice blast disease caused by the fungal Magnaporthe oryzae [144]. The mutation was stable and successfully inherited in the T2 generation. The important agronomic traits, such as plant height, length of the flag leaf, quantity of productive panicles, and number of grains in each panicle, were similar to those of the wild type. A recent investigation demonstrated that the elimination of the MAP kinase phosphatase 1 (TaMKP1) gene in wheat (T. aestivum) through CRISPR/Cas9 technology led to improved resistance against two fungal pathogens. The study showed increased protection against Blumeria graminis f. sp. tritici (Bgt), which caused powdery mildew, and Puccinia striiformis f. sp. tritici (Pst) that caused the rust disease [145]. Unexpectedly, the modified wheat plants were taller and produced more grains than their unaltered counterparts.

For the diseases manifested by the infection of oomycetes (Phytophthora), several genes related to plant immunity were edited to enhance resistance against the pathogen. One of the genes is the cacao tree (Theobroma cacao) non-expressor pathogenesis related 3 (TcNPR3). The TcNPR3 gene is a defense response repressor gene, and the knockout of this gene increased endurance to P. tropicalis [146]. In another study, Raf-like protein was targeted for CRISPR/Cas9 genome editing to enhance resistance against P. parasitica for A. thaliana. The CRISPR/Cas9 genome editing of the A. thaliana Raf36 gene resulted in a frameshift mutation, which reduced gene expression and produced a truncated Raf36 protein. When the detached leaf of the raf36 mutant was inoculated with P. parasitica, the lesion was smaller than the control, indicating enhanced resistance to the pathogen [147]. Recently, a group of scientists from China successfully increased the resistance of soybean (Glycine max L.) plant to the oomycete P. sojae via Agrobacterium-mediated CRISPR/Cas9 knockout of the soybean acetyltransferase gene (GmTAP1). Notably, the edited soybean plant exhibited similar tallness, pod number per plant, and yield per plant as the wild type in the field test, confirming that knockout of the GmTAP1 gene did not affect the agronomic traits [148].

4.6 Improving Oil Palm Resistance to Pest

The potential of CRISPR/Cas9 technology for managing insect pests was also explored and critically reviewed by Komal et al. [149]. Interestingly, CRISPR-mediated insect pest management can be achieved by modifying either plant or insect genomes, as suggested by Tyagi et al. [150]. However, this review will focus solely on CRISPR/Cas9 modification of the plant genome to provide insights into potential genes for enhancing oil palm resistance to pests. Creating insect-resistant crops through genome editing techniques will reduce farmers' reliance on pesticides. This shift is beneficial, as pesticide use can lead to various problems, including the emergence of pesticide-resistant insects, contamination of soil and water resources, and heightened expenses for managing environmental health concerns [151].

As a natural defense mechanism, plants synthesize metabolic substances in response to insect pest attacks. Among them are serotonin and salicylic acid [152]. In plants, both serotonin and salicylic acid are synthesized from chorismate, a metabolite from the shikimate pathway [153]. Isochorismate can be produced from chorismate, which can then be transformed into salicylic acid. Chorismate is also converted to tryptophan, which is subsequently converted to tryptamine for the synthesis of serotonin [153]. In a 2018 study, Lu et al. [154] demonstrated the creation of rice with enhanced resistance to insects by employing CRISPR/Cas9 techniques to inhibit the production of serotonin. They inactivated the CYP71A1 gene, which encodes the tryptamine-5-hydroxylase, an enzyme responsible for converting tryptamine into serotonin. Consequently, the lack of serotonin in rice enhanced its ability to resist stem borers and plant hoppers [154]. Subsequently, Wang et al. [155] conducted additional research on these mutants, which substantiated that rice plants with a reduced serotonin level confer increased resistance against striped stem borer.

Flavonoids are another type of plant metabolite that can protect plants from insect pests and pathogen attacks [156]. Numerous investigations have shown that CRISPR/Cas9 knockout of certain flavonoid biosynthesis genes awarded plants with insect resistance properties. For example, in the soybean cultivar Tianlong No.1, modification of the UDP-glycosyltransferase gene (GmUDP) via Agrobacterium-mediated CRISPR/Cas9 conferred enhanced resistance to the leaf-eating pests Helicoverpa armigera and Spodoptera litura [151]. The UDP-glycosyltransferase (UDP) is a cytosolic enzyme involved in generating flavonoid derivatives in the last stage of flavonoid biosynthesis. Mutation in the GmUDP gene altered the flavonoid content in the soybean leaf, and long-term feeding of H. armigera with the mutant soybean leaves reduced the larvae's immunity [151]. In addition, the Agrobacterium-mediated CRISPR/Cas9 knockout of the Nipponbare rice naringenin O-glucosyltransferase gene changed the flavonoid content in the rice. This modification leads to a reduced loss by two rice-consuming pests, brown plant hopper (Nilaparvata lugens) and rice grasshopper (Oxya hyla intricate) [102].

5. Conclusion and Prospects

The ongoing enhancement of oil palm planting materials has been facilitated by insights from oil palm physiology and molecular biology studies, which focus on genes that regulate growth, oil yield, and stress responses. This improvement process incorporates conventional breeding, genetic engineering, and RNAi-mediated gene silencing coupled with tissue culture for regeneration and propagation [13,54]. The complete mapping of the oil palm genome [16] has paved the way for the improvement of oil palm planting materials via CRISPR/Cas9 technology. Additionally, CRISPR/Cas9 genome editing studies on other crops offer valuable lessons for enhancing oil palm agronomic traits. Present efforts to apply CRISPR/Cas9 technology to improve oil palm planting materials employ various DNA delivery methods, including biolistic, Agrobacterium-mediated transformation [18,104,105], and PEG-mediated protoplast transformation [20]. While CRISPR/Cas9 technology has demonstrated successful genome editing of oil palms [17,18,20], enhancing Agrobacterium-mediated transformation efficiency would significantly accelerate the production of edited oil palms. Furthermore, developing transgene-free genome editing via Agrobacterium-mediated transformation could improve consumer acceptance of genome-edited oil palms. In essence, the strategic implementation of CRISPR/Cas9-mediated genome editing through Agrobacterium-based transformation presents significant opportunities for developing more sustainable oil palm planting materials, which could potentially contribute to the sustainability and environmental responsibility of the oil palm sector.

Acknowledgments

The authors thank the MPOB management for permission to publish this review. The authors would also like to acknowledge all the Transgenic Technology Group (TTG) members of MPOB for their advice and kind assistance.

Author Contributions

Hanin AN conceptualized the idea, conducted literature surveys, and drafted the manuscript. Masani MYA conceived the idea, edited and finalized the write-up of the manuscript, and submitted it. Rasid OA, Janna OA, and Parveez GKA reviewed and edited the manuscript. All authors read and approved the final manuscript.

Funding

No funding was applied for this review.

Competing Interests

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the literature reported in this review paper.

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