1. Introduction
Genetic engineering has significantly contributed to a fundamental and practical understanding of plant biology and genetics over the past 45 years. Notably, the potato was one of the first plant species to successfully undergo genetic transformation [
1]. Since then, numerous publications have detailed the generation of diverse transgenic potato plants carrying a wide array of engineered traits [
2,
3,
4]. Potato is an important food crop, which is cultivated not only for direct human consumption, but also as animal feed and an industrial crop for the production of alcohol, biofuel, starch, and other products. It stands as the 4th major staple crop globally, following maize, wheat, and rice, and is cultivated in over 150 countries. Faced with various production challenges, breeders are constantly making efforts to develop new varieties adapted to local agricultural needs in order to increase productivity while reducing costs [
5]. The breeding of potato is traditionally achieved through sexual hybridization between related species. However, the limiting factor in potato breeding is the long generation period, which makes it difficult to effectively introduce new traits into commercial varieties using traditional techniques of crossing. For this reason, potato genetic engineering is an important area of research, focusing on improving traits that are not easily modified by conventional breeding [
2,
3].
The generation of transgenic plants in any species hinges on the efficient selection of transgenic tissues, typically facilitated by various marker genes that confer resistance to selective substances, such as antibiotics or herbicides. However, the presence of antibiotic or herbicide resistance genes in transgenic plants intended for commercial use has raised significant consumer concerns regarding health risks and biosafety. This complicates the regulatory processes overseeing the release of biotech crops [
6]. Thus, the development of marker-free transgenic plants stands as one of the options to mitigate perceived risks and reduce public concerns.
In addressing the issue of marker gene presence, various strategies have emerged over the past decades. These include approaches that involve the direct removal of selective sequences from the transformation process or the controlled elimination of marker genes from the plant genome after the marker-assisted selection of transgenic plants is completed. The methods of removal include co-transformation, site-specific recombination, transposition, and the utilization of double right border–binary vectors or multi-auto-transformation vectors [
7,
8,
9,
10]. In co-transformation, vectors carry two separate T-DNAs: one containing the gene of interest and the other encoding a selection marker gene, both of which are introduced into the plant genome simultaneously. If insertions occur at unlinked genomic loci, they can independently segregate in subsequent generations, yielding marker-free segregants [
10]. Similarly, segregation is necessary when transgenic plants are transformed with the double right border twin T-DNA vector, featuring an additional copy of the right border sequence inserted between the marker gene and the gene of interest [
11]. Segregation-based strategies are extensively applied for various seed-propagated crops [
9,
10] but are impractical for vegetatively propagated species, such as potato.
Approaches directly applied to primary transformants, such as site-specific recombination or systems involving transposon-based and multi-auto-transformation vectors, are better suited for potato. Various self-excision site-specific recombination systems, including Cre-lox, FLP-FRT, and R/RS, have already been applied to varying degrees in vegetatively propagated horticulture crops, including apricot [
12], tomato [
13], blood orange [
14], strawberries [
15], apples [
16,
17,
18] and pears [
19]. The Cre-lox and R/RS systems have also demonstrated effectiveness in generating marker-free transgenic plants of potato. The heat shock-inducible Cre-lox systems achieved a 71% excision efficiency of the
NPTII antibiotic resistance marker gene in potato cv. ‘Desire’ [
20]; while the R/RS recombination tool exhibited lower efficacy, producing only 29% marker-free transgenic plants from the regenerated shoots of the same cultivar [
21]. The ipt (isopentenyl transferase)-type multi-auto-transformation vector has also been employed to generate marker-free disease-resistant transgenic potato plants [
22]. While these approaches have been successful, they do carry certain limitations. These include the need for designing sophisticated constructs, resulting in decreased transformation efficiency; the requirement for additional time for manipulations to re-regenerate marker-free plants after induced excision; the inability to achieve 100% excision efficiency; and unwanted chromosomal rearrangements in the plant genome, as a result of the expression of recombinase systems, leading to genetic and phenotypic changes.
An ideal approach to overcome these limitations involves a marker-free transformation procedure, where a simple expression cassette exclusively encoding the gene of interest is transferred into the plant genome via
Agrobacterium or gun-mediated transformation. In practice, only a limited number of crops, such as alfalfa [
23], peanut [
24], tobacco [
25] and wheat [
26], have been transformed using this approach, with an efficacy ranging from 0.1 to 50%. This straightforward procedure relies on the high regenerative capability of cultivated in vitro tissue to produce plants with a high frequency. Given that potato is among the highly regenerative species, markerless genetic transformation has been successfully applied to generate late blight-resistant [
27,
28], virus-resistant [
29,
30], and oxidative stress-tolerant transgenic potato lines [
31]. The primary challenge associated with markerless transformation is the necessity for the molecular screening of several hundreds of regenerated plants to discover a few transgenic events. Since regenerated plants need to be maintained in vitro, until molecular test results are obtained, transformation without selective genes becomes a time-consuming and expensive procedure.
In our current study, we analyzed the possibility of producing transgenic potato plants without using selective substances. We employed an expression construct encoding GFP or RFP to monitor the transformation process by cultivating internodal explants on both selective and non-selective media. This approach facilitated the analysis of the efficiency of chimeric and transgenic plantlet formation at various time intervals after co-cultivation with Agrobacterium and helped to compare transformation efficiencies of potato using antibiotic-free and antibiotic-assisted strategies.
2. Materials and Methods
2.1. Plant Material and General Conditions
The plant materials used in this study consisted of various potato germplasms generously provided by the Doka-Gene Technology Ltd., Russia. These included five commercial cultivars, ‘Chicago’, ‘La Strada’, ‘Lion Heart’, ‘Manhattan’ and ‘Pirol’, along with five breeding accessions, specifically #10-9-3, #10-10-10, #12-22-129, #12-36-42 and ‘Indigo’ (formerly #10-17-10). In vitro stock plants of potato were multiplicated in plastic vessels using phytohormone-free Murashige and Skoog (MS) basal medium supplemented with 3% sucrose, solidified with 7 g L−1 agar, and adjusted to a pH 5.8–5.9 before autoclaving. Vessels were maintained in a culture room at 21 ± 2 °C, subjected to a 16 h light/8 h dark cycle under artificial light (40 μmol m–2 s–1) provided by OSRAM cool white and fluora fluorescent lamps. In all experiments, internodal segments of 0.5–1 cm in length, excised from three- to four-week-old in vitro plants, were used as explants. Explants were cultured in 100 mm × 20 mm glass Petri dishes containing 25 mL of regeneration medium.
2.2. Potato Regeneration Media
All regeneration media were consisted of MS mineral salts and vitamins, supplemented with 30 g L−1 sucrose and 100 mg L−1 myo-inositol, solidified with 7 g L−1 agar, and adjusted to a pH range of 5.8–5.9. Four combinations of phytohormones were used to induce adventitious regeneration, comprising zeatin (Zea) 3 mg L−1, indoleacetic acid (IAA) 2 mg L−1, and gibberellic acid (GA) 1 mg L−1; zeatin-riboside (Zea-R) 3 mg L−1, IAA 2 mg L−1, and GA 1 mg L−1; Zea 3 mg L−1, IAA 0.5 mg L−1; Zea-R 3 mg L−1, and IAA 0.5 mg L−1. The preferred combinations of phytohormones were determined through preliminary experiments.
2.3. Agrobacterium-Mediated Genetic Transformation of Potato with and without Antibiotic Selection
In these experiments
A. tumefaciens strain AGL0 harboring pBIN-mGFP5-ER binary vector was used [
32]. T-DNA of this construct consists of the
NPTII-selectable marker gene under
NOS promoter and the modified
GFP gene driven by
CaMV 35S promoter along with a leader sequence for expression localization in the endoplasmic reticulum of the cells. Prior to transformation, colonies of bacteria were cultured overnight in liquid LB medium supplemented with 100 mg L
−1 kanamycin at 28 °C on an orbital shaker. Shortly prior to explant isolation, the agrobacterial suspension was diluted with phytohormone-free MS medium to a final density of OD600 = 0.2. Approximately 50–75 freshly cut internodal segments were immersed in 15 mL of
Agrobacterium suspension and inoculated in a 100 mL glass for 25–30 min at room temperature. Following this, the explants were placed onto sterilized paper and blotted dry for 2–3 min under laminar flow. After removing the excess of bacteria, the explants were transferred to Petri dishes containing the regeneration medium covered with sterilized filter paper, and maintained for 3 days in the dark at 25 ± 1 °C. Post-co-cultivation, groups of 10–12 explants were transferred to 100 mm × 20 mm glass Petri dishes containing 25 mL of fresh regeneration medium supplemented with 500 mg L
−1 of the antibiotic cefotaxime. Dishes were kept in the culture room at 21 ± 2 °C under a 16 h light/8 h dark cycle, with subculturing carried out every 2 weeks. All subsequent media plates contained the same cefotaxime concentration. From the third week after inoculation, plantlets 1.5–3.0 cm in length, regenerated from explants under-non selective conditions, were cut and transferred to culture vessels (ten plantlets per vessel) containing 100 mL of phytohormone–free MS medium supplemented with 150 mg L
−1 cefotaxime. Once the plantlets grew to 5–10 cm in length, shoot tips with one to two expanded leaves were moved into phytohormone–free MS medium containing 100 mg L
−1 kanamycin for the identification of transgenic events through rooting. The step-by-step scheme of the non-selective genetic transformation of potato is presented in
Figure 1.
In parallel, the antibiotic-assisted genetic transformation was carried out. After co-cultivation with
Agrobacterium in the dark for 3 days, a portion of intermodal segments was transferred to the corresponding regeneration medium supplemented with kanamycin (50 mg L
−1). Shoot regeneration and transgenic plant selection were then performed as described [
32]. To avoid duplication of transgenic lines, only one kanamycin-resistant shoot was collected from each explant.
As per the aforementioned transformation procedure (
Figure 1), two potato cultivars were subjected to transformation using the plasmid pDGB3_5453 (the gift of prof. A.Vainstain, The Hebrew University of Jerusalem), which harbors the
RFP gene driven by
CaMV 35S promoter and
NPTII-selectable marker gene driven by
NOS promoter. In contrast to previous experiments, each explant that produced a chimeric or transgenic plantlet was carefully labeled. Both the ‘mother’ explant and the resulting plantlet(s) were tracked throughout the experiment to determine the ‘standard’ transformation efficiency, calculated as the percentage of inoculated explants that regenerated transgenic plants. Four independent experiments were performed, each involving 50–55 explants for ‘Pirol’ or 91–100 explants for ‘Chicago’. Plantlets displaying any signs of red fluorescence, whether sectoral or full fluorescence, were detached and subsequently cultivated on an antibiotic-free medium. Following at least five sub-cultivations, during which the observation for RFP fluorescence was no longer carried out, all putative transgenic events underwent PCR analysis to confirm the introduction of the
RFP gene. Concurrently, these events were transferred to a kanamycin-enriched medium to confirm the introduction of the
NPTII gene from T-DNA through rooting.
2.4. Monitoring of Green and Red Fluorescence
Visual screening for transient and stable T-DNA incorporation was conducted using a ZEISS SteREO Discovery.V12 microscope (Carl Zeiss Microscopy GmbH, Jena, Germany) equipped with a PentaFluar S 120 vertical illuminator(Leistungselektronik JENA GmbH, Jena, Germany). In the GFP observations, two commercially available filter sets, namely 38 GFP BP (EX BP 470/40, BS FT 495, EM BP 525/50) and 57 GFP BP (EX BP 470/40, BS FT 495, EM LP 550), from Carl Zeiss MicroImaging GmbH (München, Germany) were used. RFP fluorescence was detected using 43 Cy3/Rhod/RFP (EX BP 545/25, BS FT 565, EM BP 606/70) from the same manufacturer. Photographs were taken using the digital Camera AxioCam MRc 5 with the help of ZEN Pro 2012 software (Carl Zeiss Microscopy GmbH, Jena, Germany).
2.5. Molecular Analysis
To analyze integrated T-DNA copies, Southern hybridization was conducted. For the blot analysis, 30 μg of potato genomic DNA was digested overnight at 37 °C with 60U
HindIII, which cleaves the T-DNA of pBIN-mGFP5-ER at a single position (5′ end of the
CaMV 35S promoter). Subsequently, the DNA was separated through gel electrophoresis in 0.9% agarose, and then transferred and immobilized onto a Hybond N+ membrane (GE Healthcare, Amersham Bioscience, Amersham, UK). Membranes were probed with alkaline phosphatase-labeled probes and detected using CDP-Star detection reagent (Amersham CDP-Star Detection reagent, GE Healthcare), as previously described [
30]. Hybridizing bands were visualized on X-ray film (Retina XBE blue sensitive, Carestream Health Inc., New York, NY, USA) at room temperature for 24 h. The DNA probe (711 bp) for hybridization was synthesized via PCR using specific primers for the coding region of the GFP gene (forward, 5′-AGTAAAGGAGAAGAACTTTTCACTGGAGTT-3′; reverse, 5′-TTTGTATAGTTCATCCATGCCATGTGT-3′) and labeled with the alkaline phosphatase using the Amersham Gene Images AlkPhos Direct Labelling and Detection System (GE Healthcare, Amersham Bioscience, Amersham, UK).
The transgenic status of plants, which were discovered after the initial RFP monitoring, was validated using PCR with the following primers: RFP forward 5′-CATCACCGAGTTCATGCGCTTCAAG-3′, RFP reverse 5′-GGCTTCTTGGCCATGTAGATGGACT-3′; the size of the amplified fragment was 537 bp. PCR conditions included preheating to 95 °C for 2 min, followed by 35 cycles with denaturation at 95 °C for 20 s, annealing at 61 °C for 20 s, elongation at 72 °C for 45 s, and ending with 5 min at 72 °C. The PCR products were analyzed in 0.8% (w/v) agarose gel stained with ethidium bromide.
2.6. Statistical Analysis
The data presented are the mean ± SD. Significant differences were determined via t-test with p < 0.05 as a threshold. Within experiments, data were analyzed by Statistica10 software (©StatSoft Inc., Tulsa, OK, USA) using analysis of variance (ANOVA), followed by Tukey’s HSD (Duncan’s) test.
4. Discussion
The large number of scientific reports published since the late 1980s and worldwide commercial releases of GM varieties confirm that potato is a relevant crop for improvement through biotechnology [
2,
3,
4,
5]. The successful genetic transformation of potato depends on the efficient plant regeneration protocol and the optimized method of recognizing transgenic tissues. Since it is assumed that the likelihood of obtaining transgenic events is higher when more cells are able to differentiate into shoots, we have preliminarily screened ten potato cultivars for the regeneration potential to choose better ones for antibiotic-free transformations. As a rule, a two-stage regeneration protocol is used in potato, when the stage of regeneration of shoots is preceded by the stage of callus induction [
4]. In most cases, cytokinins are of paramount importance to initiate morphogenesis in potato. Although BAP, kinetin, and TDZ are known to stimulate regeneration in potato, currently zeatin is the most popular cytokinin for generation of transgenic potato plants. Most transformation protocols include the supplementation of 1–5 mg L
−1 of zeatin in combination with a low auxin level into the regeneration medium.
Several zeatin-containing variants of regeneration medium combined with different auxins were used in the present study. Experiments also included twin variants, when zeatin was replaced with zeatin ribozide. The latter was reported to be superior to zeatin in terms of regeneration frequency and even allowed the one-step transformation of potato [
33]. Tested varieties positively reacted to the various plant phytohormone combinations, although the two variants were more effective in practice. The combination of 3 mg L
−1 Zea and 0.5 mg IAA L
−1 was the best for five cultivars, while the combination of the same level of zeatin with a significantly higher concentration of IAA (2 mg L
−1) and the additional incorporation of gibberellic acid (1 mg L
−1) to support the better outgrowth of morphogenic buds was essential for successful regeneration in ‘Chicago’, ‘Lion Heart’, and #10-9-3. The replacement with the more expensive zeatin ribozide generally had no significant effect in listed above varieties as they were already able to produce plants with 95–100% efficiency using zeatin. Nonetheless, zeatin ribozide was more successful in two cultivars (‘Indigo’, ‘La Strada’) and this observation supports the early notion that its application is a really good alternative for particular varieties to achieve increased efficiency of regeneration [
33].
Experiments have also shown that the timeline of plantlet regeneration from internodal explants is an important aspect to pay attention to. We observed significant differences between genotypes in the speed of adventitious shoot formation. Some varieties, such as ‘Chicago’ and #12-22-129, started to generate plantlets much earlier than the others. In contrast, the ‘late’ cultivars such as Pirol’, #10-9-3, ‘Indigo’, and ‘Lion Heart’ begin to develop plantlets when the early regenerative cultivars had already produced a maximum of shoots. This genotype-specific property could be used when potato cultivars were subjected to marker less transformation. Our results indicate that early regenerative cultivars produced the most transgenic plants (~75%) between 30 and 60 days after inoculation with
Agrobacterium, while the late regenerative cultivars preferably generate transgenic events during the 50–80 days of cultivation. The cultivars with an intermediate regeneration timeline generate most transgenic plants between 40 and 70 days after co-cultivation with
Agrobacterium. This could be considered as a means to reduce the number of tested plantlets, as a bunch of manipulations, such as DNA extraction, PCR analysis, and prolonged in vitro cultivation of each regenerated plant, are required to detect transgenics. Our data are in agreement with those of Jo et al. 2014 [
27], who under non-selective conditions and also observed differences between three potato cultivars in the number of PCR-positive plants over the number of analyzed regenerated shoots. Unlike the present study, shoots were collected only at three-week intervals, and only a part of generated shoots were analyzed; however, the timeline-dependent effect was clearly observed, as a higher portion of PCR positive plants of ‘Potae9’ and ‘Bintje’ was found between 31–50 and 31–70 days, correspondently, while explants of ‘Atlantic’ produced a significant portion of transgenic plants during the 50–90 days [
27].
There is general agreement that regeneration without selective pressure leads to a problem of chimerism, when the shoots are composed of both transgenic and non-transgenic cells. Through the in vivo monitoring of
GFP or
RFP fluorescence, we found that a substantial portion of plants (from a third to a half) displaying visible fluorescent signals represent chimeras of varying degrees (
Figure 4C and
Figure 7A). Even though chimeric plants were more prevalent during the first period of regeneration, they continued to appear during the later stages of transformation. Our findings suggest that sequential cultivation of chimera shoot tips helps overcome the problem of chimerism. Five cycles of multiplications enable the stabilization of putative transgenic plants. During this period, chimeras containing the transgenic meristem turn into completely transgenic plants, while the majority of chimeras (approximately 80–95%) exhibiting sectoral fluorescence transform into non transgenic plants.
An additional consideration is the possible transgenic chimerism of regenerated potato plants. Direct regeneration may result in transgenic plants composed of cells with diverse T-DNA introduction events. Analysis of transgene insertions indicated a low number of transgene copies in the resulting transgenic potato plants, with mostly one to three independent insertions identified (
Figure 5). Observed patterns of integrations align with the prevalent type of transgene insertions reported by various authors when producing transgenic potato plants with the aid of selectable marker genes [
20,
26,
34,
35,
36,
37]. This finding prompts us to propose that chimerism issues initially observed in plants collected without selective pressure could be effectively addressed through the application of standard tissue culture methods, such as tip sub-culturing. This practice yields transgenic potato plants that consistently demonstrate the presence of transgenes, confirmed by molecular analysis (PCR or southern-blot) or the expression of introduced genes (red or green fluorescence of tissues, rooting on medium supplemented with kanamycin). In our prior study [
29], where marker-free intragenic plants of ‘Pirol’ were regenerated using the same procedure, the transgenic status remained stable over five years of in vitro propagation and was regularly confirmed by qRT-PCR and virus resistance.
The Southern blot analysis corroborated that the majority of the regenerated plants represent independent events, even if they originate from the same explant. Our tracking of explants producing transgenic plantlets showed the possibility of duplicating the same transgenic event in the case of morphogenic transgenic cluster formation (
Figure 7E). Continuous in vivo monitoring for
RFP fluorescence, however, indicated that the duplication was rarely observed, giving the low rate of callus formation in our study. It is plausible that the direct induction of buds at various sites of the explant (
Figure 4F) could augment the generation of independent events. This notion is supported by the fact that most of the cultivars used for antibiotic-free transformation exhibited the ability to regenerate shoots on both sides of the internodal explant (
Figure 2), thereby increasing the likelihood of the independent production of transgenic events from the same explant.
Our results are consistent with previous studies, underscoring that antibiotic-free transformation is less genotype-dependent compared to antibiotic-assisted transformation [
25,
27]. In the present study, antibiotic-assisted transformation across five cultivars varied from 44 to 100% (
Table 2), whereas the efficiency of antibiotic-free transformation was within a narrow range of 0.8 and 2.8% (per 100 plants). A similar trend was previously observed following the
Agrobacterium-mediated transformation of ‘Atlantic’, ‘Potae9’, and ‘Bintje’ potato cultivars [
27], demonstrating high variation in the efficiency of kanamycin-assisted transformation (ranging from 10 to 71%) and low variation in markerless transformation efficiency (0.6–2.4 plants per 100 tested plants). An average marker-free transformation efficiency of 2.2% was reported for cv. ‘Superior’ [
30], where leaf explants were used instead of intermodal segments for plantlet regeneration. In another report, the highly transformable cv. ‘Karnico’ achieved a slightly higher efficiency, reaching 4.5% of markerless transformation, while the cultivars with lower marker-assisted transformation abilities showed a lower percentage of PCR-positive shoot recovery (0.6–2.4%) [
26]. There was no such correlation in our study. For instance, ‘Chicago’, the cultivar with remarkably high efficiency of antibiotic-assisted selection (100%), demonstrated the lowest antibiotic-free transformation (0.8–0.9%) calculated per 100 detached plantlets. By contrast, cultivars ‘Pirol’ and ‘La Strada’, with a lower kanamycin-assisted transformation efficiency of 44–47%, produced more transgenic plants without selective pressure (1.8–2.0 per 100 plants) than ‘Chicago’ (
Table 2). It is pertinent to note that the marker-free transformation, calculated relative to the total number of plants tested, may not be directly comparable for the same cultivar, as the efficiency of antibiotic-assisted transformation is typically defined as the percentage of explants producing transgenic plants. Consequently, the ability to generate more or fewer plantlets from the same number of cultured explants can influence the difference in marker-free transformation efficiency per 100 tested plants in a specific cultivar. This was further affirmed in our study of the ‘standard’ transformation efficiency by tracking all inoculated explants/transgenic plantlets using in vivo
RFP fluorescence. The outcomes indicated that the previously mentioned cultivars, ‘Pirol’ and Chicago’, which differ in antibiotic–assisted transformation, displayed nearly equivalent efficiency of antibiotic free transformation, defined as the percentage of initial explants producing transgenic plants (
Table 3). We found that approximately every tenth explant of both cultivars is capable of producing a transgenic plant, although the efficiency in individual experiments could vary from 7.3 to 13%.
Despite the simplicity of marker-less transformation, the chances of recovering transgenic plants are usually low [
22,
23,
24,
27,
28,
29], as there is the supposition that without the application of selective substances the fraction of
Agrobacterium-treated cells that may become transgenic is limited. In our study, the number of explants displayed that
GFP fluorescence until 30 days after agrobacterial inoculation of four potato cultivars was surprisingly equal or even higher than without the selective pressure. Only cultivar ‘La Strada’ displayed a better transient expression when the kanamycin-assisted selection was used; however, the efficiency of stable genetic transformation was only 47%, lower than in other genotypes. These results, on the one hand, indicate that a high level of transient expression does not necessarily lead to high efficiency of transformation in potato, while the presence of explants with high transient expression, regardless of selective pressure, makes the generation of fully transgenic plants in the absence of marker-assisted selection realistic.
Although the ability to generate transgenic elite cultivars of potato without using selectable marker genes is not as effective as using a marker-assisted selection, we believe it will facilitate the potential commercial release of new biotech potato varieties produced by cisgenic and intragenic approaches of genetic transformation.