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Review

Genomic Innovations and Marker-Assisted Breeding in Echinacea Species: Insights and Applications

by
Fatemeh Ahmadi
UWA School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
Sci 2025, 7(2), 43; https://doi.org/10.3390/sci7020043
Submission received: 2 October 2024 / Revised: 25 February 2025 / Accepted: 25 March 2025 / Published: 2 April 2025
(This article belongs to the Section Biology Research and Life Sciences)
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Abstract

:
The genus echinacea has attracted attention for its diverse medicinal properties, including its ability to enhance immunity, reduce inflammation, and combat microorganisms. Despite its popularity in herbal medicine, the varying concentrations of active compounds among different echinacea species and products create obstacles for achieving uniform quality and reliable efficacy. This study investigates the genetic and molecular mechanisms responsible for producing key bioactive substances such as alkamides, chicoric acid, and complex carbohydrates, which are essential for echinacea’s therapeutic effects. Furthermore, the research explores recent advancements in plant breeding methodologies, including the use of DNA-based selection techniques and cutting-edge genomic tools like CRISPR-Cas9. These innovative approaches seek to develop echinacea varieties with improved tolerance to environmental challenges, heightened disease resistance, and enhanced production of valuable phytochemicals. Additionally, this review addresses the impact of environmental factors, including abiotic stresses like drought and salinity, on gene expression related to secondary metabolite production. These insights are crucial for optimizing both cultivation practices and breeding programs. The conclusions suggest that integrating traditional breeding methods with modern genomic tools holds great promise for improving the consistency and quality of echinacea products, which is essential for their sustained use in global herbal medicine markets.

1. Introduction

The name “Echinacea” stems from the Greek “Echinos”, referencing sea urchins or hedgehogs, due to the plant’s spiky appearance [1]. This genus, indigenous to North America, thrives naturally in areas east of the Rocky Mountains, specifically in the Atlantic drainage regions of the U.S. and Canada. Echinacea cultivation is believed to cover thousands of hectares around the world [2]. The popularity of herbal remedies has surged recently, with usage increasing from 15% to 35%, and echinacea joining garlic as a top choice for self-care [3]. Among herbal extracts in North America, echinacea leads the market. Its annual sales surpass USD 158 million in the USA, with global figures estimated at USD 1300 million. Three echinacea species are primarily used for their medicinal properties: E. purpurea Moench (whole plant), E. angustifolia DC (roots), and E. pallida Nutt (roots) [4]. Echinacea crops can produce over 50 tons of fresh material or 10 tons when dried per hectare, with E. purpurea typically being the most productive [5]. The conversion ratio from fresh to dry weight for echinacea generally falls between 2.5 and 5.1, with roots having a lower ratio due to their higher dry matter content [6].
Echinacea species have been utilized globally for their therapeutic properties, addressing a wide range of ailments from venomous bites to malignancies and from dental pain to viral infections [7]. Indigenous communities pioneered the medicinal applications of echinacea long before Western medical practitioners documented its use. However, the advent of antibiotics in the 20th century temporarily overshadowed echinacea’s popularity as an herbal remedy for infections [8]. The medicinal effects of echinacea are believed to stem from its ability to enhance immune function by promoting T-cell production, increasing phagocytosis and lymphocytic activity, and exhibiting antioxidant properties against tumor cells [9]. Additionally, it may inhibit hyaluronidase enzyme secretion. Market research consistently places echinacea among the top 10 best-selling herbal products [10]. Echinacea-based products are derived from various plant parts, including roots, flower heads, seeds, and whole plant extracts [11]. The resurgence in echinacea usage, sourced from both wild and cultivated plants, can be attributed in part to the extensive pharmacological and clinical studies conducted since the early 1980s [12,13]. Currently, natural health products containing echinacea are at the forefront of the movement towards preventive healthcare and alternatives to synthetic pharmaceuticals [14].
The diverse array of bioactive compounds found in echinacea species contributes to their wide-ranging therapeutic potential [15]. Historically, these plants have been valued for their ability to boost immune function, reduce inflammation, and combat microbial infections [16]. Echinacea’s pharmacological profile includes several key component classes: phenolic acids, alkamides, polyacetylenes, glycoproteins, and polysaccharides. These various compounds are believed to work in concert, producing the medicinal effects associated with echinacea preparations [17]. However, the precise mechanisms and interactions between these components remain an active area of scientific inquiry, with researchers continuing to explore the complex synergies at play [18].
Echinacea species contain various phenolic compounds, with caffeic acid derivatives being particularly noteworthy [19]. For instance, chicoric acid is found in E. purpurea and E. pallida, while echinacoside is present in E. angustifolia. These compounds have garnered attention due to their potential antioxidant, anti-inflammatory, and immune-modulating properties [20]. However, the levels of these phenolic substances can fluctuate considerably based on factors such as the specific echinacea species, the plant part utilized, and environmental growing conditions [21].
Recent studies have raised important questions regarding the bioavailability and absorption of these phytochemicals [18]. While compounds like chicoric acid and echinacoside are indeed present in echinacea preparations, current research suggests that they may not be absorbed into the bloodstream in quantities sufficient to directly exert significant medicinal effects [14]. This finding has implications for understanding the mechanisms behind Echinacea’s reported health benefits and highlights the need for further investigation into how these compounds interact with the human body [22].
In contrast, alkamides, another group of active compounds in echinacea, have been proposed as key candidates for the medicinal efficacy of the plant [23]. These lipophilic molecules not only exhibit anti-inflammatory and immunomodulatory effects but also show higher bioavailability, with studies indicating that alkamides are more easily absorbed and metabolized in the human body compared to phenolic acids [24]. Alkamides also act on the endocannabinoid system, which may further explain their role in modulating immune responses and inflammation [25].
The composition of echinacea products varies widely, posing a significant obstacle to achieving standardization and consistent therapeutic outcomes. This variability stems from several factors, including differences in the plant material used, the extraction techniques employed, and the inclusion of additional components or excipients [26]. Some commercial preparations utilize the entire plant, while others focus on specific parts such as roots or flowers, each offering a unique profile of active compounds. Furthermore, the choice of extraction method—whether using alcohol, water, or CO2—can significantly impact the yield of bioactive substances, particularly alkamides and phenolic acids [27]. This lack of uniformity across products makes it challenging to establish standardized dosages and complicates comparisons of efficacy between different echinacea formulations [28]. The inconsistency in product composition underscores the need for more rigorous standardization practices in the production of echinacea supplements. It also highlights the importance of further research to better understand how different preparation methods affect the therapeutic potential of echinacea products [29]. The main alkamides and phenylpropanoids in echinacea species are shown in Figure 1. The most abundant alkamides and caffeic acid derivatives of echinacea species are listed in Table 1 and Table 2, respectively.
Studies [30] have shown that E. purpurea roots contain up to 0.2% essential oil, with key components including caryophyllene, humulene, and caryophyllene epoxide (Figure 2). The aerial parts of this plant contain less than 0.1% essential oil, featuring compounds such as borneol, bornyl acetate, germacrene D, and caryophyllene and its epoxide, which are also found in E. pallida and E. angustifolia aerial parts [31,32]. Research on E. purpurea achenes has identified various compounds, including a-pinene, b-farnesene, myrcene, and limonene [33]. A comprehensive analysis of volatile components in different plant parts of E. angustifolia, E. pallida, and E. purpurea revealed over 70 compounds, with camphene, b-pinene, and limonene being prevalent across all tissues and species [34,35]. The composition of essential oils varies between plant parts. Aerial parts contain additional compounds like b-myrcene, a-pinene, and trans-ocimene. α-Phellandrene is a major component in E. purpurea and E. angustifolia rhizomes but absent in E. pallida [36]. Aldehydes are more concentrated in rhizome tissue, while terpenoids dominate in flowers and stems [37,38]. This diversity in essential oil composition across different Echinacea species and plant parts contributes to the complex phytochemical profile of these plants, potentially influencing their therapeutic properties [39].

2. Factors That Affect Echinacea Phytochemistry

Genetic diversity plays a crucial role in determining the bioactive compound profiles of Echinacea species. Variations in genetic makeup, both between and within species, can lead to significant differences in the levels of key compounds such as alkylamides, caffeic acid derivatives (including echinacoside and chicoric acid), and polysaccharides [40]. The three most commonly used medicinal species—E. purpurea, E. angustifolia, and E. pallida—which possess distinct chemical signatures. To optimize the therapeutic potential of echinacea, plant breeders and researchers are exploring selective breeding techniques and genetic enhancement strategies [41]. These approaches aim to develop echinacea cultivars with elevated concentrations of targeted bioactive substances, potentially improving their medicinal efficacy [42].
The method of cultivation plays an important role in the accumulation of bioactive compounds [43]. Organic farming practices that avoid synthetic pesticides and fertilizers have been associated with higher levels of certain phytochemicals, possibly due to increased plant stress, which stimulates the production of defense-related compounds [44]. Additionally, harvesting time and the plant’s growth stage at harvest have a profound impact on the content of bioactive substances. Research suggests that harvesting at the optimal stage of flowering maximizes the concentration of echinacoside and other phenolic compounds [45].
The bioactive compounds in echinacea are also affected by post-harvest handling, drying methods, and storage conditions [46]. Improper handling during drying or prolonged exposure to heat and light can lead to the degradation of temperature-sensitive compounds like alkylamides and chicoric acid [47]. Moreover, extended storage times or high humidity during storage may reduce the potency of echinacea extracts. To preserve the integrity of bioactive compounds, standardized extraction methods, and appropriate storage practices are critical [48]. Advanced drying technologies such as freeze-drying can help retain higher levels of bioactive constituents, making them more effective in commercial formulations [49].
Environmental stressors significantly impact the phytochemical profile of echinacea species. These abiotic factors include temperature fluctuations, water scarcity, soil salinity, and nutrient availability [50]. For example, water-deficient conditions often trigger increased production of secondary metabolites like phenolic acids and flavonoids in echinacea plants. This response is believed to be a protective mechanism against oxidative stress caused by reactive oxygen species [51]. Soil salinity is another environmental factor that can alter the biosynthesis of important compounds in echinacea, particularly caffeic acid derivatives such as echinacoside and chicoric acid. Interestingly, echinacea purpurea has shown elevated levels of these compounds when cultivated in saline environments [52]. This finding suggests that controlled exposure to salt stress could potentially be used as a method to enhance the medicinal properties of echinacea crops. Understanding these plant-environment interactions offers opportunities for optimizing cultivation practices to maximize the therapeutic potential of echinacea species [53].
Temperature fluctuations also influence the plant’s metabolic processes. Low temperatures tend to slow down metabolic reactions, which may decrease the biosynthesis of certain bioactive compounds [54]. Conversely, high temperatures, particularly heat stress, can either inhibit the accumulation of some phytochemicals or trigger the overproduction of others, depending on the duration and severity of the stress [55]. Nutrient availability in the soil is another essential factor; for example, nitrogen and phosphorus levels can influence the synthesis of bioactive compounds in echinacea [56]. Higher concentrations of nitrogen may stimulate the production of alkaloids and terpenoids, while phosphorus limitation can lead to enhanced production of phenolics [57].
Biotic factors, such as herbivory, pathogens, and microbial interactions, also significantly affect echinacea phytochemistry [58]. In response to herbivory, plants often upregulate the production of defense-related secondary metabolites [59]. When echinacea species are subjected to herbivore attacks, they can increase the biosynthesis of alkaloids, phenolic acids, and terpenoids, which act as deterrents to herbivores by being toxic or unpalatable [60]. These compounds also serve as signaling molecules, activating various defense pathways within the plant to mitigate further damage [61].
Pathogen infections, caused by fungi, bacteria, or viruses, can also alter the phytochemical profile of echinacea. For example, when exposed to fungal pathogens, echinacea plants may increase the production of phenolic compounds, which serve as antimicrobial agents [62]. These phytochemicals help to protect the plant tissues from pathogen invasion, while also enhancing the plant’s overall resilience to biotic stress. Recent studies have shown that microbial interactions, such as symbiosis with mycorrhizal fungi, can positively affect the concentration of secondary metabolites in echinacea [63]. Mycorrhizal associations are known to improve nutrient uptake, especially under nutrient-deficient conditions, which can lead to the increased biosynthesis of medicinally valuable compounds like caffeic acid derivatives and alkamides [64].
In nature, echinacea often faces multiple biotic and abiotic stresses simultaneously, which can have synergistic or antagonistic effects on its phytochemistry [65]. For instance, plants experiencing both drought stress and pathogen attack may exhibit a compounded increase in secondary metabolite production, as the same pathways are often involved in responding to both types of stress [66]. On the other hand, certain combinations of stresses may lead to trade-offs, where the plant allocates more resources toward mitigating one type of stress over another, thereby altering the balance of phytochemicals produced [67]. Understanding the interactions between different stresses is vital for optimizing the cultivation of echinacea for medicinal purposes, as controlled stress can be used to maximize the production of bioactive compounds sustainably [68].

3. Genetic Engineering and Transgenic Echinacea

Genetic engineering is an advanced scientific technique that enables researchers to manipulate an organism’s genetic material [69]. This process involves modifying DNA through the insertion, deletion, or alteration of genes. The application of this technology has become widespread in agricultural and medical fields, allowing for the development of organisms with specific desirable characteristics [32]. These traits may include enhanced resistance to diseases, improved crop yields, or increased production of targeted compounds. By harnessing the power of genetic engineering, scientists can potentially create more resilient and productive varieties of plants, including medicinal herbs like Echinacea [70]. Transgenic plants have genes from other species inserted into their genomes, enabling them to express new traits [71]. This process is typically facilitated using a bacterial vector like Agrobacterium tumefaciens, which can transfer foreign DNA into plant cells [72].
The application of genetic engineering in agriculture presents numerous opportunities for creating high-value crops. This technology also enables researchers to investigate regulatory mechanisms in plant development and biosynthesis by introducing foreign genes [73]. However, genetic engineering research on echinacea species remains limited, with only a few studies reporting successful creation of transgenic hairy roots and plants. The efficiency of echinacea transformation is influenced by several factors, including the choice of plant tissue (explant), co-cultivation methods, selection processes, and regeneration techniques for transformed tissues [74]. These variables play crucial roles in determining the success rate of genetic modifications in echinacea species [75]. Transgenic echinacea, specifically E. purpurea, has been the subject of genetic engineering experiments aimed at enhancing its medicinal properties [76]. Echinacea is well known for its bioactive compounds, including caffeic acid derivatives, which have immune-boosting, antiviral, and antioxidant effects. By employing genetic engineering, scientists aim to increase the production of these beneficial compounds and enhance echinacea’s ability to resist diseases or environmental stresses [77]. While research on transgenic echinacea is still developing, the application of genetic engineering to this medicinal plant holds great potential for improving its use in herbal medicine [78].
Research has shown the potential for genetic modification in echinacea species, particularly E. purpurea, using Agrobacterium-mediated transformation techniques [79,80]. These methods have been employed to create transgenic hairy root cultures and whole plants with enhanced characteristics [81,82]. One approach involves using Agrobacterium rhizogenes to induce hairy root cultures in E. purpurea. These cultures have shown promise in increasing the production of secondary metabolites, especially caffeic acid derivatives (CADs) like chicoric and caftaric acids [83]. Some transgenic lines exhibited improved growth and higher CAD content compared to non-transgenic counterparts. Another study utilized Agrobacterium tumefaciens to introduce herbicide resistance (bar gene) and fungal resistance (chitinase gene) into E. purpurea. This resulted in the successful regeneration of transgenic plants resistant to glufosinate ammonium herbicide, representing a significant advancement in echinacea biotechnology [84,85]. Further research using A. rhizogene-induced hairy roots in E. purpurea aimed to enhance secondary metabolite production. The most successful transgenic line showed significantly increased levels of chicoric and chlorogenic acids compared to non-transgenic plants [86,87]. These studies demonstrate the potential of genetic engineering to improve the medicinal properties of echinacea by increasing the concentration of valuable bioactive compounds [88,89,90].
Research on Agrobacterium rhizogene-mediated transformation of E. purpurea has yielded mixed results, with some studies reporting limited growth and atypical morphology in transgenic roots [54]. However, recent advancements have led to more efficient protocols for initiating and propagating hairy roots, which show promise for isolating medicinally active compounds. In one study, leaf explants of E. purpurea transformed with A. rhizogenes (ATCC 43057) produced hairy roots that achieved maximum dry biomass in MS basal medium within 40 days [63]. HPLC analysis of these roots revealed significant levels of important caffeic acid derivatives (CADs), including chicoric acid, caftaric acid, and chlorogenic acid. Notably, CAD production in these hairy root cultures was comparable to levels found in the source plant [46]. Further research demonstrated that light exposure enhanced CAD biosynthesis in E. purpurea hairy roots, suggesting their potential as a model system for studying CAD biosynthetic pathways and as an efficient production method for these compounds [36]. Recent developments include the creation of transgenic echinacea plants using Agrobacterium-mediated transformation with modified expression vectors. For instance, one study replaced the β-glucuronidase (GUS) reporter gene with the Petunia chalcone synthase (CHS) gene, creating a model system for studying secondary metabolite accumulation in echinacea [52]. These advancements in genetic engineering techniques for echinacea highlight the potential for improving growth characteristics and enhancing beneficial compound production, making it a promising subject for further research in medicinal plant biotechnology [75].

4. Molecular Markers and Genomic Resources in Echinacea

The genetic research on echinacea is relatively new compared to other aspects such as its phytochemistry or therapeutic effects [91]. A survey of over 200 articles published between 1998 and 2002 reveals that only about 3% of the literature focuses on genetics, while most studies explore its medicinal properties. Despite the growing popularity of echinacea as a medicinal plant, limited genetic studies have been conducted, even though genetic research is crucial for understanding the molecular, biochemical, and environmental factors that control its beneficial traits [92,93].
The study of molecular markers in echinacea has provided invaluable insights into its genetic diversity, population structure, and evolutionary relationships [94]. Molecular markers are DNA sequences that reflect genetic variations within or between species, making them useful for identifying genetic traits, characterizing populations, and selecting breeding strategies. In echinacea, several types of markers have been utilized, including random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and microsatellites (simple sequence repeats, SSRs). These markers offer researchers the tools to investigate genetic diversity, structure, and lineage, aiding in conservation and breeding efforts [95]. Random amplified polymorphic DNA markers have been widely used to assess genetic diversity within echinacea species. Random amplified polymorphic DNA analysis is simple, cost-effective, and capable of detecting polymorphisms without prior knowledge of the genomic sequence. In E. purpurea, E. angustifolia, and E. pallida, RAPD markers have helped differentiate species and identify genetic variations between populations [96]. For instance, Previous research demonstrated the utility of RAPD markers in distinguishing commercial species and identifying genetic diversity among echinacea populations [97].
AFLP markers have proven valuable in genetic studies of echinacea. This technique has revealed significant diversity within commercial E. purpurea compared to wild species like E. angustifolia and E. pallida [90]. AFLP offers greater sensitivity than RAPD, enabling finer distinctions between individuals and populations. Its high-throughput nature suits large-scale studies, though it requires more specialized equipment and expertise. AFLP’s sensitivity stems from selective amplification of restriction fragments from genomic DNA. The process involves DNA digestion with two restriction enzymes, adapter ligation, and PCR amplification using primers with selective nucleotides [84]. This approach generates unique genetic fingerprints for each individual. The technique’s strength lies in its ability to screen multiple genomic regions simultaneously, detecting more polymorphic loci than other methods. AFLP can identify single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) affecting restriction sites or primer binding [63]. This comprehensive genomic sampling provides a detailed representation of genetic diversity in echinacea, making it particularly useful for distinguishing between commercial cultivars and wild populations [98].
Microsatellite markers (SSRs) are highly polymorphic, co-dominant markers that provide detailed information on genetic relationships [99]. Although they have not been as widely applied in echinacea studies as RAPD and AFLP, SSR markers offer the potential for precise population genetics analysis, especially for fine-scale diversity studies [100]. They are ideal for tracking allelic variations within breeding programs, which is crucial for improving echinacea cultivars. Previous research reported that in E. purpurea, SSR markers were successfully used to assess genetic diversity across different populations. The study highlighted that SSRs provided more detailed and reliable genetic fingerprinting compared to RAPD markers [101]. Furthermore, they found that SSRs were instrumental in identifying specific alleles linked to higher concentrations of medicinal compounds like alkamides and chichoric acid. This genetic information has been pivotal for breeding programs aimed at enhancing the phytochemical properties of E. purpurea [102]. Similarly, previous research noted that SSR markers were effective in tracking genetic variations among E. angustifolia populations. The markers helped identify distinct genetic clusters within the species, which were not detectable through phenotypic traits alone [103]. These findings have been essential for conservation efforts, ensuring that diverse genetic material is preserved in breeding and cultivation. Previous research applied SSR markers to analyze hybridization events between E. pallida and E. purpurea. Their research revealed complex hybridization patterns that were undetectable through traditional morphological methods [104]. Simple sequence repeats markers enabled the identification of introgression lines, which are hybrids with traits inherited from both parent species, providing valuable insights into the evolutionary history of echinacea [105].
Previous researchers conducted a study where SSR markers were used to differentiate between several commercial echinacea species. The study revealed that E. purpurea, E. angustifolia, and E. pallida exhibited distinct genetic signatures based on SSR data, which allowed for more accurate species identification in commercial preparations [106]. This was particularly significant because many herbal products labeled as echinacea often contain misidentified or mixed species, leading to variability in their medicinal efficacy [107]. By applying SSR markers, the researchers could ensure the genetic purity of cultivated echinacea plants, contributing to the standardization of herbal products sold in the market [108]. Previous research explored the genetic relationships between echinacea species using SSR markers to resolve taxonomic ambiguities [109]. The study found that SSR markers provided higher resolution in distinguishing closely related species and populations compared to traditional morphological classification [110]. This was especially useful in analyzing populations of E. Pallida and E. simulata, two species that are morphologically similar but genetically distinct [111]. SSR markers were able to confirm the species’ genetic separation, which has implications for both conservation and commercial cultivation, ensuring that pure strains of each species are preserved and utilized [95]. Previous research utilized SSR markers to investigate the genetic diversity of rare and widespread echinacea species. The results indicated that the rare E. tennesseensis exhibited lower genetic diversity compared to the more widespread E. angustifolia [93]. This study emphasized the importance of maintaining genetic diversity within small populations of rare echinacea species, as the reduced diversity could make them more susceptible to environmental changes and diseases [101]. SSR markers, by providing precise measures of allelic diversity, played a crucial role in identifying conservation priorities and developing strategies for preserving the genetic integrity of endangered echinacea species [97]. SSR markers exhibit high polymorphism due to DNA replication errors, particularly slippage, which affects the number of repeat units. These variations result in length differences detectable through PCR amplification. As co-dominant markers, SSRs provide a more comprehensive view of genetic diversity by identifying heterozygotes, surpassing dominant markers like RAPD or AFLP in accuracy. Their species-specific nature makes SSRs especially valuable for differentiating between closely related echinacea species and identifying hybrid plants. The frequent mutations in SSRs, along with their widespread presence across the genome, allow researchers to observe recent evolutionary changes and detailed population structures. This capability proves crucial in clarifying taxonomic uncertainties, evaluating the genetic authenticity of commercial echinacea products, and formulating conservation plans for endangered echinacea species. The unique attributes of SSR markers significantly enhance our understanding of echinacea genetics and support various practical applications in this field of study.
Furthermore, in a comprehensive study of genetic variation among wild and cultivated echinacea populations, previous research applied SSR markers to investigate the effects of cultivation on genetic diversity [94]. The study showed that cultivated populations of E. purpurea exhibited reduced genetic diversity compared to their wild counterparts. This reduction in genetic diversity was attributed to the selection pressures of cultivation, where specific traits such as high biomass and medicinal compound concentration were favored [95]. The use of SSR markers allowed for detailed tracking of these genetic changes, providing important insights for breeding programs that aim to maintain genetic diversity while selecting desirable traits [106]. Similarly, previous research used SSR markers to analyze the population structure of E. purpurea in Europe, where the species has been cultivated extensively. The study found significant genetic differentiation between European and North American populations, likely due to founder effects and genetic drift in the smaller European gene pool [99]. These findings highlight the role that SSR markers can play in monitoring the genetic integrity of echinacea populations that are geographically isolated from their native range, ensuring that breeding programs can incorporate diverse genetic material to avoid the negative effects of inbreeding [91]. Previous research utilized SSR markers to evaluate the genetic stability of echinacea hybrids in controlled breeding experiments. The researchers investigated hybrids between E. purpurea and E. angustifolia, assessing the inheritance of key traits such as flower color and medicinal compound content. SSR markers enabled the precise tracking of alleles inherited from each parent species, helping to identify hybrid lines with the best combination of desirable traits [110]. This work contributed to the development of new echinacea cultivars that combine the high yield and medicinal properties of E. purpurea with the stress tolerance of E. angustifolia [96].
In addition to breeding applications, SSR markers have also been used in conservation genetics to prioritize populations for protection. For example, previous research demonstrated how SSR markers can be applied to assess the genetic health of small populations [99]. The study revealed low levels of genetic variation within isolated populations of E. tennesseensis, underscoring the need for genetic monitoring and management to prevent further loss of diversity [100]. The application of SSR markers enabled conservationists to identify genetically distinct populations that should be prioritized for habitat protection and restoration efforts [94]. In a study focused on understanding the genetic basis of phytochemical production, previous research used SSR markers to correlate specific alleles with the concentration of medicinal compounds such as alkamides and caffeic acid derivatives in echinacea roots [103]. By linking SSR marker data with phytochemical analysis, the researchers identified genetic markers associated with high levels of bioactive compounds, providing a valuable tool for selecting echinacea plants with enhanced medicinal properties for commercial cultivation [111]. This integration of genetic and chemical data has significant implications for the herbal medicine industry, where consistency in medicinal compound levels is crucial for product efficacy [107].
Simple sequence repeats markers have proven to be a powerful tool in echinacea research, offering insights into genetic diversity, population structure, and the inheritance of key traits [95]. By providing high-resolution data on genetic variation, SSR markers have supported breeding programs, conservation efforts, and the standardization of commercial echinacea products [106]. As molecular techniques continue to advance, SSR markers, combined with next-generation sequencing technologies, will play an increasingly important role in unraveling the genetic complexities of echinacea and improving its use as a medicinal plant [110].

5. Advances in Echinacea Breeding Programs

Echinacea breeding programs focus on enhancing key traits like phytochemical production, resistance to diseases, and tolerance to environmental stresses [111]. While conventional breeding methods have contributed to developing high-yield varieties, contemporary approaches increasingly utilize molecular techniques, such as marker-assisted selection, to boost breeding efficiency [112]. The rising demand for consistent, high-quality echinacea products in the herbal medicine market has intensified efforts to refine breeding strategies [113]. These strategies aim to ensure reliable production of important bioactive compounds, including alkamides, caffeic acid derivatives, and polysaccharides, which are crucial for echinacea’s medicinal properties [114].
Several key studies have significantly advanced echinacea breeding programs. Early research using RAPD markers assessed genetic diversity among E. purpurea, E. angustifolia, and E. pallida, revealing substantial genetic variability both within and between these species [115]. This work provided crucial insights into genetic resources available for breeding programs, laying the foundation for strategies that balance genetic diversity with high-yield cultivar selection. Further research utilized amplified fragment length polymorphism (AFLP) markers to investigate hybridization between E. purpurea and E. angustifolia, contributing to our understanding of interspecific breeding potential in echinacea. These studies collectively have enhanced our ability to develop improved echinacea varieties for medicinal use [116]. The hybrids exhibited hybrid vigor, showing enhanced growth and yield compared to their parent species [117]. The use of AFLP markers allowed the researchers to track allelic inheritance from both parent species, offering valuable information for the selection of hybrid lines that combine the medicinal properties of E. purpurea with the stress tolerance of E. angustifolia [118]. This approach has been further refined in subsequent studies, demonstrating the potential of hybridization to produce superior echinacea cultivars [119].
Molecular marker-assisted selection (MAS) has emerged as a significant technological advancement in echinacea breeding. Research has shown the effectiveness of simple sequence repeat (SSR) markers in identifying genetic traits linked to increased production of alkamides and caffeic acid derivatives in E. purpurea. This approach has enhanced breeders’ ability to select plants with desirable medicinal properties more efficiently [120]. By using SSR markers, the researchers were able to screen large populations more efficiently and select individuals who possessed the genetic traits linked to elevated concentrations of these medicinal compounds [121]. This marked a significant shift in breeding practices, as it enabled breeders to focus on phytochemical content at the genetic level, making the breeding process more efficient and targeted [122]. Hybrid breeding has also played a central role in echinacea breeding programs, particularly in efforts to combine desirable traits from different species. Previous research reported the successful development of hybrid lines between E. pallida and E. angustifolia that exhibited greater resistance to fungal diseases like root rot [123]. This research demonstrated that hybrid breeding could be used to introduce disease resistance into susceptible echinacea species, thus reducing the need for chemical interventions in cultivation [124]. The development of disease-resistant cultivars is crucial for both organic and conventional farming practices, where minimizing the use of pesticides is a priority [125].
In recent years, advances in genomic technologies have further propelled echinacea breeding programs [126]. Next-generation sequencing (NGS) has allowed researchers to conduct more detailed genetic analyses, identifying quantitative trait loci (QTL) that are associated with complex traits such as drought tolerance and phytochemical biosynthesis. Previous research utilized NGS to explore the genetic basis of drought tolerance in E. purpurea, identifying several candidate genes that regulate water-use efficiency and stress response mechanisms [113]. These findings are being applied to develop new echinacea cultivars that can thrive in arid environments, thereby expanding the cultivation range of the plant and making it more resilient to climate change [115]. In addition to advances in molecular tools, traditional breeding techniques continue to play an important role in echinacea breeding programs [125]. For instance, the selection of plants based on phenotypic traits such as flower size, biomass, and root yield remain a key component of many breeding strategies [126]. However, the integration of molecular markers has greatly enhanced the efficiency of traditional breeding by allowing breeders to select traits that are not easily observable in the phenotype [127]. Previous research emphasized the importance of combining traditional and molecular breeding approaches, noting that while molecular markers are valuable for genetic analysis, phenotypic selection remains essential for ensuring that desired traits are expressed under field conditions [113].
The development of new echinacea cultivars is not without its challenges. One of the major obstacles in echinacea breeding is the high level of genetic variability within the species, which can complicate efforts to produce consistent and uniform plants [119]. Additionally, the long breeding cycle of perennial echinacea plants presents a challenge for breeders who seek to introduce new cultivars quickly [128]. To address these issues, researchers are exploring the use of tissue culture and other biotechnological methods to accelerate the breeding process and reduce generation times [115]. As genomic resources for echinacea continue to expand, there is potential for even more rapid advancements in breeding programs, particularly through the application of genome editing technologies like CRISPR-Cas9 [115].
Echinacea breeding programs have advanced considerably in recent years, benefiting from progress in molecular genetics, hybrid breeding, and genomic technologies. Research using various molecular markers has enhanced our understanding of genetic diversity and trait inheritance in echinacea species, leading to more focused and efficient breeding efforts [115]. Hybridization has proven effective in combining medicinal properties and stress tolerance from different species. Additionally, next-generation sequencing has opened new possibilities for investigating the genetic foundations of complex traits like drought tolerance and phytochemical production [120]. As these breeding programs continue to develop, they will be instrumental in ensuring a steady supply of high-quality echinacea cultivars to meet the increasing global demand for medicinal plants [129].

6. Advances in Gene-Editing and Genomic Tools in Echinacea

The application of biotechnology in echinacea genetics has opened new frontiers for improving this valuable medicinal plant [129]. Recent advancements in gene-editing technologies, such as CRISPR-Cas9, along with other molecular techniques, have enabled precise manipulation of the echinacea genome, facilitating targeted improvements in phytochemical production, disease resistance, and environmental stress tolerance [130]. These technologies offer exciting possibilities for enhancing the medicinal properties of echinacea while reducing reliance on traditional, time-consuming breeding methods. CRISPR and associated Cas9 proteins have revolutionized plant genetics by providing a precise, efficient, and cost-effective tool for genome editing. CRISPR allows for targeted modifications of specific genes involved in key biological pathways, making it possible to enhance traits such as the biosynthesis of bioactive compounds. For instance, CRISPR could be applied to upregulate genes involved in the production of important phytochemicals like alkamides and caffeic acid derivatives, thereby increasing the medicinal potency of echinacea extracts [131]. While specific applications of CRISPR in echinacea are still in their infancy, the potential for this technology in plant improvement is immense, as evidenced by its successful use in other medicinal plants like Artemisia and Cannabis [132].
Gene-editing technologies also enable the downregulation or removal of undesirable traits. In echinacea, this could involve knocking out genes associated with susceptibility to pathogens or stressors. This approach has already been demonstrated in other medicinal crops, where targeted mutations have led to improved stress tolerance and resistance to both biotic and abiotic factors [133,134]. In addition to CRISPR, other gene-editing technologies, such as TALENs (transcription activator-like effector nucleases) and ZFNs (zinc finger n), have also been applied in plant genomics, offering complementary tools for modifying echinacea genetics. These methods provide alternative approaches for targeted gene modification, especially in cases where CRISPR is less efficient [135]. For example, TALENs have been used to enhance the production of secondary metabolites in various medicinal plants, and similar applications could be envisioned for echinacea, particularly in optimizing the pathways responsible for the biosynthesis of bioactive compounds like echinacoside and chicoric acid [136]. Another biotechnological approach that holds promise for echinacea improvement is RNA interference (RNAi). RNAi technology allows for the silencing of specific genes, thereby enabling researchers to study gene function and control the expression of undesirable traits. In the case of echinacea, RNAi could be employed to downregulate genes involved in negative stress responses or to control pathways that inhibit the synthesis of medicinal compounds [137]. This technique has already been used in various medicinal plants to enhance desirable traits, such as increased alkaloid production in Papaver [129].
Advancements in biotechnological tools are also being used in tandem with traditional breeding methods. Marker-assisted selection, for instance, continues to play a critical role in improving echinacea cultivars [135]. Recent advancements in molecular biology are reshaping echinacea breeding strategies. Researchers are now exploring the potential of combining molecular markers for specific traits with gene-editing technologies to develop enhanced cultivars. Genome-wide association studies (GWASs) and quantitative trait loci (QTL) mapping are being employed to identify crucial genetic regions for targeted improvements, offering deeper insights into echinacea’s genetic architecture and enabling more effective breeding approaches [136]. In the field of synthetic biology, plant transformation systems and metabolic engineering are gaining prominence in echinacea research. Metabolic engineering focuses on modifying biosynthetic pathways to boost the production of specific compounds [132]. For echinacea, this could involve increasing the yield of therapeutically valuable secondary metabolites, such as phenolic compounds and alkamides. These innovative approaches hold promise for developing echinacea varieties with enhanced medicinal properties and improved agronomic traits [137]. Synthetic biology techniques are already being applied in medicinal plants like Taxus and Catharanthus, and similar methodologies could be adapted to optimize echinacea’s metabolic pathways [133].
Tissue culture techniques, including somatic embryogenesis and micropropagation, have also seen advancements in echinacea biotechnology [132]. These methods provide an efficient way to propagate genetically modified plants and ensure the uniformity of desirable traits [137]. Tissue culture has been widely used to propagate elite echinacea plants with enhanced phytochemical content, ensuring that the high-quality traits selected through gene editing or MAS are retained in large-scale cultivation [129]. Furthermore, tissue culture is critical for producing transgenic plants, as it facilitates the integration of foreign DNA into the echinacea genome, a process that is essential for the application of CRISPR and other gene-editing tools [138]. While these biotechnological applications hold significant promise, challenges remain in the commercialization and public acceptance of genetically modified echinacea plants [139]. Regulatory hurdles, especially concerning CRISPR-edited crops, must be addressed to ensure that these advancements can be translated into real-world applications [136]. Nevertheless, the future of echinacea improvement lies in the integration of these advanced biotechnological tools, which will enable the development of high-quality cultivars with enhanced medicinal properties, stress tolerance, and disease resistance [139].
The advancements in biotechnological tools, such as CRISPR-Cas9, TALEN, RNAi, and synthetic biology, represent a transformative shift in echinacea breeding and genetic improvement [140]. These technologies offer precise and efficient methods for enhancing traits that are vital for the plant’s medicinal efficacy and cultivation resilience. As gene-editing techniques continue to evolve, echinacea stands to benefit from targeted improvements in phytochemical biosynthesis, disease resistance, and environmental stress tolerance. The integration of these tools into breeding programs will shape the future of echinacea as both a medicinal crop and a model for plant biotechnology.

7. Conclusions and Future Perspective on Echinacea Research

Over the last few decades, echinacea has emerged as one of the most studied and widely utilized medicinal plants. The diverse therapeutic applications of echinacea species, particularly in the fields of immunomodulation, anti-inflammatory, and antimicrobial treatments, highlight its significance in modern herbal medicine [141,142]. Research has made substantial progress in understanding the plant’s phytochemistry, with key bioactive compounds such as alkamides, phenolic acids, and polysaccharides being identified [143]. These compounds, working in synergy, contribute to echinacea’s health benefits, although there remain challenges in standardizing their content in commercial products. The variability in bioactive compounds due to genetic, environmental, and agronomic factors has complicated efforts to ensure consistent efficacy in echinacea-based therapies [144].
Looking ahead, there are several promising avenues for future research and development in echinacea cultivation, phytochemistry, and therapeutic applications. The advent of genomic resources, including molecular markers and next-generation sequencing (NGS) technologies, offers exciting possibilities for enhancing echinacea breeding programs [145]. Modern breeding techniques are enhancing echinacea cultivation. Marker-assisted selection (MAS) and genome-wide association studies (GWASs) help identify genetic markers associated with desirable traits such as increased phytochemical production and improved stress tolerance. These advanced methods allow breeders to develop enhanced echinacea varieties more efficiently, potentially leading to cultivars with superior medicinal properties and resilience to environmental challenges [146]. Techniques like CRISPR/Cas9 and RNA interference (RNAi) hold the potential to modify key genes that govern the biosynthesis of medicinal compounds, enhancing the plant’s therapeutic properties [147].
Echinacea cultivation can be improved using advanced agricultural techniques like controlled salinity, organic farming, and precision agriculture, all of which support the production of bioactive compounds. Additionally, gaining insights into how biotic and abiotic factors—such as drought conditions and microbial interactions—affect the plant’s phytochemical profile can further enhance its medicinal properties, particularly in large-scale cultivation systems. One of the significant challenges in echinacea production remains the inconsistency in bioactive compound levels across different products. As more sophisticated analytical tools become available, standardization efforts can ensure that commercial echinacea preparations deliver consistent levels of alkamides, phenolic acids, and other key compounds [148]. This is essential for ensuring the reproducibility of therapeutic effects and for building consumer trust in herbal products.
Biotechnological innovations, such as tissue culture and metabolic engineering, offer new pathways for optimizing echinacea cultivation. These methods not only improve the consistency of phytochemical production but also enable the mass propagation of genetically superior plants. Transgenic approaches, while still in the early stages, could be leveraged to enhance the medicinal efficacy of echinacea while minimizing susceptibility to environmental stressors and diseases. As the global demand for herbal medicines grows, echinacea is poised to play an even greater role in the healthcare landscape. Future research should focus on elucidating the mechanisms of action of echinacea bioactive compounds and conducting large-scale clinical trials to validate its efficacy in treating specific conditions [149]. Additionally, exploring new applications of echinacea in fields such as oncology and neuroprotection could expand its therapeutic repertoire. In conclusion, echinacea continues to be a valuable medicinal plant, with a wealth of untapped potential. The integration of modern biotechnological tools and advanced breeding programs offers a path toward enhancing its medicinal properties and ensuring its consistent use in herbal medicine. By addressing the current challenges in cultivation, standardization, and product efficacy, echinacea can cement its role as a cornerstone of natural health therapies in the future [149].

Funding

This research received no external funding or grants.

Data Availability Statement

Data are available upon request.

Conflicts of Interest

The author declares no conflicts of interest.

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Figure 1. (A) Echinacea species and (B) representative phytochemicals (alkamides and phenylpropanoids) are present in echinacea species (figure drawn by F. Ahmadi).
Figure 1. (A) Echinacea species and (B) representative phytochemicals (alkamides and phenylpropanoids) are present in echinacea species (figure drawn by F. Ahmadi).
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Figure 2. Essential oil compounds in echinacea species (figure drawn by F. Ahmadi).
Figure 2. Essential oil compounds in echinacea species (figure drawn by F. Ahmadi).
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Table 1. Most abundant alkamides in the root of echinacea species [29].
Table 1. Most abundant alkamides in the root of echinacea species [29].
Alkamide CompoundsMolecular Weight (g/mol)Echinacea Species
Undeca-2E,4Z-diene-8,10-diynoic acid isobutylamide229.32E. purpurea, E. angustifolia
Undeca-2Z,4E-diene-8,10-diynoic acid isobutylamide229.32E. purpurea
Undeca-2E-ene-8,10-diynoic acid isobutylamide231.34E. purpurea
Undeca-2E,4Z-diene-8,10-diynoic acid 2-methylbutylamide243.35E. purpurea
Undeca-2Z,4E-diene-8,10-diynoic acid 2-methylbutylamide243.35E. purpurea
Dodeca-2Z,4E-diene-8,10-diynoic acid isobutylamide243.35E. purpurea
Dodeca-2E,4Z-diene-8,10-diynoic acid isobutylamide243.35E. purpurea
Dodeca-2E,4E-diene-8,10-diynoic acid isobutylamide245.37E. purpurea
Dodeca-2E,4Z,10E-triene-8-ynoic acid isobutylamide245.37E. purpurea
Dodeca-2E-ene-8,10-diynoic acid isobutylamide245.37E. angustifolia
Dodeca-2E,4E,8Z,10E-tetraenoic acid isobutylamide247.38E. angustifolia
Dodeca-2E,4E,8Z,10Z-tetraenoic acid isobutylamide247.38E. purpurea
Dodeca-2E,4E,8E,10Z-tetraenoic acid isobutylamide249.40E. purpurea
Dodeca-2E,4E-dienoic acid isobutylamide251.41E. purpurea
Trideca-2E,7Z-diene-8,10-diynoic acid isobutylamide257.38E. purpurea
Dodeca-2E,4Z-diene-8,10-diynoic acid 2-methylbutylamide257.38E. purpurea
Dodeca-2,4,8,10-tetraenoic acid 2-methylbutylamide261.41E. purpurea
Table 2. Distribution of caffeic acid contents in flowers, leaves, and rhizomes of E. pallida [30].
Table 2. Distribution of caffeic acid contents in flowers, leaves, and rhizomes of E. pallida [30].
Caffeic Acid ConjugatesFlowerLeafRhizome a
Chlorogenic acid (5-O-caffeoylquinic acid)++++++
3,5-O-Dicaffeoylquinic acid++++
4,5-O-Dicaffeoylquinic acid++++
Chicoric acid (2,3-O-dicaffeoyltartaric acid)+++++++++
2-O-Caffeoyl-3-O-feruloyltartaric acid?++?
Caftaric acid (2-O-caffeoyltartaric acid)++++++
2-O-Caffeoyl-3-O-5-[a-carboxy-b-(3,4-dihydroxyphenyl)ethyl]caffeoyltartaric acid-++-
2,3-O-Di-5-[a-carboxy-b-(3,4-dihydroxyphenyl)ethyl]caffeoyltartaric acid-++-
b-(3,4-Dihydroxyphenyl)-ethyl-O-4-O-caffeoyl-b-D-glucopyranoside(desrhamnosylverbascoside)++++
b-(3,4-Dihydroxyphenyl)ethyl-O-a-L-rhamnopyranosyl(1Æ3)-4-O-caffeoyl-b-Dglucopyranoside (verbascoside)++++
b-(3,4-Dihydroxyphenyl)ethyl-O-a-L-rhamnopyranosyl(1Æ3)-b-Dglucopyranoside(1Æ6)-4-O-caffeoyl-b-D-glucopyranoside (echinacoside)++++++
b-(3,4-Dihydroxyphenyl)ethyl-O-a-L-rhamnopyranosyl(1Æ3)(6-O-caffeoyl-b-Dglucopyranosyl(1Æ6)-4-O-caffeoyl-b-D-glucopyranoside (6-Ocaffeoylechinacoside)--++
a Referred to as roots in the source; ? means not reported; + means the presence of the compound; - means without the compound. One, two, and three positive signs mean less, moderate, and high concentrations, respectively.
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Ahmadi, F. Genomic Innovations and Marker-Assisted Breeding in Echinacea Species: Insights and Applications. Sci 2025, 7, 43. https://doi.org/10.3390/sci7020043

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Ahmadi F. Genomic Innovations and Marker-Assisted Breeding in Echinacea Species: Insights and Applications. Sci. 2025; 7(2):43. https://doi.org/10.3390/sci7020043

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Ahmadi, Fatemeh. 2025. "Genomic Innovations and Marker-Assisted Breeding in Echinacea Species: Insights and Applications" Sci 7, no. 2: 43. https://doi.org/10.3390/sci7020043

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Ahmadi, F. (2025). Genomic Innovations and Marker-Assisted Breeding in Echinacea Species: Insights and Applications. Sci, 7(2), 43. https://doi.org/10.3390/sci7020043

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