1 Introduction

Pine species, such as limber pine (Pinus flexilis) and sugar pine (Pinus lambertiana), are keystone species in their respective ecosystems, playing crucial roles in maintaining ecological balance and biodiversity. However, these species face significant threats from various pathogens, including the non-native white pine blister rust (Cronartium ribicola) and fusiform rust disease (Wilcox et al., 1996; Liu et al., 2019). The introduction of these pathogens has led to high infection rates and mortality, severely impacting pine populations and forest health (Liu et al., 2019; Wright et al., 2022). Understanding and enhancing disease resistance in pines is therefore of paramount importance for forest conservation and management.

Despite advances in genetic mapping and molecular biology, managing disease resistance in pines remains challenging. Traditional genetic analysis has often failed to identify discrete resistance factors, leading to the assumption that effective long-term resistance is polygenic. However, recent studies have shown that single dominant genes can confer significant resistance, challenging previous assumptions (Wilcox et al., 1996). Additionally, the complexity of forest pathosystems and the long generation times of trees complicate breeding programs and the development of resistant strains (Sun et al., 2023). The identification of quantitative trait loci (QTL) and the integration of genomic tools have provided new insights, but the practical application of these findings in breeding programs is still in its early stages (Sniezko et al., 2014; Weiss et al., 2020).

This study aims to provide a comprehensive overview of the current state of research on disease resistance in pines, focusing on the genetic and molecular mechanisms underlying resistance to major pathogens such as white pine blister rust and fusiform rust. By synthesizing findings from recent studies, this study will highlight the progress made in identifying resistance genes and the potential for genomic tools to enhance breeding programs. The expectation is to offer insights into the practical applications of these findings in forest management and conservation, ultimately contributing to the development of more resilient pine populations.

2 Molecular Mechanisms of Disease Resistance in Pines

2.1 Pathogen recognition and signal transduction pathways

Pathogen recognition in pines involves a complex interplay of molecular mechanisms that enable the plant to detect and respond to pathogenic threats. Pines utilize pattern recognition receptors (PRRs) to identify pathogen-associated molecular patterns (PAMPs), which are conserved microbial signatures. Upon recognition, these PRRs initiate a cascade of signal transduction pathways that activate defense responses. For instance, the study on limber pine (Pinus flexilis) identified numerous receptor-like protein kinase genes (RLKs) that play a crucial role in pathogen recognition and subsequent signal transduction (Liu et al., 2019). These RLKs are essential for the activation of downstream defense mechanisms, highlighting their importance in the early stages of pathogen detection.

2.2 Role of disease resistance (R) genes in pines

Disease resistance (R) genes are pivotal in the defense against pathogens in pines. These genes encode proteins that can recognize specific pathogen effectors and trigger robust immune responses. The genetic mapping of limber pine revealed the presence of numerous nucleotide-binding site leucine-rich repeat (NBS-LRR) genes, which are a major class of R genes involved in pathogen recognition and resistance (Liu et al., 2019). Additionally, the PmPR10-3.1 gene in western white pine (Pinus monticola) has been identified as a significant contributor to quantitative disease resistance (QDR) against white pine blister rust, demonstrating the critical role of R genes in conferring resistance to specific pathogens (Liu et al., 2021).

2.3 Defense mechanisms activated by R genes

Upon activation by R genes, pines deploy a variety of defense mechanisms to combat pathogen invasion. These mechanisms include the production of pathogenesis-related (PR) proteins, which have antimicrobial properties. For example, the PmPR10-3.1 gene in western white pine encodes a PR10 protein that exhibits inhibitory effects on the growth of fungal pathogens, thereby contributing to the plant's defense (Figure 1) (Liu et al., 2021). Furthermore, the disruption of susceptibility (S) genes using genome editing tools like CRISPR/Cas9 has been shown to enhance disease resistance by interfering with pathogen compatibility, providing a transgene-free approach to developing durable disease-resistant pine varieties (Zaidi et al., 2018). These defense responses are crucial for maintaining the health and survival of pine species in the face of pathogenic threats.

Figure 1 Micrographs showing the effects of PmPR10-3.1 on spore germination of fungal pathogens (Adopted from Liu et al., 2021) Image caption: Conidiospores of Phoma exigua (isolate PFC 2705) were treated by pure PmPR10-3.1 protein for 18 h and photographs were taken at 63× magnification DIC. (a) Desalt buffer control; (b) 10 μg/mL PR10-3.1; (c) 42 μg/mL PR10; (d) 75 μg/mL PR10; (e) 100 μg/mL PR10-3.1. Urediniospores of Cronartium ribicola were treated with pure PmPR10-3.1 protein for 24 h and photographs were taken at 200× using Nimarsky filter: (f) desalt buffer control; (g) 100 μg/mL PR10-3.1. Bars in insets represent 100 μm. Arrows indicate reduced hyphal growth and swelling at hyphal tips due to PmPR10-3.1 (Adopted from Liu et al., 2021)

Liu et al. (2021) illustrates the impact of PmPR10-3.1 protein on spore germination of fungal pathogens, specifically Phoma exigua and Cronartium ribicola. Micrographs (a) through (e) show conidiospores of P. exigua treated with varying concentrations of PmPR10-3.1 for 18 hours, displaying inhibited hyphal growth and swelling at hyphal tips, especially at higher concentrations (b to e). Similarly, images (f) and (g) depict urediniospores of C. ribicola treated for 24 hours, with the treated spores (g) showing reduced hyphal growth compared to the control (f). These observations highlight PmPR10-3.1's potential as an antifungal agent, effectively hampering fungal development and providing a promising avenue for enhancing plant disease resistance.

3 Genome Editing Technologies for Pine Disease Resistance

3.1 CRISPR/Cas9 system

3.1.1 Principles and mechanisms

The CRISPR/Cas9 system, derived from the adaptive immune system of bacteria, has revolutionized genome editing due to its simplicity, efficiency, and precision. The system uses a guide RNA (gRNA) to direct the Cas9 nuclease to a specific DNA sequence, where it creates a double-strand break. This break can then be repaired by the cell's natural repair mechanisms, leading to targeted modifications such as insertions, deletions, or substitutions (Manghwar et al., 2019; Rodriguez-Rodriguez et al., 2019; Sharma et al., 2020). The CRISPR/Cas9 system's ability to make precise edits has made it a powerful tool for genetic research and therapeutic applications (El-Mounadi et al., 2020; Li et al., 2021).

3.1.2 Applications in plant genomics

CRISPR/Cas9 has been widely adopted in plant genomics for its ability to introduce precise genetic modifications. It has been used to enhance disease resistance in various crops by targeting and modifying susceptibility genes. For instance, CRISPR/Cas9 has been employed to develop resistance against viral, fungal, and bacterial diseases in model plants and crops such as rice, tomato, wheat, and citrus (Borrelli et al., 2018; Charlesworth et al., 2018; Ahmad et al., 2020). The technology's versatility and efficiency make it an ideal tool for improving disease resistance in pine trees, potentially leading to more resilient forestry practices.

3.2 Other genome editing tools (TALENs, ZFNs)

In addition to CRISPR/Cas9, other genome editing tools such as Transcription Activator-Like Effector Nucleases (TALENs) and Zinc Finger Nucleases (ZFNs) have been used for precise genetic modifications. TALENs and ZFNs function by creating double-strand breaks at specific DNA sequences, similar to CRISPR/Cas9, but they use different mechanisms for DNA recognition and binding. TALENs use customizable DNA-binding domains derived from transcription activator-like effectors, while ZFNs use zinc finger domains to recognize specific DNA sequences (Borrelli et al., 2018; Charlesworth et al., 2018). Although these tools have been effective in various applications, CRISPR/Cas9 has largely overtaken them due to its ease of design, higher success rate, and lower cost (Charlesworth et al., 2018; Manghwar et al., 2019).

3.3 Delivery methods for genome editing in pines

Effective delivery of genome editing components into pine cells is crucial for successful genetic modifications. Various delivery methods have been explored, including Agrobacterium-mediated transformation, biolistic particle delivery (gene gun), and protoplast transfection. Agrobacterium-mediated transformation is commonly used for its efficiency in delivering DNA into plant cells, although it is more challenging in gymnosperms like pines. Biolistic particle delivery involves shooting DNA-coated particles into plant tissues, which can be effective for species that are recalcitrant to Agrobacterium transformation. Protoplast transfection, which involves the introduction of DNA into isolated plant cells without cell walls, offers another alternative but requires efficient regeneration protocols to produce whole plants from edited cells (Charlesworth et al., 2018; Ahmad et al., 2020; Li et al., 2021). Each method has its advantages and limitations, and the choice of delivery method may depend on the specific requirements of the pine species and the desired genetic modification.

4 Identification and Characterization of Disease Resistance Genes

4.1 Techniques for gene discovery

The discovery of disease resistance genes (R genes) in plants has evolved significantly over the past few decades. Traditional biochemical methods, such as cloning and mutagenesis, have been foundational in identifying these genes. However, with the advent of next-generation sequencing (NGS) and bioinformatics, the landscape of gene discovery has expanded dramatically. NGS allows for the rapid sequencing of entire genomes, facilitating the identification of R genes through comparative genomics and transcriptomics (Hadjadj et al., 2019). Bioinformatic tools have become indispensable, enabling researchers to predict R genes by analyzing sequence data for characteristic domains such as nucleotide-binding sites (NBS) and leucine-rich repeats (LRR) (Figure 2) (Fernandez-Gutierrez and Gutierrez-Gonzalez, 2021). These methods are complemented by functional genomics approaches, which involve the use of transposon mutagenesis and metagenomics to uncover new resistance mechanisms (Hadjadj et al., 2019).

Figure 2 Overview of protocols for NLR discovering pipelines (Adopted from Fernandez-Gutierrez and Gutierrez-Gonzalez, 2021) Image caption: Equal and differential steps are lined up to highlight the similarities/differences. WT: wild type. NGS: next generation sequencing. SNV: single nucleotide variant. A figure legend is on the upper right corner (Adopted from Fernandez-Gutierrez and Gutierrez-Gonzalez, 2021)

4.2 Functional genomics approaches

Functional genomics plays a crucial role in understanding the mechanisms by which R genes confer disease resistance. This field employs various techniques to elucidate gene function, including gene knockout and overexpression studies, RNA interference (RNAi), and CRISPR-Cas9 mediated gene editing. These approaches allow researchers to observe the phenotypic effects of specific gene modifications, thereby linking gene sequences to their functional roles in disease resistance (Hadjadj et al., 2019). Additionally, functional genomics can involve the use of transcriptomic and proteomic analyses to study gene expression patterns and protein interactions under pathogen attack, providing insights into the dynamic responses of plants to infections (Fernandez-Gutierrez and Gutierrez-Gonzalez, 2021).

4.3 Case studies of identified R genes in pines

Several R genes have been identified and characterized in pine species, providing valuable insights into their mechanisms of action. For instance, the meta-analysis of 314 cloned R genes has revealed that the majority encode cell surface or intracellular receptors, which can detect pathogen-derived molecules either directly or indirectly (Kourelis and Hoorn, 2018). These receptors often belong to the NBS-LRR family, which is the largest group of plant resistance genes and is crucial for initiating immune responses. Specific case studies in pines have demonstrated the effectiveness of pyramiding multiple R genes to enhance resistance durability, thereby reducing the need for chemical pesticides and promoting sustainable forestry practices (Fernandez-Gutierrez and Gutierrez-Gonzalez, 2021). The identification of these genes and their functional validation through various genomic and bioinformatic approaches underscores the potential for rational engineering of disease-resistant pine varieties.

Fernandez-Gutierrez and Gutierrez-Gonzalez (2021) presents an overview of four protocols--RenSeq, MutRenSeq, MutChromSeq, and AgRenSeq--for discovering nucleotide-binding leucine-rich repeat (NLR) genes. Each pipeline starts with different inputs: wild-type plants, mutagenesis, and a diversity panel. All protocols involve DNA fragmentation, hybridization with biotinylated oligonucleotide baits, and enrichment of target sequences, followed by next-generation sequencing (NGS). RenSeq directly identifies NLRs from wild-type samples. MutRenSeq and MutChromSeq include mutagenesis steps and focus on mapping to wild-type assemblies for single nucleotide variant (SNV) identification. AgRenSeq uses a diversity panel and k-mer filtering to associate genetic variations with phenotypes. These protocols, with their similarities and differences, offer robust methods for NLR gene discovery, each tailored for specific research needs in plant genetics and disease resistance studies.

5 Strategies for Precise Gene Editing

5.1 Targeted mutagenesis

Targeted mutagenesis is a powerful strategy for precise gene editing, primarily utilizing the CRISPR/Cas9 system. This method involves creating specific mutations at targeted genomic loci to disrupt gene function, which can confer disease resistance in plants. For instance, the CRISPR/Cas9 system was employed to knockout the Os8N3 gene in rice, resulting in enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo). The mutations were stably transmitted across generations, and the edited plants displayed no significant differences in agronomic traits compared to non-transgenic controls (Kim et al., 2019). Similarly, CRISPR/Cas9-mediated mutagenesis of the VvMLO3 gene in grapevine led to enhanced resistance to powdery mildew, demonstrating the effectiveness of this approach in improving disease resistance in economically important crops (Wan et al., 2020).

5.2 Homology-directed repair (HDR)

Homology-Directed Repair (HDR) is another precise gene editing strategy that leverages the cell's natural repair mechanisms. When a double-strand break (DSB) is introduced at a specific genomic location, a donor template with homologous sequences can be provided to guide the repair process, allowing for precise insertion, deletion, or replacement of DNA sequences. This method is particularly useful for introducing specific genetic changes or correcting mutations. Although HDR is less efficient than non-homologous end joining (NHEJ), advancements in CRISPR/Cas9 technology and the development of novel donor templates are improving its efficiency and applicability in plant genome editing.

5.3 Base editing and prime editing

Base editing and prime editing are innovative gene editing techniques that enable precise nucleotide changes without introducing DSBs. Base editing uses engineered deaminases to convert specific DNA bases, such as cytosine to thymine or adenine to guanine, directly at the target site. This method has been successfully applied to create point mutations that confer disease resistance in plants. Prime editing, on the other hand, uses a reverse transcriptase enzyme fused to a modified Cas9 protein to introduce small insertions, deletions, or base substitutions guided by a prime editing guide RNA (pegRNA). These techniques offer higher precision and reduced off-target effects compared to traditional CRISPR/Cas9 methods, making them promising tools for functional genomics and crop improvement.

6 Functional Verification of Edited Genes

6.1 In vitro assays

In vitro assays are crucial for the initial functional verification of edited genes. These assays allow researchers to observe the direct effects of gene edits in a controlled environment. For instance, the PmPR10-3.1 gene from Pinus monticola was expressed in Escherichia coli, and the purified recombinant protein exhibited inhibitory effects on the spore hyphal growth of fungal pathogens such as Cronartium ribicola, Phoma exigua, and P. argillacea. This demonstrates the potential of the edited gene in conferring disease resistance. Additionally, in vitro assays can help identify the physiological roles of pathogenesis-related (PR) proteins, which are essential in plant defense responses (Liu et al., 2021).

6.2 Transgenic pine models

Creating transgenic pine models is a critical step in verifying the functionality of edited genes in a living organism. These models help in understanding how the edited genes perform in the complex biological systems of pine trees. For example, the use of genome editing tools like CRISPR has enabled the development of transgene-free, disease-resistant crop varieties by targeting susceptibility (S) genes (Zaidi et al., 2018). In the context of pine trees, transgenic models can be used to study the expression and impact of edited genes such as PmPR10-3.1 in response to pathogen infection, providing insights into their role in quantitative disease resistance (Weiss et al., 2020; Liu et al., 2021).

6.3 Field trials and environmental assessments

Field trials and environmental assessments are essential for evaluating the real-world applicability and effectiveness of edited genes. These trials help in understanding how the edited genes perform under natural environmental conditions and in the presence of various biotic and abiotic stressors. For instance, the genomic architecture of quantitative disease resistance in white pine species has been studied to facilitate marker-assisted disease resistance breeding (Weiss et al., 2020). Field trials can validate the effectiveness of edited genes like PmPR10-3.1 in providing resistance to diseases such as white pine blister rust, thereby confirming their potential for practical applications in forestry and agriculture (Liu et al., 2019; Weiss et al., 2020; Liu et al., 2021).

7 Case Studies and Success Stories

7.1 Successful gene edits conferring disease resistance

Recent advancements in gene editing have demonstrated significant success in conferring disease resistance in pine species. One notable example is the use of the CRISPR/Cas9 system, which has been applied extensively in tree genetic studies to develop new disease-resistant cultivars. This system has shown great potential in regulating lignin biosynthesis and shortening the breeding cycle of forest trees, thereby enhancing their resistance to various diseases (Chen and Lu, 2020).

Another successful application of gene editing is the identification and functional characterization of the PmPR10-3.1 gene in western white pine (Pinus monticola). This gene was found to play a crucial role in quantitative disease resistance (QDR) to white pine blister rust. The purified recombinant protein of PmPR10-3.1 exhibited inhibitory effects on the growth of fungal pathogens, providing valuable insights into the genetic architecture underlying QDR in conifers (Liu et al., 2021).

Prime editing, a novel genome editing technology, has also shown promise in correcting genetic defects and conferring disease resistance. For instance, prime editing has been used to generate precise in-frame deletions in the CTNNB1 gene, mimicking mechanisms of disease development and functionally recovering disease-causing mutations in organoid models. This technology offers greater precision than traditional methods and holds therapeutic potential for various plant diseases (Schene et al., 2020).

7.2 Comparative analysis of edited vs. non-edited pines

Comparative studies between edited and non-edited pines have provided compelling evidence of the benefits of gene editing in enhancing disease resistance. For example, a study on sugar pine (Pinus lambertiana) revealed that single nucleotide polymorphisms (SNPs) associated with the Cr1R gene, a major gene for resistance to white pine blister rust, exhibited a strong association with disease resistance. This association was validated through PCR-based genotyping, demonstrating the potential of SNP markers in identifying resistant individuals and expediting forest restoration efforts (Table 1) (Wright et al., 2022).

Table 1 Fit of observed (O) diploid genotype frequencies to expected (E) Hardy–Weinberg proportions in a random sample of putatively susceptible, Cr1r trees and in a selected sample of resistant, Cr1R treesa (Adopted from Wright et al., 2022) Note: NS, not significant (P < 0.45); *P < 9.5 × 10–9; A haplotype (restriction sites 1, 2, and 6): 81 and 359 bp; B haplotype (1, 2, and 6 plus 3 and 4): 81 30 86 and 243 bp; and C haplotype (1, 2, and 6 plus 5): 81 187 and 172 bp

Wright et al. (2022) compares observed (O) and expected (E) diploid genotype frequencies under Hardy-Weinberg equilibrium in a random sample of putatively susceptible Cr1^r trees and a selected sample of resistant Cr1^R trees. In the random sample, the observed frequencies closely match the expected ones, indicating no significant deviation from Hardy-Weinberg proportions (P < 0.45). However, in the selected sample of resistant trees, significant deviations are observed (P < 9.5 × 10^–9), particularly with the A/C and B/C genotypes showing substantial differences between observed and expected frequencies. This suggests strong selection pressure for resistance traits. The haplotypes are defined by restriction sites, highlighting genetic variations influencing disease resistance. This research underscores the importance of specific haplotypes in breeding programs aimed at enhancing disease resistance in Cr1^R trees.

In another study, the genomic architecture of quantitative disease resistance in sugar pine was investigated using quantitative trait loci mapping and genome-wide association studies. The study identified 453 SNPs involved in various biological functions, including disease resistance. These findings suggest that newly reported genes may have partial resistance or epistatic effects on qualitative disease resistance genes, providing a deeper understanding of the complex genomic architecture of disease resistance in long-generation trees (Weiss et al., 2020).

Furthermore, the application of the CRISPR/Cas9 system in developing disease-resistant cultivars has been systematically reviewed, highlighting its versatility and effectiveness in editing genes and noncoding sequences. This study underscores the potential of CRISPR/Cas9 in promoting tolerance to multiple abiotic and biotic stresses, thereby improving the overall health and resilience of pine species (Nascimento et al., 2023).

8 Challenges and Future Perspectives

8.1 Technical challenges in pine genome editing

Genome editing in pine species presents several technical challenges. One significant issue is the complexity of the pine genome, which is large and highly repetitive, making precise editing difficult (Liu et al., 2019). Additionally, the long generation time of pine trees complicates the process of validating edits and observing phenotypic changes (Weiss et al., 2020). The efficiency of current genome editing tools, such as CRISPR/Cas9, is also a concern, as these tools need to be optimized for the unique characteristics of pine genomes (Mushtaq et al., 2019). Furthermore, the delivery of genome editing components into pine cells is challenging due to the thick cell walls and the recalcitrant nature of pine tissues to transformation (Mishra et al., 2021).

8.2 Regulatory and ethical considerations

The application of genome editing in pine species raises several regulatory and ethical issues. Regulatory frameworks for genetically modified organisms (GMOs) vary widely across different countries, and the classification of genome-edited plants under these regulations is still a matter of debate (Yin and Qiu, 2019; Mushtaq et al., 2019). There is also public concern about the environmental impact of releasing genetically edited trees into the wild, particularly regarding gene flow to wild relatives and potential effects on biodiversity (Proudfoot et al., 2019). Ethical considerations include the long-term ecological consequences and the potential for unintended off-target effects, which necessitate thorough risk assessments and transparent communication with the public (Mushtaq et al., 2019; Schene et al., 2020).

8.3 Future directions for research

Future research in pine genome editing should focus on improving the precision and efficiency of editing tools. This includes developing more sophisticated delivery methods for genome editing components and optimizing protocols for pine species (Mushtaq et al., 2019; Mishra et al., 2021). Advances in bioinformatics and computational tools, such as the PINES framework, can aid in predicting the functional impact of edits and identifying target genes for disease resistance (Bodea et al., 2018). Additionally, integrating genome editing with traditional breeding methods and marker-assisted selection can accelerate the development of disease-resistant pine varieties (Liu et al., 2019; Weiss et al., 2020). Collaborative efforts between researchers, regulatory bodies, and the public are essential to address regulatory and ethical concerns and to ensure the responsible application of genome editing technologies in forestry (Yin and Qiu, 2019; Mushtaq et al., 2019; Proudfoot et al., 2019).

9 Concluding Remarks

The research on precise editing and functional verification of pine disease resistance genes has yielded several significant findings. Genome editing technologies, particularly CRISPR/Cas9, have been instrumental in developing disease-resistant plant varieties by enabling precise, targeted modifications of plant genomes. Studies have demonstrated the successful application of genome editing to disrupt susceptibility (S) genes, thereby conferring broad-spectrum and durable disease resistance in various crops. Additionally, the construction of high-density genetic maps in pine species has provided valuable insights into the genetic basis of disease resistance, identifying key genes involved in defense responses and systemic resistance to pathogens. The use of base editors, such as adenine and cytidine base editors, has further enhanced the precision of genome editing, allowing for targeted point mutations without introducing double-stranded DNA breaks.

The advancements in genome editing technologies have profound implications for pine disease management. By leveraging CRISPR/Cas9 and other genome editing tools, researchers can now develop pine varieties with enhanced resistance to diseases such as white pine blister rust, which has significantly impacted pine populations in North America. The ability to precisely edit disease resistance genes and disrupt susceptibility genes offers a promising strategy for creating durable and broad-spectrum resistance in pine species. Furthermore, the development of high-density genetic maps and the identification of key resistance genes provide a robust foundation for marker-assisted breeding programs, facilitating the selection and propagation of disease-resistant pine varieties. These advancements not only contribute to the conservation of pine ecosystems but also enhance the sustainability and productivity of forestry practices.

The integration of genome editing technologies into pine disease resistance research marks a significant milestone in plant biotechnology. The precise editing capabilities of CRISPR/Cas9 and base editors have revolutionized the field, enabling the development of disease-resistant pine varieties with unprecedented accuracy and efficiency. As we continue to refine these technologies and expand our understanding of the genetic basis of disease resistance, the potential for creating resilient and sustainable pine forests becomes increasingly attainable. Future research should focus on optimizing genome editing protocols, exploring the long-term effects of edited genes on pine health and ecology, and ensuring the responsible deployment of these technologies in forestry practices. The collaborative efforts of researchers, policymakers, and stakeholders will be crucial in harnessing the full potential of genome editing for the benefit of pine ecosystems and the broader environment.

Acknowledgments

The authors appreciate the feedback from two anonymous peer reviewers on the manuscript of this study.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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