1 Introduction

Figs (Ficus carica L.) have been a staple in human agriculture and diet for millennia, recognized for their nutritional value and versatility. As one of the oldest domesticated fruit species, figs are cultivated globally, particularly in regions with Mediterranean climates. The fruit is rich in essential nutrients, including vitamins, minerals, and antioxidants, making it a valuable component of a balanced diet. Additionally, fig seeds have been identified as a significant source of minor oils with high unsaturation levels and potent antioxidant properties, further enhancing their nutritional profile (Irchad et al., 2023). The phenotypic diversity observed in fig cultivars underscores their potential for various applications in food and health industries (Irchad et al., 2023).

Understanding the domestication history and genetic diversity of figs is crucial for several reasons. It provides insights into the evolutionary processes that have shaped the current fig varieties, which are essential for conservation and breeding programs. Traditional agroecosystems, such as those in Morocco, serve as conservatories and incubators of fig varietal diversity, maintaining a rich genetic pool that is vital for the species’ adaptability and resilience (Achtak et al., 2010). Moreover, advancements in genomics, such as the development of a high-quality reference genome for figs, have opened new avenues for research into the relationship between genetic and epigenetic changes and phenotypic traits (Usai et al., 2019). These genomic resources are invaluable for breeding programs aimed at improving fig cultivars for better yield, disease resistance, and nutritional quality.

This study is to consolidate current knowledge on the domestication history, genetic diversity, and genomics progress of figs. By synthesizing findings from various studies, this study will provide a comprehensive understanding of the factors influencing fig cultivation and improvement. We expect this study to highlight the significant genetic resources available within fig germplasm, the role of traditional agroecosystems in preserving genetic diversity, and the latest advancements in fig genomics, contributing to the sustainable cultivation and utilization of figs in agriculture and diet.

2 Historical Context of Fig Domestication

2.1 Archaeological evidence of early fig cultivation

The domestication of figs is a significant milestone in the history of agriculture, with evidence suggesting that figs may have been one of the earliest domesticated plants. Archaeological findings from the Lower Jordan Valley, particularly at sites such as Gilgal I and Netiv Hagdud, indicate that fig cultivation dates back to the second half of the twelfth millennium BP. Kislev et al. (2006a) presented evidence of human use of parthenocarpic female figs (Ficus carica var. domestica) from these sites, suggesting that these figs were propagated vegetatively, a practice that was likely widespread throughout the Fertile Crescent during this period (Denham, 2007). This evidence is supported by the discovery of nine carbonized fig fruits (Figure 1) and hundreds of drupelets at Gilgal I, which date to approximately 11 400 to 11 200 years ago. These findings suggest that fig trees were grown from intentionally planted branches, indicating a form of early horticulture that predates cereal domestication by about a thousand years (Kislev et al., 2006a).

Figure 1 Carbonized fig fruit (Ficus carica var. domestica) from Gilgal I, broken lengthwise (Adopted from Kislev et al., 2006a) Image caption: Orifice (A) surrounded by scales (B). The fruit skin (C) covers the thin fruit flesh (D) and its inner part (E), which includes the empty drupelets (F). Scale bar, 5 mm (Adopted from Kislev et al., 2006a)

Further analysis of these archaeological remains has led to the conclusion that the simplicity of fig tree propagation likely contributed to its early domestication. Unlike cereal crops, which required repeated sowing, fig trees could be propagated through cuttings, making them an attractive option for early Neolithic farmers (Kislev et al., 2006b). This early cultivation of figs represents a significant shift from the gathering of wild food to the deliberate planting and management of food-producing plants, marking an important step in the development of agriculture (Gibbons, 2006).

2.2 Geographic spread and ancient trade routes associated with figs

The domestication and subsequent spread of figs were closely tied to the development of ancient trade routes and the geographic expansion of early agricultural societies. The Near East, particularly the Fertile Crescent, is recognized as the primary region where fig domestication began. From this region, the cultivation of figs spread to other parts of the Mediterranean and beyond, facilitated by the trade networks that connected different civilizations.

The spread of fig cultivation can be traced through the examination of genetic diversity in modern fig populations and their wild relatives. Studies have shown that the genetic makeup of domesticated figs reflects a history of multiple origins and extensive gene flow, likely driven by human-mediated movement of fig plants along trade routes (Olsen and Gross, 2008). This genetic evidence aligns with archaeological data, which suggests that the domestication of figs was a geographically diffuse process, involving long-term use and management of wild fig populations across a wide area of the Near East (Olsen and Gross, 2008).

3 Genetic Diversity in Wild and Domesticated Fig Populations

3.1 Comparative analysis of genetic variability

The genetic variability between wild and domesticated fig populations can be understood through comparative population genomics. Studies have shown that domestication generally leads to a reduction in genetic diversity due to selective breeding and population bottlenecks. For instance, research on various crops and animals has demonstrated that domesticated species exhibit lower genetic diversity compared to their wild counterparts (Liu et al., 2019).

In figs, similar trends are expected. The domestication process, driven by human selection for desirable traits, likely resulted in a genetic bottleneck, reducing the overall genetic diversity. This reduction in diversity can be attributed to selective sweeps, where favorable alleles are fixed in the population, leading to a loss of other genetic variants (Burban et al., 2021). Comparative studies in other crops, such as cotton and maize, have shown that domestication not only reduces genetic diversity but also alters gene expression patterns and regulatory networks, further impacting the genetic architecture of domesticated species (Hufford et al., 2012; Wang et al., 2017).

3.2 Impact of domestication on genetic diversity

The impact of domestication on genetic diversity is profound and multifaceted. Domestication often involves a series of genetic changes that result in the so-called “domestication syndrome”, characterized by traits that are advantageous for cultivation and human use. These traits include changes in plant structure, seed dispersal mechanisms, and palatability, which are selected for during the domestication process (Smýkal et al., 2018). However, this selection process also leads to a reduction in genetic diversity, as only a subset of the original genetic variation is retained in the domesticated population.

Research has shown that domesticated species tend to have higher proportions of deleterious genetic variants compared to their wild relatives. This is due to the population bottlenecks and reduced effective population sizes associated with domestication, which decrease the efficacy of natural selection in purging harmful alleles. For example, studies on domestic animals and plants have found elevated levels of nonsynonymous amino acid changes and damaging single nucleotide polymorphisms (SNPs) in domesticated species (Makino et al., 2018).

The demographic history of domestication plays a crucial role in shaping the genetic diversity of domesticated species. Extended periods of pre-domestication cultivation and subsequent dispersal to new regions can introduce additional genetic variation through hybridization and introgression from wild relatives (Gaut et al., 2018). In figs, this complex history of domestication and dispersal likely contributed to the current genetic diversity observed in cultivated populations.

4 Genomics Progress in Fig Research

4.1 Advances in sequencing technologies and their application to fig genomics

The advent of next-generation sequencing (NGS) technologies has significantly advanced our understanding of complex genomes, including those of non-model plants like figs (Ficus carica L.). One notable application of these technologies is the assembly of a high-quality reference genome for figs using Pacific Biosciences single-molecule, real-time sequencing. This approach has enabled the successful assembly of the fig genome, which is approximately 333 Mbp in size, with 80% of the genome anchored to 13 chromosomes (Figure 2). This high-quality reference genome provides a crucial resource for fig breeding and fundamental research into the relationship between epigenetic changes and phenotype (Usai et al., 2019).

Figure 2 Distribution of genomic and epigenomic features of the fig genome (Adopted from Usai et al., 2019) Image caption: (a) The 13 pseudomolecules. The black label on each pseudomolecule represents the putative centromeric region. Pseudomolecules are divided into 1 Mbp intervals. (b) Heterozygosity. (c) Histogram representing gene density. (d) Histogram representing TEs density. (e) Heat map representing 4mC modification levels. (f) Heat map representing 6mA modification levels (Adopted from Usai et al., 2019)

Next-generation sequencing has also facilitated the rapid domestication of new plant species and the efficient identification and capture of novel genetic variation from related species. For instance, re-sequencing of domesticated genotypes can identify regions of low diversity associated with domestication, and whole-genome shotgun sequencing of related wild species can provide species-specific data. These advancements have been applied to various crops, including rice, sugarcane, and Eucalypts, demonstrating the broad applicability of NGS in crop improvement and domestication studies (Henry, 2012).

4.2 Key genomic discoveries that have impacted understanding of fig biology

Several key genomic discoveries have significantly enhanced our understanding of fig biology. The high-quality reference genome of figs has revealed important epigenetic patterns, including high levels of methylation in both genes and transposable elements. This discovery underscores the prevalence of methylated over non-methylated genes in figs and has led to the identification of a species-specific motif, ANHGA, which is prevalent in both genes and transposable elements. Additionally, the identification of 13 putative centromeric regions in the fig genome provides valuable insights into the structural organization of the fig genome (Usai et al., 2019).

Furthermore, population genomics approaches have been applied to study the intraspecies genomic divergence of fig-associated species, such as fig wasps. These studies have revealed how geographic barriers and adaptation influence genetic divergence at the population level, thereby increasing our knowledge of potential speciation in non-model organisms. For example, the genetic divergence between populations of fig wasps on Hainan Island and the mainland has been attributed to both geographic isolation and environmental adaptation, highlighting the complex interplay of factors driving genetic diversity in fig-associated species (Xu et al., 2021).

5 Molecular Markers and Breeding Techniques

5.1 Description of molecular markers used in fig research

Molecular markers are essential tools in plant genetics and breeding, providing insights into genetic diversity, trait inheritance, and the domestication process. In fig research, several types of molecular markers have been employed, including restriction fragment length polymorphisms (RFLPs), microsatellites, and single nucleotide polymorphisms (SNPs). These markers are polymorphic, meaning they exhibit variation at specific loci within the genome, which can be used to distinguish between different genotypes (Beuzen et al., 2000).

Recent advancements in next-generation sequencing (NGS) technologies have significantly enhanced the development and application of molecular markers. Techniques such as genotype-by-sequencing (GBS) and whole genome resequencing allow for the identification of thousands to millions of SNPs across the genome, providing a comprehensive view of genetic variation (García and Piñero, 2017; Ramesh et al., 2020). These high-throughput methods facilitate the discovery of functional markers (FMMs) that are directly associated with traits of interest, thereby improving the efficiency of breeding programs (Ramesh et al., 2020).

5.2 Breeding markers that promote ideal traits

Molecular markers play a crucial role in breeding programs by enabling marker-assisted selection (MAS). MAS involves using DNA markers to select plants with desirable traits, thereby accelerating the breeding process and increasing the precision of selection. For instance, SNP markers identified through GBS can be used to map quantitative trait loci (QTL) associated with important agronomic traits such as yield, disease resistance, and stress tolerance (Li et al., 2022).

The integration of molecular markers with traditional breeding techniques allows for the efficient exploitation of genetic diversity. By identifying and selecting for specific alleles associated with desirable traits, breeders can develop new cultivars with improved performance and adaptability (Charcosset and Moreau, 2004). This approach has been particularly effective in addressing complex traits that are controlled by multiple genes, as it allows for the simultaneous selection of multiple loci (Eathington et al., 2007).

Moreover, molecular markers facilitate the study of domestication and evolutionary history by revealing patterns of genetic diversity and selection. For example, genomic regions with signatures of selection can be identified, providing insights into the genetic changes that occurred during domestication (Geleta and Ortiz, 2016). This information is valuable for understanding the genetic basis of domestication syndrome traits and for guiding future breeding efforts to enhance crop performance and resilience.

6 Role of Epigenetics in Fig Domestication

6.1 Overview of epigenetic factors influencing fig characteristics

Epigenetics, the study of heritable changes in gene expression that do not involve changes to the underlying DNA sequence, plays a crucial role in the domestication of figs (Ficus carica L.). Epigenetic mechanisms such as DNA methylation and histone modifications can significantly influence phenotypic traits by regulating gene expression. In figs, genome-wide analysis has revealed high levels of DNA methylation in both genes and transposable elements, indicating that epigenetic modifications are prevalent and potentially influential in fig domestication (Usai et al., 2019).

Epigenetic diversity can compensate for the loss of genetic diversity, which is particularly important in domesticated species that often undergo bottlenecks and reduced genetic variation due to selective breeding (Dar et al., 2022). This diversity can influence various traits, including growth, stress tolerance, and reproductive success, by modulating gene expression in response to environmental cues (Jensen, 2015; Shi and Lai, 2015).

6.2 Case studies demonstrating the impact of epigenetics

Several studies have highlighted the impact of epigenetics on the domestication of various species, providing insights that are applicable to figs. For instance, in soybean domestication, differentially methylated regions (DMRs) were identified, which exhibited higher genetic diversity and were associated with important metabolic pathways (Shen et al., 2018). In figs, the high-quality genome reference and methylation profiles provide a valuable resource for understanding how epigenetic changes influence phenotypic traits. The identification of species-specific methylation motifs and the prevalence of methylated genes suggest that epigenetic regulation is a key factor in fig domestication (Usai et al., 2019). These findings underscore the potential for epigenetic mechanisms to drive rapid phenotypic changes in figs as well.

7 Biotechnological Advances and Genetic Engineering

7.1 Recent biotechnological interventions in fig cultivation

Recent advancements in biotechnology have significantly impacted the cultivation of figs, focusing on enhancing genetic diversity, disease resistance, and overall crop yield. The completion of reference genome sequences for many crops, including figs, has provided a foundation for high-throughput resequencing, which accelerates crop improvement by enabling detailed comparisons of individual plant genomes (Morrell et al., 2011). This genomic data facilitates the identification of genetic variations that can be harnessed to improve fig cultivation.

Moreover, the development of novel genetic tools, such as plasmid-based systems and CRISPR/Cas9, has revolutionized the field of plant biotechnology. These tools allow for precise genetic modifications, enabling the introduction of desirable traits such as increased resistance to pests and diseases, improved fruit quality, and enhanced environmental adaptability (Riley and Guss, 2021). The integration of these advanced biotechnological methods into fig cultivation practices promises to optimize growth conditions and improve overall productivity.

7.2 Genetic engineering techniques employed in fig research

Genetic engineering techniques have become indispensable in fig research, providing the means to manipulate the fig genome with high precision. One of the primary methods employed is the use of CRISPR/Cas9, a powerful genome-editing tool that allows for targeted modifications at specific genetic loci. This technique has been instrumental in introducing beneficial traits and studying gene function in figs (Nora et al., 2019).

Additionally, the use of recombinant DNA methods, guided by genomic data, has enabled the domestication of figs in ways that mimic conventional breeding but with greater efficiency and precision. This approach involves the insertion of transgenes to confer desired traits, such as improved fruit size, flavor, and resistance to environmental stresses (Strauss, 2003). However, the regulatory landscape for field trials of genetically modified organisms (GMOs) remains a significant challenge, potentially hindering the widespread adoption of these technologies.

Gene stacking, which involves the introduction of multiple genes to achieve complex trait improvements, is another technique being explored in fig research. Despite its potential, gene stacking faces technical challenges, such as ensuring stable expression and int (eraction of multiple transgenes within the plant genome (Halpin, 2005). Overcoming these hurdles will be crucial for the successful application of genetic engineering in fig cultivation.

8 Case Study: Genomic Insights into Mediterranean Fig Cultivation

8.1 Background on Mediterranean fig varieties

The fig tree (Ficus carica L.) is a significant fruit crop in the Mediterranean region, valued for its nutritional and pharmaceutical properties. Historically, figs, along with olives and grapes, were among the first fruit trees domesticated in the Near East. The domestication process involved a shift from sexual reproduction in the wild to vegetative propagation under cultivation, which facilitated the rapid buildup of variation in domesticated crops through introgression from wild gene pools. This historical context underscores the importance of figs in early Mediterranean agriculture and their continued relevance today.

8.2 Genomic studies on Mediterranean figs and their impact on agricultural practices

Recent genomic studies have provided valuable insights into the genetic diversity and structure of fig populations in the Mediterranean basin. An ex situ collection of 60 fig accessions, including 41 indigenous Greek and 19 from other Mediterranean countries, was analyzed using simple sequence repeat (SSR) markers (Figure 3). The study revealed relatively low allelic variation among Greek fig genotypes but highlighted an excess of heterozygosity and extensive outbreeding, indicating a weak genetic structure with significant variation within individual clusters (Sclavounos et al., 2021). This genetic diversity is crucial for sustainable fig production and breeding efforts.

Figure 3 Analysis of the 60 fig accessions based on SSR markers (Adopted from Sclavounos et al., 2021) Image caption: (A) Principal coordinate analysis (PCoA) of the 60 fig accessions based on eight SSR markers. (B) Estimation of the number of populations K=3 by calculating delta K values. (C) STRUCTURE plot depicting sub-populations. Inferred population structure for K=3. Each individual is represented by bars partitioned into K segments representing the membership fraction in K clusters. The bars are arranged based on geographical eastern approximate coordinate of the accessions (right: most western accession, Italy; left: most eastern accession, Cyprus) (Adopted from Sclavounos et al., 2021)

The development of a comprehensive genomic variation map for olive trees, another key Mediterranean crop, has set a precedent for similar studies in figs. The olive tree study identified candidate genes associated with key agronomic traits, such as fruit yield and oil quality, through genome-wide association analyses (Bazakos et al., 2023). These methodologies can be applied to figs to uncover genetic markers linked to desirable traits, thereby enhancing breeding programs and agricultural practices.

8.3 Lessons from genomics research and applications for future breeding strategies

The lessons learned from genomics research on Mediterranean crops like olives and carobs can be directly applied to figs. For instance, the olive tree’s domestication involved recurrent genetic admixture events with wild populations, which maintained genetic diversity and facilitated adaptation to different environments (Díez et al., 2015; Julca et al., 2020). Similarly, fig breeding programs can benefit from incorporating wild genetic material to enhance resilience and adaptability.

Moreover, the carob tree study demonstrated the importance of preserving genetic resources from both wild and cultivated populations to maintain genetic diversity and support future breeding efforts (Baumel et al., 2021). This approach is equally relevant for figs, where ex situ collections and conservation of diverse germplasm are essential for long-term sustainability.

9 Future Directions in Fig Genomics

9.1 Potential genetic technologies and breeding strategies for future fig improvement

The future of fig improvement lies in the integration of advanced genetic technologies and innovative breeding strategies. Genome editing technologies, such as CRISPR/Cas9, offer promising avenues for the de novo domestication of figs by allowing precise modifications to the genome, bypassing the limitations of traditional breeding methods that rely on random mutagenesis or intraspecific diversity (Bartlett et al., 2022). This approach can accelerate the domestication process and enhance desirable traits in figs, such as disease resistance, fruit quality, and yield.

Next-generation sequencing (NGS) technologies have revolutionized our understanding of plant genomes and can be leveraged to identify key genetic loci responsible for important agronomic traits in figs (Singh et al., 2020; Ashraf et al., 2022). By combining NGS with genome-wide association studies (GWAS) and quantitative trait loci (QTL) mapping, researchers can pinpoint specific genes and genomic regions that control traits of interest, facilitating marker-assisted selection (MAS) and genomic selection (GS) in fig breeding programs (Tang et al., 2010; Turner-Hissong et al., 2019).

Meanwhile, the integration of bioinformatics tools and molecular techniques, such as de novo genome assembly and pan-genome analysis, can provide a comprehensive understanding of the genetic diversity within fig populations. This knowledge can be used to develop breeding strategies that optimize the accumulation of beneficial alleles while purging deleterious ones, ultimately leading to the creation of superior fig cultivars (Brozynska et al., 2016; Varshney et al., 2021).

9.2 Integration of biotechnological tools for enhanced cultivation and production

The integration of biotechnological tools into fig cultivation and production systems holds significant potential for enhancing productivity and sustainability. Genomic-assisted breeding (GAB) has already shown its effectiveness in other crops and can be adapted for figs to fast-track the development of climate-smart cultivars with improved nutritional value. This approach involves the use of high-throughput genotyping and precision editing to create novel genetic diversity and incorporate it efficiently into breeding programs.

Biotechnological innovations, such as metabolomics and transcriptomics, can also play a crucial role in understanding the metabolic pathways and gene expression profiles associated with stress tolerance and fruit quality in figs. By identifying key metabolites and regulatory genes, researchers can develop strategies to enhance fig resilience to biotic and abiotic stresses, thereby improving overall yield and quality (Wang et al., 2023).

The application of genome editing technologies, such as CRISPR/Cas9, in combination with traditional breeding methods, can facilitate the rapid development of figs with enhanced traits. This integrated approach can lead to more efficient and targeted breeding efforts, ultimately resulting in the production of high-quality figs that meet the demands of both growers and consumers (Østerberg et al., 2017).

10 Concluding Remarks

This study summarizes the domestication history, genetic diversity, and genomics progress of the fig (Ficus carica L.). As one of the early fruits domesticated in the Near East, figs exhibit a transition from sexual reproduction in the wild to asexual propagation under cultivation, a process that has facilitated the rapid accumulation of genetic variation. Regarding genetic diversity, research has revealed that, despite the constraints of traditional breeding methods, fig populations have maintained significant genetic variation. Additionally, advances in genomics, particularly the assembly of high-quality genomes and the study of epigenetic markers, have provided new perspectives on understanding the genetic and phenotypic characteristics of figs.

With the continuous advancements in genomic technologies, sustained investment in fig genomic research is crucial for the sustainability and enhancement of fig agriculture. Genomic studies not only reveal the genes and epigenetic mechanisms that lead to genetic diversity but also enable the identification of key genetic loci associated with important agronomic traits, driving targeted breeding strategies. Furthermore, a deeper understanding of the fig genome will aid in developing new varieties resistant to diseases and adaptable to various environmental stresses, which are essential for addressing climate change and preserving biodiversity.

The expansion of genomic research can optimize existing breeding programs and has significant implications for ensuring the long-term sustainability of the global fig industry. As our knowledge of this ancient crop's genetic foundation deepens, the future of fig breeding and cultivation looks increasingly promising. Through these studies, we can better utilize the genetic resources of figs to provide innovative solutions for agricultural production, meeting the growing market demands.

Acknowledgments

EcoEvo Publisher thanks the anonymous reviewers for their insightful comments and suggestions that improved the manuscript.

Conflict of Interest Disclosure

The author affirms 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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