TADs, CGVs, and compartmentalization in genomes: Providing a new way for crop domestication and improvement

ABSTRACT

Genetic variation underlying phenotypic diversity between wild and domesticated species has been extensively studied, the contribution of higher‐order chromatin architecture to these processes remains less explored. Advances in Hi‐C and related genomic technologies have revealed that plant genomes exhibit complex three‐dimensional (3D) genome organization, hierarchically structured into A/B compartments, and topologically associated domains (TADs). TADs represent self‐interacting genomic regions that can constrain or regulate without directly determining transcriptional outcomes. Alterations to TAD organization or boundary have been associated with changes in chromatin interactions and gene regulatory potential in specific developmental or environmental contexts. In plants, emerging evidence indicates that TAD structure can be genetically and environmentally modulated, despite the absence of canonical architectural proteins such as CTCF. Both environmental stress and genetic perturbations have been shown to remodel chromatin organization, with context‐dependent changes in gene expression. Such plasticity in chromatin dynamics that contribute to adaptive responses raises a potential link between 3D genomic structure and cryptic genetic variations (CGVs). CGVs remain phenotypically silent under normal conditions but can be revealed under environmental or genetic perturbations, representing an additional layer of regulatory potential in plant genomes. Here, we propose that stress‐induced chromatin organization, including changes in TAD organization and chromatin compartmentalization, may influence accessibility and expression of CGVs in a context‐dependent manner. While a direct mechanistic link between TADs and CGVs remains largely unexplored. Here, we reviewed recent findings from model plants and major crops to highlight how variation in 3D genome organization can contribute to transcriptional plasticity, stress responses, and lineage‐specific regulatory evolution. By integrating 3D genomics, chromatin accessibility, and multi‐omics data, we outline a conceptual framework for generating hypotheses and open questions on how TAD‐associated chromatin dynamics and CGVs together may shape transcriptional plasticity, stress responses, and long‐term adaptive evolution in plants with implications for future crop improvement strategies.

This review discusses how environmentally responsive modulation of 3D genome architecture may contribute to adaptive traits and crop improvement. In parallel, under unusual environmental conditions, cryptic genetic variations in plants play a role in adaptation, although how higher‐order chromatin structure influences this remains unclear.

EXPLORING GENOMIC STRUCTURE: UNLOCKING THE NEW ERA OF CROP DOMESTICATION

Advanced molecular tools played an important role in finding the genetic variations in plants accumulated through natural or selective processes. A high level of variation associated with novel phenotypes arises as a result of perturbation throughout the domestication process, which might be an essential source of physiological and evolutionary potential (Gibson and Dworkin, 2004). Throughout the evolutionary processes, environmental or forced perturbations led to changes in the phenotype of the population as standing genetic variations or cryptic genetic variations (CGVs). Accumulation of CGVs in duplicated genes can alter the functional consequences, which influence the trajectories and reorganize the associated interaction network (Dibyachintan et al., 2025). In principle, CGVs strongly influence the natural populations to adapt to a new environment (Paaby and Rockman, 2014). How such variations potentially intersect the higher‐order chromatin organization and transcriptional plasticity under environmental or forced adaptation. In the modern era, it is worth studying the CGV to determine how plants respond to mutational changes, artificial selection through breeding, and how it rewrites the 3D structure of the genome.

Three‐dimensional (3D) folding of the eukaryotic genome results in self‐interacting regions packaged in chromatin loops, forming topologically associated domains, A/B compartments (Lieberman‐Aiden et al., 2009), and chromosome territories (CTs) (Cremer and Cremer, 2010). The 3D spatial organization of the genome can be partitioned into two types of chromatins, referred to as active (A) and inactive (B) compartments (Ouyang et al., 2020). These structural features exhibit chromosomal characteristics and chromatin interaction patterns. Unlike mammalian TAD, plant genomes display TAD domains whose structural and functional properties vary across the species and genomic contexts. In several plant species, these TAD domains have been reported to be enriched in active genes, open chromatin features (DNase I hypersensitive sites [DHSs]), and epigenetic marks (Dong et al., 2017; Liu et al., 2017; Göbel et al., 2024), whereas in other species, such enrichment is less evident (Karaaslan et al., 2020). Plant TAD domains are associated with regulatory contacts between enhancers and promoters, particularly near domain boundaries; however, such interactions are context‐dependent and are not universally conserved.

Compartment A is generally characterized by a high gene density and epigenetic modification associated with transcriptionally active euchromatin and splicing speckles, whereas compartment B is enriched in transposable elements (TE) and transcriptionally inactive heterochromatin, often localized near the nucleolus (Ouyang et al., 2020; Pei et al., 2021). Global nuclear organization reflects a high level of compartmentalization and spatial organization, which can influence the regulatory landscape by constraining or permitting long‐range regulator interactions, rather than directly determining transcriptional outcomes. Consistent with this view, studies in 3D genomics indicate that chromatin status is directly correlated with DNA replication (Dekker and Heard, 2015; Pei et al., 2021), cell type‐specific gene expression, and other biological functions (Dekker et al., 2013).

As conserved feature of genome organization, TADs define chromatin architecture (Szabo et al., 2019), suggesting a role in shaping higher‐order chromosomal organization while constraining DNA‐dependent regulatory landscape, rather than directly determining gene expression outcomes (Lieberman‐Aiden et al., 2009; Beagan and Phillips‐Cremins, 2020). TADs are widely observed in plants and are unlikely to be associated with genome size. TAD has been observed together with distinct epigenetic features in many plant species, including in Marchantia polymorpha (Karaaslan et al., 2020), rice (Liu et al., 2017; Dong et al., 2018), pitaya (Zaman et al., 2025), Brassica (Xie et al., 2019), cotton (Wang et al., 2018), maize, tomato, sorghum, foxtail millet (Dong et al., 2017), and soybean (Ni et al., 2023). Generally, TADs are characterized by a higher frequency of interactions among regions within a domain than between adjacent domains, although the strength and regulatory consequences of such interactions vary across species and genomic context (Dixon et al., 2012; Nuebler et al., 2018).

Chromatin organization in the form of TAD can assist long‐range chromatin interactions and influence the target specificity of promoter elements in plant genomes (Doğan and Liu, 2018). Mammalian TADs are highly conserved between different cell types and tissues and even across species; however, genes contained within a given TAD in plant species are often not conserved in corresponding domains of another plant species. For example, none of the sorghum TADs were identified in the maize genome, whereas 8.23% of foxtail millet TADs revealed a syntenic relationship with the sorghum genome. Other than plant species, TAD showed 30%–40% conservation between Drosophila melanogaster and Drosophila pseudoobscura, and approximately 43% of the human genome exhibits syntenic relationships with the closest chimpanzees (Eres et al., 2019). Most of the mammalian TADs are enriched with conserved binding proteins (CTCF); however, in plants, domain function occurs in the absence of CTCF and is mediated by an alternative plant‐specific mechanism (Dong et al., 2017). TAD corner loops in mammalian genomes are enriched at the boundary, while similar corner loops in maize are located outside the domain and interact with active compartment (A) and are separated by condensed heterochromatin (compartment B) (Dong et al., 2017). Notably, recent work in rice demonstrates that CCCTC‐containing elements can act as a functional insulator like sequences, and targeted modulation of chromatin loop extrusion at specific loci can influence gene expression and agronomic traits, despite the absence of canonical CTCF in plants (Liu et al., 2025).

Domestication through long‐term artificial selection, together with crop breeding, genomic variation, and phenotypic diversification, has had a sustainable impact on agrobiodiversity, socio‐economic, and food security, while enabling the accumulation of beneficial alleles in diverse landraces. Recent advances in Hi‐C and related chromosome conformation capture techniques have enabled detailed exploration of hierarchical chromatin interaction, A/B compartmentalization, and TAD. These approaches have begun to provide insights into genome organization that may complement conventional genetic and genomic strategies, rather than directly delivering predictive breeding outcomes. Accordingly, 3D genomic information has the potential to speed up the plant breeding and trait improvement efforts, particularly when integrated with functional genomics and population genetics, but its application to domestication and breeding remains largely exploratory at present.

Evolutionary origin and boundary characteristics of TAD

Formation of TADs and their boundaries increases the complexity of transcriptional regulation and might reflect the sophistication of higher‐order chromatin structures. These structures appear to represent a recurrent organizational principle across eukaryotes (Szabo et al., 2019). In mammals, loop extrusion and compartmentalization suggest that both operate jointly to maintain the spatial organization of the genome. However, TAD domains and compartmentalization have also been observed in plants, but the mechanism of formation largely remains unknown (Doğan and Liu, 2018). Wang and colleagues (Wang et al., 2015) called the TAD “positive strips”, which show special structural features and distinct epigenetic marks in the Arabidopsis thaliana genome at 2‐kb resolution of the Hi‐C map. Unlike those found in A. thaliana, TAD structures in rice, Brassica, and cotton had different sizes and accounted for 25%–93% of their genomic length. A recent study in rice demonstrates that CCCTC‐containing cis‐elements can function as a boundary insulator via zinc finger protein (Yin‐Yang homolog‐OsYY1), which mediates chromatin looping and loop extrusion in a context‐dependent manner (Liu et al., 2025). These CCCTC‐associated loops in plants are dynamically regulated by environmental inputs, including nitrogen availability, and exhibit allele‐specific and tissue‐specific effects on gene expression. Such plasticity contrasts with the relatively stable and evolutionary conserved CTCF‐bound TAD boundaries in mammals, suggesting that plant TAD domains may be more responsive to developmental and environmental cues. These findings suggested that plant chromatin domains are stabilized through a combination of transcription factors (TCP, bZIP, YY1), chromatin states, and environmental signaling. This can facilitate rapid regulatory rewiring during the adaptation and domestication of plant species.

A recent study in Arabidopsis elucidated the plant‐specific mechanism. Mutations in cohesion regulatory factor PDS5 lead to enhanced formation and stabilization of TAD domains, demonstrating that plant chromatin is genetically tunable and context‐dependent (Göbel et al., 2024). Any change in chromatin structure can contribute to or constrain transcriptional regulation and genome evolution. Genes within the TAD tend to have more conserved expression patterns and alteration or disruption in these domains by evolutionary changes can lead to shifts in expression profile (Krefting et al., 2018). Long and colleagues found that genes occupying TAD singly are functionally enriched and exhibited a strong association with the developmental and evolutionary process (Long et al., 2022). These TAD structures were similar to mammalian TAD as their cis‐interactions and were enriched in the domain interior, but active genes and histone modifications were enriched in the domain border (Liu et al., 2017; Wang et al., 2018). In Arabidopsis, the disruption of loops between the promoter and transcription termination site results in decreased FLC gene expression (Crevillén et al., 2013). In Marchantia polymorpha, loss of TCP1 does not disrupt the TAD architecture but leads to increased expression fold changes for genes within the TCP1‐rich TADs, indicating that plant TADs modulate the magnitude of transcriptional responses rather than activating or repressing gene expression (Karaaslan et al., 2020). In rice, 1,763 TADs were detected with a median size of 45 kb, which collectively comprised 25% of the genome. In addition, TAD boundaries were enriched with a plant‐specific family of TCP TF, which was positively correlated with higher than average gene expression (Liu et al., 2017). Pepper TAD domains were enriched by genes that act to connect genes via gene‐to‐gene loops, leading to the spatial clustering of active genes (Liao et al., 2022). Previous work revealed substantial differences in 3D genome organization in pitaya species with 2,031 TAD in polyploid pitaya (Selenicereus megalanthus) and 3,376 TAD in diploid pitaya (Selenicereus undatus) (Zaman et al., 2025). In red‐peel pitaya, 24,384 genes were distributed across 3,376 TADs, while in yellow pitaya, 2,031 TADs comprised 24,775 genes. In red‐peel pitaya, TAD boundaries were enriched for motifs, such as PHYPA_DRAFT_64121, RAV1, WRKY60, and WRKY18, whereas yellow pitaya showed enrichment of WRKY75, WRKY60, RAV1, and MYB3. These structural features were proposed to influence the expression of key betalain biosynthesis genes.

A recent study on cotton has demonstrated that drought‐tolerant and drought‐susceptible varieties exhibit distinct patterns of higher chromatin organization under stress, including differences in A/B compartment switching and TAD boundary variation. Notably, stress‐induced changes in TAD architecture were associated with differential expression of drought‐responsive genes and with phenotypic resilience, while the majority of TAD boundaries remained stable, highlighting a model of chromatin plasticity rather than reorganization. These findings support the view that environmentally responsive modulation of 3D genome architecture can be relevant to adaptive traits and crop improvement, without implying deterministic control of gene expression (Zhang et al., 2024). In Arabidopsis, it is demonstrated that despite the absence of canonical mammalian TAD, plant genomes are organized into smaller, gene‐centered chromatin domains anchored by transcriptional start and termination sites (Lee and Seo, 2023). These gene domains function as basic structural units of 3D genome organization and dynamically respond to transcriptional and heat stress, indicating that chromatin architecture in plants is highly plastic and initiates context‐dependent regulation. Similarly, genetic perturbations of chromatin architectural regulators further support the functional relevance of TAD organization in plants. Mutations in PDS5 genes, which regulate the cohesion dynamics, enhance the formation and insulation of TAD domains in Arabidopsis without inducing uniform transcriptional changes across the genome. Instead, these mutations alter the domain architecture, and are associated with context‐specific transcriptional regulation (Göbel et al., 2024). These findings demonstrate that plant chromatin architecture is a dynamic, environmentally responsive regulator layer that modulates gene expression in a context‐dependent manner, rather than acting as a deterministic control mechanism.

Beyond the model system, studies in diverse plant species illustrate that changes in TAD organization can be associated with lineage‐specific regulatory evolution, thereby linking chromatin topology to the broader narrative of plant genome evolution (Clark, 2023). In addition, studies in Gossypium species have shown that the number of conserved TAD decreases with phylogenetic divergence, suggesting that TAD stabilization can act both as a conservative force and as a source of regulatory variation over evolutionary time (Li et al., 2023). Similarly, in pitaya, species‐specific differences in TAD positioning correlate with differential gene expression, indicating that TAD architecture may contribute to lineage‐specific regulatory evolution (Zaman et al., 2025). These findings collectively illustrate that formation is not merely structural but a dynamic unit in the evolutionary toolkit of plant genomes.

Intensive functional verifications are required to characterize the potential role of proteins at TAD boundaries, which might be shaping plant traits. The substantial variation of TAD boundaries in different plant species suggests that chromatin organization might be more diverse in plants, being affected more by gene density, linear distribution of genes, and TE (Stam et al., 2019) than in multicellular metazoans.

Functional association between TADs and cryptic genetic variations: Open questions and bridging the gap from structure to variation

Transition to new environments is often associated with phenotypic diversification. A change in the genetic background or environment generates phenotypic variations in populations (Paaby and Rockman, 2014). Unusual environmental conditions reveal phenotypic differences arising from underlying genetic variations termed cryptic genetic variations (CGVs) (Donnelly et al., 2018). CGVs are genetic variations that are invisible under normal conditions but manifest phenotypically under specific genetic or environmental changes. Various studies have investigated these genetic variations at a population level, which are often masked by epistatic effects, yet can contribute to phenotypic diversity and play a role in adaptation and speciation.

Well‐known examples illustrating the contribution of CGVs to phenotypic diversification come from the domesticated maize derived from teosinte after centuries of artificial selection (Doebley et al., 1995). TE inserted into the regulatory region of TB1 acts as an enhancer in domesticated maize (Studer et al., 2011). Quantitative trait loci (QTL) mapping of multiple traits in teosinte provided evidence that loci identified between teosinte and maize harbor cryptic variations for the same trait in teosinte populations (Paaby and Rockman, 2014). Advances in QTL mapping, genome‐wide association studies, and genome sequencing technologies have facilitated the identification of genes contributing to domestication and genome evolution. Cryptic mutations have little or no effect under normal conditions, but these CGVs are important contributors that shape the evolution of the genome by both natural and artificial selection.

In tomatoes, the natural hypomorphic SlCLE9 allele existed as a cryptic variant in wild progenitors, and its interaction with the Slwus allele contributed to increased fruit size during domestication. This appears to have had a quantitative effect due to a combination of idiosyncratic interaction with cryptic gain of function of the Slwus allele and alleviation of dose‐dependent suppression by cryptic hypomorphic SlCLE9 (Aguirre et al., 2023). Similarly, experimental studies have shown that populations carrying RNA enzymes with accumulated cryptic variation can adapt more rapidly to a changing environment than populations lacking such variation (Hayden et al., 2011).

Besides the CGVs, TADs are also considered structural units of the genome organization that can exert conditional regulatory consequences during evolution (Dixon et al., 2016). Importantly, alterations in TAD structure or boundary features do not necessarily lead to uniform changes in gene expression, but may be associated with differential or variable transcriptional responses, depending on the genomic and cellular state. Recently, using TAC‐C, Kang and colleagues (2025) demonstrated that chromatin interaction hubs and looped regulatory domains are significantly enriched for QTLs and eQTLs in wheat, rice, maize, and sorghum (Kang et al., 2025). Importantly, distal regulatory variants exhibited larger phenotypic differences when physically connected to target genes through chromatin loops, indicating that the 3D genome might modulate CGVs. In addition, recent genetic evidence in Arabidopsis thaliana demonstrated that substantial changes in the TAD domain can occur without uniform or widespread transcriptional effects (Karaaslan et al., 2020; Göbel et al., 2024). In this sense, CGVs and TADs share a conceptual similarity in that both can remain phenotypically silent under favorable conditions but may indirectly contribute to phenotypic variation in response to environmental or regulatory perturbations (Figure 1).

Figure 1.

Conceptual framework linking cryptic genetic variations (CGVs) and three‐dimensional genome organization

CGVs represent genetic variants that are silent under normal conditions but can contribute to phenotypic variations when genetic or environmental perturbations occur. Higher‐chromatin organization, including A/B compartments and topologically associated domains, defines structural features of the genome that can influence regulatory interactions without deterministically controlling gene expression. Alterations in chromatin structure or regulatory components do not necessarily result in uniform transcriptional changes but may modulate the variability of gene expression responses. In this framework, TADs are proposed to provide chromatin environments that can influence whether CGVs remain silent or become expressed under selective or environmental stress, thereby contributing to adaptation and evolution.

Given the importance of both CGVs and chromatin architecture in genome evolution and plant adaptation, it remains unclear how higher‐order chromatin structure influences the manifestation of cryptic genetic variation. How do chromosomal rearrangements, cis‐regulatory mutations, or changes in TAD boundary properties affect the CGVs in evolving or domesticated plant genomes? Are CGVs harbored within the genomic regions associated with inactive (B) compartments, or can they reside in both A and B compartments depending on the regulatory context? Rather than being structural entities themselves, could TAD provide a chromatin environment that modulates whether CGVs remain silent or become expressed under selection or environmental stress? As the environmental or genetic perturbations alter cis‐regulatory activity or transcription factor occupancy within the TAD, genes respond differentially, potentially resulting in an obvious phenotype, not observed under normal conditions (Schlichting, 2008). In broader terms, the relative contributions of chromatin architecture and CGV, and their potential interplay, remain open questions that warrant further investigation to better understand genome evolution, compartmentalization, and plant adaptation.

Context‐dependent trait improvement framework based on TADs

Agriculture continues to face major challenges driven by population growth, climate variability, and increasing environmental stresses, which require grounded strategies for crop improvement. Advances in genomics and genome sequencing technologies have accelerated the identification of genes involved in domestication and agronomic traits in both cultivated crops and their wild relatives. 3D genome organization provides an additional layer that shapes gene expression in a context‐dependent manner (Huang et al., 2023). The presence of TAD regions along the diagonal of the Hi‐C matrix regulates gene expression via regulatory elements within their target genes (Dixon et al., 2016; Junaid et al., 2024). Increasing evidence indicates that 3D genome organization represents a dynamic regulatory layer that responds to developmental and environmental cues rather than a stable architectural scaffold. In plants, TAD domains and their boundaries can reorganize under stress conditions, leading to altered enhancer promoter contacts and context‐specific transcriptional responses (Huang et al., 2023; Göbel et al., 2024). These observations suggest that chromatin topology contributes to phenotypic plasticity by modulating gene regulation in an environment‐dependent manner.

From a crop improvement perspective, this plasticity implies that the same genotype grown in distinct climatic zones can exhibit different TAD configurations and regulatory interactions. Such environment‐specific chromatin states can expose regulatory links that remain cryptic under normal growth conditions, analogous to the environmentally induced expression of CGVs. This comparative analysis of 3D genome organization between cultivated and their wild relatives or across environments helps to identify the novel genes that are transcriptionally constrained in one environment but play their key role in another environment. Rearrangement in genome architecture that occurred during evolution may have functional and evolutionary consequences arising from 3D chromatin architecture, including chromosomal territories, A & B compartments, and TAD (Li et al., 2023). In cotton, it is elaborated that allopolyploidization is associated with extensive switching and reorganization of A/B compartments and TAD‐like domains, particularly in open chromatin regions, and that such reorganization correlates with coordinated changes in gene expression (Wang et al., 2018). Karaaslan and colleagues (2020) have found that mutations in TCP1‐rich TAD boundary lines explained significant changes in the expression of the genes located within the TAD (Karaaslan et al., 2020). In addition to domain boundaries, long‐chromatin interactions within active chromatin regions also contribute to transcriptional regulation of agronomic traits. In maize, genes involved in higher‐frequency chromatin interactions tend to exhibit elevated expression levels, and chromatin interaction network (ChIN) analysis has enabled the prioritization of candidate genes associated with quantitative traits (Li et al., 2019). Together, these observations suggest that TADs and the associated interaction network can be used to contextualize regulatory variation and prioritize candidate loci. By combining these ideas, genes within the active TAD can be predicted at specific stages of plant development and can be directly manipulated using modern breeding methods, particularly the CRISPR system (Zaman et al., 2023, 2024). Recent studies further demonstrated that environmental stresses such as heat and drought can induce reorganization of chromatin interactions, including the formation of stress‐specific enhancer‐promoter links and modulation of TAD boundaries, which are accompanied by transcriptional changes (Sun et al., 2020; Lee and Seo, 2023; Zhang et al., 2024). Li and colleagues (2026) found that TAD structures increased slightly under heat stress, and the expression of genes at the boundaries of partitioned TAD was significantly higher compared to the genes at the boundaries of homologous TAD structures. These partitioned TAD structures were associated with enhanced transcriptional activity (Li et al., 2026).

From a crop improvement perspective, TAD‐based analysis can be viewed as complementary to existing genomics‐assisted strategies. Conventional approaches such as marker‐assisted selection (MAS) have enabled rapid identification of trait‐associated loci, but their effectiveness can be limited to population specificity, incomplete marker trait association, and the need for repeated backcrossing to remove undesirable genetic backgrounds. In this context, integrating 3D genome organization with transcriptomic and chromatin accessibility data may help prioritize candidate genes that are conditionally active in specific varieties, tissues, and agro‐climatic zones. In principle, combining Hi‐C with tissue‐ or stage‐specific transcriptomic data enables the identification of genes in permissive chromatin contexts that are transcriptionally constrained in one environment but responsive in another, thereby highlighting candidates for functional validation. Targeted perturbations of regulatory elements within the TAD, including boundary association regions, can then be used to validate the interaction of chromatin and gene expression as demonstrated in Marchantia (Karaaslan et al., 2020). Recent high‐resolution analysis of open chromatin interactions in crops further supports the role of 3D genome organization in shaping the trait‐associated genetic effects. Integration of chromatin interaction maps with QTL and eQTL data revealed that distal regulatory variants located at chromatin interaction hubs often exhibit larger phenotypic effects than the variants lacking physical contacts with target genes (Kang et al., 2025).

Progressing from genomics‐assisted breeding strategies (Varshney et al., 2005) and term TAD‐based trait improvement should therefore be viewed not as a deterministic breeding approach, but as a framework to explore how stress‐induced chromatin configuration influences the gene regulation in a specific climatic zone. When the same cultivar is grown across the different climatic zones, stress‐responsive changes in TAD organization and regulatory contacts could reveal regulatory interactions that remain cryptic under normal conditions. Comparison of TAD structures and associated chromatin interactions in cultivated and wild progenitors can reveal extensive genome content and regulatory variation between the species. Along with TADs, CGVs can be detected, which can serve as a source of genetic diversity and phenotypic plasticity under environmental perturbations. Integrating 3D genome architecture with multiomics data under defined stress conditions, therefore, can assist in prioritizing candidate loci for functional validation (Figure 2).

Figure 2.

Overview of the TAD‐based trait improvement

(A) Comparative analysis of wild progenitors and cultivated species or the same cultivar grown in different agro‐ecological zones may assist in context‐dependent differences in genome organization. (B) Identification of A/B compartments of contrasting species or cultivars and finding the differences of topologically associated domains (TADs) at the chromosomal scale. Compare the motifs from TAD boundaries that contribute to differential chromatin insulation and influence transcriptional regulation. (C) Identification of compartmentalization and TADs reveals switching of compartments from A to B, or B to A, TAD reorganization, highlighting genes in active or repressed chromatin states and differential chromatin interactions. (D) CCCTC‐like motifs and TAD boundary‐associated transcription factors can enable, restrain, or rewire chromatin loops within TADs, influencing gene expression and potentially revealing the CGVs under changing environmental conditions. These changes can reinforce or weaken the TAD reorganization and modulate the associated interactions. (E) Integration of TADs, loops, and epigenetic modifications, with CRISPR‐based functional validation, can assist in prioritizing the candidate gene within the TADs formed under changing environmental conditions. Gene validation and trait improvement can assist in releasing the elite line and reveal the chromatin interactions adapted to the local environment.

Thus, TAD‐based trait improvement represents a hypothesis‐driven strategy to investigate how genome architecture contributes to phenotypic variation by linking dynamic TAD organization with conditional expression of CGVs, offering insights into the adaptive potential relevant to crop domestication and improvement. Recent Hi‐C studies in Arabidopsis and cotton show environment‐associated changes in 3D genome organization and gene regulation (Göbel et al., 2024; Zhang et al., 2024), underscoring the potential of targeting chromatin structure and dynamics as a strategy for breeding of crops (Li et al., 2026).

Utilizing TAD chromatin organization to empower crop domestication and improvement

In the past, the domestication of crops has been considered a key historical innovation that enabled the selection of plants with large and complex genomes suitable for taste, storage, production, and cultivation (Chen et al., 2015). Domesticated traits are common to all members of domesticated species and mutations in a population may have originated from structural variants in an ancestral population. The conventional model of genome evolution assumes that when a novel phenotype is favored by the alteration in the environment, the population responds by relying on standing genetic variations, mutations, and past hybridization events (Barrett and Schluter, 2008). If a substantial phenotype change is needed to respond to drastic environmental stresses, adaptive genetic variations or cryptic variations arise and respond to adaptive changes. Identification of these variations and tapping the untapped potential of genes could facilitate crop domestication and trait improvement. High‐quality reference genomes, pan‐genomes, compartmentalization within the genomes, and identification of TAD and sub‐TAD have enabled researchers to directly identify the candidate genes regulating specific traits (Li et al., 2019) and link the genome structures to functions by simultaneous application of single‐cell Hi‐C and RNA sequencing (Liu et al., 2023). Specific genes regulating specific traits within the TAD can be targeted by genome editing for functional validation of traits associated with dynamic regulation. Mutations in TCP1‐rich transcription factors have been shown to alter the gene expression within the TADs. Similarly, perturbations of regulatory elements within TADs influence gene expression in a context‐dependent manner. TAD expression can be altered for desired trait improvement. Genome editing has greatly improved the crop traits and is widely adopted in diploid and polyploid crops (Zaman et al., 2019) using diverse CRISPR‐associated proteins (Zaman et al., 2024). After identifying candidate genes and regulatory regions within the chromatin interaction networks, CRISPR‐based approaches can be applied to validate their functional roles. Genome‐edited plants can be multiplied using speed breeding to get the required number of generations in a shorter duration (Figure 2). Recently, a simple and efficient method of “RAPID” transformation has been developed to induce the CRISPR expression cassettes in host tissues without the tissue culture procedures (Mei et al., 2024). TAD‐based trait improvement method may complement existing domestication strategies. Alteration in gene expression has been observed following experimental perturbations of boundary‐associated regulatory elements under specific conditions. TAD‐based trait improvement methods can directly help to prioritize the active TAD and ChIN analysis can facilitate identifying the whole network of regulatory pathways that are affecting the phenotype. Together, these approaches highlight the potential of integrating 3D genome organization with functional genomics and modern breeding tools to prioritize candidate loci for crop improvement.

CONCLUDING REMARKS

Understanding the genetic basis and phenotypic variation between domesticated and wild species has provided new opportunities for crop improvement. Genomic resources have expanded the toolbox available for plant breeders and trait improvement efforts by enabling changes at desired loci with great precision. Recent advancement in Hi‐C techniques has enabled the exploration of hierarchical chromatin interaction, A/B compartmentalization, TAD, and sub‐TAD, which are thought to contribute to gene regulation by facilitating the enhancer‐promoter interactions. Many plant species (cotton, foxtail millet, maize, pitaya, rice, sorghum, and tomato) have distinctly observed TAD boundaries that are enriched for active chromatin features and transcription factor occupancy. The association of transcription, epigenetic marks, and TAD boundaries (TCP and bZIP‐rich transcription factors) represents recurrent features associated with TAD boundaries in several plant species. Identifying the putative candidate genes regulating desired traits in plants can be exploited for TAD‐based trait improvement programs and potential biological questions (Figures 1, 2) that can be solved from the perspective of CGVs and TAD relationships. CGVs may act as an evolutionary element, buffering TADs and releasing them for phenotypic expression during stress‐induced 3D conformational changes. This TAD‐based trait improvement provides a complementary framework to conventional breeding stategies including the marker‐assisted breeding method, which is laborious and takes years for mapping, and most of the time predicts many genes at a single QTL. TAD‐based method combined with GEd and speed‐breeding techniques can start a new era of crop domestication, can become a resource of genetic diversity, may help the untapped potential of CGVs, and could ensure the sustainability of agriculture by developing new and better crops under a changing climate. These approaches extend beyond MAS in plant breeding because higher‐order features, including compartments and TAD domains, provide an additional regulatory layer that can be integrated with existing genomic approaches. Compared with conventional methods, TAD‐based strategies may facilitate more to identify candidate genes and ChINs underlying the desired phenotypes. TAD‐based trait improvement is a potential sustainable approach to enhance the productivity of the specific cultivar grown in specific climates and already adapted to local environmental conditions.

CONFLICTS OF INTEREST

The authors declare no conflicts of interest.

AUTHOR CONTIBUTIONS

Q.U.Z. conceptualized the idea and drafted the manuscript. R.J.H. and Z.M. contributed to manuscript revision. S.S. critically reviewed and edited the manuscript. J.L. and R.K.V. supervised the study and contributed to scholarly input. All authors read and approved the contents of this article.

Biographies

Zaman, Q.U ., Henry, R.J ., Mu, Z ., Shen, S ., Luo, J ., and Varshney, R.K . (2026). TADs, CGVs, and compartmentalization in genomes: Providing a new way for crop domestication and improvement. J. Integr. Plant Biol. 68: 2827–2837.