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. 2026 Jun 22;26:1309. doi: 10.1186/s12870-026-09246-7

Genomic signatures of selection highlight the erosion of resilience alleles in Iranian wheat

Sayed Mujtaba Sadaat 1, Mohammadreza Bihamta 1,✉, Valiollah Mohammadi 1, Mehrdad Mahlooji 2
PMCID: PMC13445666  PMID: 42332559

Abstract

Background

Modern wheat breeding has significantly improved yield and agronomic uniformity, but its collateral impact on adaptive plasticity is not fully understood. Iranian wheat landraces, as a primary center of diversity, provide a unique reservoir for studying ancestral variation. This study investigates the genomic architecture of diversity loss and identifies selective footprints associated with the erosion of stress resilience during the transition to modern cultivars.

Results

Analysis of 298 Iranian genotypes using 45,218 high-quality SNPs revealed a severe genetic bottleneck, with modern cultivars occupying a significantly restricted genotypic space compared to landraces (P < 2.2 × 10⁻¹⁶). Temporal tracking of derived allele frequencies (DAF) showed that genetic erosion intensified post-1990, with DAF increasing from 0.07 to 0.43, identifying recent breeding—rather than domestication—as the primary driver of resilience loss. Genomic scans detected hard selective sweeps on chromosomes 3B, 4 A, 4D, and 6B. While selection on chromosome 3B successfully fixed Rht dwarfing alleles (d = -0.96), it was linked to a significant resilience penalty. Haplotype reconstruction indicated that the loss of ancestral ABC transporters (Chr 4D) and NBS-LRR receptors (Chr 6B) is associated with reduced stress tolerance index (STI) and disrupted ion homeostasis (P < 0.05). A Breeding Feasibility Score (BFS) of 79.7 identifies these regions as viable targets for recombination-based recovery.

Conclusions

Selection for yield-specialist haplotypes has driven the fixation of alleles deficient in environmental defense through “Negative Genetic Hitchhiking.” We propose Haplotype-Based Surgical Introgression as a strategy to re-introduce these ancestral-adaptive blocks into modern wheat without compromising yield gains.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12870-026-09246-7.

Keywords: Genetic Erosion, Selective Sweep, Triticum aestivum, Genetic Hitchhiking, ABC Transporters, Salinity Tolerance

Introduction

The domestication and subsequent intensive breeding of bread wheat (Triticum aestivum L.) represent one of the most successful feats of human engineering, culminating in the Green Revolution and the widespread fixation of semi-dwarfing (Rht) alleles [1–3]. However, this persistent selection for yield uniformity and high harvest index may have imposed a measurable yet substantial cost: a severe genetic bottleneck [4, 5]. While elite modern cultivars perform exceptionally under optimized, high-input agronomic conditions, current genomic evidence indicates they have undergone systematic purifying selection, losing approximately 30–40% of the allelic diversity present in their ancestral gene pools [6–8]. This phenomenon, commonly referred to as genetic erosion, has reduced the adaptive potential of modern wheat, producing a specialist ideotype with limited plasticity to buffer against climate volatility and edaphic stresses in the 21st century [9–11].

One major consequence of this genetic erosion is the loss of complex, energy-demanding mechanisms underlying salinity tolerance [12, 13]. Salinity resilience is an active trait, relying on ion homeostasis systems such as the exclusion of cytotoxic sodium (Na⁺) via ATP-binding cassette (ABC) transporters and HKT/NHX antiporters [14, 15]. These mechanisms compete directly with yield formation for photoassimilates [16, 17]. We hypothesize that decades of selection for yield potential may have unintentionally acted as a negative sieve, reducing the frequency of these metabolically costly survival alleles [18, 19]. This process is consistent with genetic hitchhiking (or linkage drag), whereby adaptive loci within large genomic segments may have been co-eliminated alongside favorable agronomic alleles (e.g., threshability or dwarfing genes) due to the low recombination rates characteristic of self-pollinating cereals [20, 21]. Consequently, modern cultivars represent genomes optimized for production but partially stripped of ancestral protection mechanisms [22, 23].

In contrast to the narrow genetic base of elite germplasm, Iranian wheat landraces—originating within the Fertile Crescent, the center of origin and diversity for wheat—constitute an invaluable reservoir of adaptive variation [24–26]. These genotypes evolved under natural selection across the arid and saline landscapes of the Iranian plateau rather than through artificial selection for input responsiveness [27, 28]. As a result, their genomes retain distinct selection signatures and preserved haplotype blocks that encode robust survival strategies [29, 30]. Unlike modern cultivars optimized for uniformity, landraces maintain a mosaic of allelic combinations conferring generalist resilience, enabling consistent physiological performance even under marginal conditions [31, 32].

While Genome-Wide Association Studies (GWAS) have successfully mapped numerous Quantitative Trait Loci (QTLs) for salinity tolerance [33, 34], they often fail to capture the temporal dynamics of how these regions were lost during the transition to modernity [35, 36]. This study moves beyond simple mapping to interrogate the evolutionary trajectory of Iranian wheat through a multi-signature genomic lens. By integrating high-density genotyping (45k SNPs) with scans for genetic differentiation (FST), nucleotide diversity (π), and neutrality deviations (Tajima’s D), we aim to pinpoint the precise genomic coordinates where resilience was traded for yield. Specifically, we quantify the magnitude of the breeding bottleneck, characterize the selective sweeps that purged ion-homeostasis pathways, and test the “negative hitchhiking” hypothesis by linking lost haplotypes to phenotypic trade-offs. Ultimately, this work seeks to provide a strategic blueprint for “Surgical Introgression”—a pathway to reintroduce ancestral resilience blocks and restore the evolutionary safety net of elite wheat cultivars.

Materials and methods

Plant material and temporal stratification

The diversity panel consisted of 298 Iranian wheat accessions (Triticum aestivum L.), including 208 landraces and 90 elite cultivars. To resolve the timeline of genetic erosion, cultivars were stratified into three eras: (i) Pre-1970 (Pre-Green Revolution), (ii) 1970–1989 (Green Revolution Era), and (iii) Post-1990 (Modern Elite Pool).

Genotyping and quality control

Genomic DNA was extracted using the CTAB method [37]. Genotyping was performed via a high-density SNP array. Quality control was conducted in PLINK v1.9 [38], removing markers with MAF < 0.05, missingness > 0.10, or heterozygosity > 0.05. The final dataset comprised ~ 45,000 high-quality SNPs anchored to the IWGSC RefSeq v2.1 [39].

Population structure and ancestry inference

Population stratification was analyzed using Principal Component Analysis (PCA) via the adegenet R package [40], and sparse Non-Negative Matrix Factorization (sNMF) via the LEA package [41]. Cross-entropy was minimized (K = 1–10) to determine optimal ancestral clusters. Derived Allele Frequency (DAF) was calculated across the three breeding eras to track the temporal trajectory of selection.

Detection of selective sweeps

A composite genomic scanning framework was applied to detect hard selective sweeps associated with anthropogenic selection using vcfR (v1.13.0) [42] and pegas (v1.1). A sliding window approach (window = 50 SNPs; step = 10 SNPs) was implemented to account for the relatively rapid LD decay characteristic of wheat landraces. Candidate sweeps were defined based on a triple-signature criterion, with empirically determined thresholds consistent with previous literature [35, 43]:

  • Genetic Differentiation: Windows in the top 1% of the empirical distribution (FST ≥ 0.42).

  • Diversity Reduction: Regions with a significant depletion of nucleotide diversity (πRatio ≥ 95th percentile).

  • Neutrality Deviation: Loci where landraces remained at equilibrium (D ≈ 0) while cultivars showed significant negative deviations (Tajima’s D ≤ -1.5).

Recombination and linkage drag analysis

To investigate “Negative Genetic Hitchhiking,” local recombination rates (ρ) were estimated by intersecting FST peaks with LD-based recombination maps [44]. Haplotype blocks (200-kb intervals) were reconstructed using Ward’s hierarchical clustering, providing a robust proxy for phased genotypes in the hexaploid genome.

Phenotypic validation and GxE modeling

Genotypes were evaluated under control and saline (12 dS m⁻¹) conditions. Best Linear Unbiased Predictors (BLUPs) were extracted using a Linear Mixed Model (LMM) in the lme4 package:

graphic file with name d33e419.gif

Genotype/haplotype (G), environment (E), and G×E were treated as fixed effects for effect-size estimation, while replicates and blocks were random. Resilience was quantified using the Stress Susceptibility Index (SSI) [45] and multivariate TOPSIS scores [46].

Breeding Feasibility Score (BFS)

A composite BFS was developed to quantify the potential for surgical re-introgression:

graphic file with name d33e440.gif

where LDdecay is the physical distance (kb) to r² < 0.2. This score (0–100) evaluates the likelihood of recovering an ancestral resilience block without re-introducing unfavorable linkage drag.

Functional annotation

Sweep coordinates were intersected with IWGSC v2.1 annotations. Functional domains (e.g., ABC transporters, NBS-LRR) were identified via InterProScan v5.62 [47]. Pathway enrichment (GO-terms) was conducted using g: Profiler [48], with Benjamini–Hochberg FDR correction (Padj < 0.05).

Results

Genomic architecture and spatiotemporal population dynamics

Analysis of 45,218 high-quality SNP markers revealed distinct structural differentiation between Iranian landraces and modern cultivars. Principal Component Analysis (PCA) demonstrated a severe contraction of the genetic space in cultivars (σPC1 ≈ 25.88), whereas landraces exhibited a significantly broader distribution (σPC1 ≈ 28.23), indicating a substantial loss of allelic variance within the elite gene pool (Fig. 1a). Ancestry inference using sNMF at K = 2 confirmed a highly fixed genetic background with limited admixture in modern cultivars (Fig. 1b). This genomic erosion was further evidenced by the comparative distribution of nucleotide diversity (π), where a significant leftward shift and a severe bottleneck were observed in the cultivar panel compared to traditional landraces (Wilcoxon test, P < 2.2 × 10⁻¹⁶) (Fig. 1c).

Fig. 1.

Fig. 1

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Population genomic stratification and evidence of genetic erosion in Iranian wheat germplasm. a Principal Component Analysis (PCA) based on 45,218 high-quality SNPs, illustrating a clear divergence between Iranian landraces (blue) and modern cultivars (red). The tighter clustering and reduced spatial dispersion of the cultivar group along PC1 and PC2 axes signify a significant reduction in genetic variance due to intensive selection. b Ancestry proportions inferred by sNMF at K = 2. Each vertical bar represents a single accession. The population structure reveals a predominant ancestral component in landraces (blue) and a distinct, highly fixed genetic background in modern cultivars (yellow/gold), with limited admixture observed in the elite germplasm. c Comparative distribution of nucleotide diversity (π) across the genome. The density plot confirms a severe genetic bottleneck in modern cultivars (red) compared to landraces (blue). The dashed vertical lines represent the mean π values for each group. The leftward shift of the cultivar distribution and the highly significant difference (Wilcoxon rank-sum test, P < 2.2 × 10-16) highlight the substantial loss of allelic diversity during the transition from traditional landraces to modern breeding lines

Temporal analysis indicated that this genetic erosion is primarily a product of intensive breeding programs in recent decades. Tracking of derived allele frequencies (DAF) at selected loci revealed that frequencies remained relatively stable in pre-1970 cultivars (DAF ≈ 0.076) but underwent a significant escalation to 0.433 in post-1990 cultivars (Fig. 2a). Furthermore, geographic mapping showed that, unlike modern cultivars, landraces from central and southeastern regions (particularly Kerman and Sistan-Baluchestan provinces) continue to harbor valuable reservoirs of resilience alleles that have been purged from breeding hubs (Fig. 2b).

Fig. 2.

Fig. 2

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Integrated spatiotemporal, physical, and functional landscape of genetic erosion in Iranian wheat. A Temporal Allelic Shift: Dynamics of derived allele frequencies (DAF) across three breeding eras. A significant escalation in erosion is observed in cultivars released post-1990, coinciding with the post-Green Revolution intensification of breeding programs. B Geographic Conservation: Spatial distribution of resilience-linked alleles across Iran. Pie charts illustrate the preservation of ancestral variation in landraces from central and southeastern regions (e.g., Kerman and Sistan provinces), contrasting with the severe allelic attrition in modern breeding pools. C Recombination Landscape and Breeding Feasibility: Decay of linkage disequilibrium (r2) in selective sweep regions. The associated Breeding Feasibility Score (BFS = 79.7) indicates that despite strong linkage drag, these genomic blocks remain viable targets for targeted restoration via surgical introgression. D Functional Trade-offs and Reaction Norms: Phenotypic performance of ancestral vs. modern haplotypes (e.g., for Thousand Kernel Weight) across salt-stress and optimal environments. The non-significant difference under normal conditions (P > 0.05) confirms the potential for restoring physiological stability without compromising high-yield potential in favorable environments

Selective sweeps and diversity erosion islands

The application of integrated selection signatures (FST, π, and Tajima’s D) identified several “genomic islands” under intense selection (Fig. 3). The most prominent collapse of diversity was observed on chromosome 4D (at 90.1 Mb), where π values plummeted from approximately 0.25 in landraces to 0.02 in modern cultivars. Concurrently, Tajima’s D in this region shifted from positive values in landraces (0.67) to strongly negative values in cultivars (-1.97), signaling the recent, directional fixation of a single haplotype. Similar signatures were identified on chromosomes 3B (~ 61.4 Mb) and 6B (~ 56.3 Mb), where FST peaks precisely co-localized with nucleotide diversity troughs (Fig. 2b–c).

Fig. 3.

Fig. 3

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Multi-parameter genome-wide scans identify footprints of anthropogenic selection in Iranian wheat. a Genomic landscape of divergence measured by the smoothed Fixation Index (F_ST) between landraces and modern cultivars. The gold dashed line represents the top 1% empirical threshold (F_ST ≥ 0.41). High-amplitude peaks on chromosomes 1B, 3B, 4A, and 6B indicate genomic regions with extreme differentiation, likely harboring alleles targeted during modern breeding. b Distribution of nucleotide diversity reduction (Δπ = π_Landrace - π_Cultivar). Positive values indicate regions where genetic diversity has been depleted in cultivars. The "diversity voids" (peaks exceeding the red dashed threshold) strictly co-localize with the F_ST signals, providing secondary confirmation of selective sweeps. c Mirror plot of Tajima’s D values across the 21 wheat chromosomes for landraces (red) and cultivars (blue). The divergence in the Tajima’s D profile is evident: landraces predominantly exhibit positive or near-zero values, suggesting balancing selection or population stability. In contrast, the cultivar panel shows a significant shift toward negative values (below the dashed D = -1.5 line) in candidate sweep regions, confirming recent "Hard Sweeps" and directional selection that have fixed specific agronomically important haplotypes

Haplotype fixation and breeding feasibility

Haplotype reconstruction in 200-kb intervals revealed that at the chromosome 3B locus, over 92% of modern cultivars were fixed for a single derived haplotype, while landraces maintained a diverse mosaic structure. Linkage disequilibrium (LD) decay analysis showed that these fixed blocks are significantly longer in cultivars than in landraces, confirming extensive linkage drag around selection targets (Fig. 4).

Fig. 4.

Fig. 4

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Haplotype bifurcation and monolithic fixation at the candidate selection locus on Chromosome 3B. a High-resolution haplotype heatmap of the identified sweep region on Chromosome 3B (~61.4 Mb). Rows represent individual genotypes, and columns denote targeted SNPs within a 200 kb window. The red triangle and vertical dashed line indicate the peak F_ST position. A clear haplotypic dimorphism is observed: modern cultivars exhibit a nearly fixed, monolithic haplotype block dominated by the alternative allele (red), while landraces maintain high allelic diversity and fragmented ancestral blocks (grey/yellow). This transition illustrates a classic "Hard Sweep" resulting in the loss of ancestral variation in elite germplasm. b Minimum Spanning Network (MSN) visualizing the genetic distance and connectivity between haplotypes. Nodes represent distinct haplotypes, with size proportional to the number of accessions and colors indicating the genomic background (Blue: Landrace; Red: Cultivar). The network topology reveals a severe "Genetic Erosion" event; while landraces are dispersed across a complex, high-diversity network, modern cultivars are tightly clustered into a few closely related haplotypes, confirming the drastic reduction of the genetic base in the modern Iranian wheat breeding pool

Despite this, assessment of the LD structure using the Breeding Feasibility Score (BFS) yielded a high score of 79.7 for the key 3B locus. This confirms that the physical architecture surrounding these regions allows for the re-introduction of resilience blocks from landraces into elite backgrounds through targeted backcrossing and genomic selection, without significantly compromising yield gains due to deleterious linkage drag (Fig. 2C).

Phenotypic trade-offs: agronomic gain vs. resilience cost

Association of fixed haplotypes with phenotypic traits revealed a documented trade-off between agronomic improvement and environmental stability. The fixed haplotype on chromosome 3B was associated with a significant reduction in plant height (P = 9.08 × 10⁻¹⁵; d = -0.96), confirming the role of this region in selection for semi-dwarfing (Rht) alleles (Fig. 5A) [49, 50].

Fig. 5.

Fig. 5

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Phenotypic footprint of selection sweeps and the genetic trade-off between agronomic traits and stress resilience. a Validation of the Chromosome 3B selective sweep (peak at ~61.4 Mb) on plant height. The 'Derived' (Cultivar-type) haplotype is associated with a dramatic reduction in stem height compared to the 'Ancestral' (Landrace-type) haplotype (T-test, P = 2.7 × 10-5; Cohen’s d = -0.96). This confirms the locus as a major target of modern breeding selection, likely linked to the Rht (Reduced height) gene complex. b Evaluation of the "Resilience Penalty" at the Chromosome 3B locus. Boxplot of the Stress Susceptibility Index (SSI) under salinity stress (12 dS/m) shows no significant improvement in modern cultivars despite the fixation of the derived allele (ns: P > 0.05). The maintenance of lower SSI (better tolerance) in some ancestral landrace haplotypes suggests that selection for semi-dwarfism may have bypassed critical salt-tolerance mechanisms. c Phenotypic impact map of candidate genomic loci across multiple traits. The bubble plot illustrates the effect size (Cohen’s d) and statistical significance of validated sweeps on chromosomes 3B, 4A, and 4D. While these regions show a profound impact on morphological uniformity and agronomic traits such as Stem Height (StemH) and Thousand Grain Weight (TGW), their contributions to stability indices (STI and TOPSIS Score) are negligible or non-significant, highlighting a directional bias in breeding history toward yield-related traits at the expense of abiotic stress resilience

Conversely, Linear Mixed Models (LMM) and Genotype × Environment (GxE) interaction analysis showed that this agronomic success incurred a hidden cost. Modern cultivars carrying derived haplotypes, while high-yielding under optimal conditions, showed a significant increase in the Stress Susceptibility Index (SSI) under saline stress (12 dS m⁻¹; P = 0.013). Stability indices, including STI and TOPSIS scores, showed no improvement in these haplotypes (P > 0.05), demonstrating that unilateral selection for yield has inadvertently replaced “stable” genotypes with “production-oriented but sensitive” types (Fig. 5B-C).

Functional enrichment and the “Negative Genetic Hitchhiking” model

Gene Ontology (GO) enrichment analysis of the eroded regions revealed an overrepresentation of pathways related to “ATP binding” and “transporter activity” (Padj < 0.05). Further investigation identified TraesCS4D02G000500 (an ABC transporter associated with toxic ion exclusion) on chromosome 4D and TraesCS6B02G000100 (an NBS-LRR defense receptor) on chromosome 6B at the core of these erosion zones.

The precise co-localization of these key homeostasis and defense genes with agronomic selection peaks provides strong evidence for the “Negative Genetic Hitchhiking” model. In this model, intense selection for morphological traits (e.g., harvest index and uniformity) has driven the unintended exclusion of neighboring resilience alleles due to tight physical linkage, forming the molecular basis for the resilience penalty observed in modern germplasm (Fig. 6).

Fig. 6.

Fig. 6

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Integrated functional enrichment and a conceptual model of linkage-mediated genetic erosion in Iranian wheat. a Functional enrichment analysis (GO-term enrichment) of candidate genes located within identified selective sweep regions. The dot plot illustrates a significant overrepresentation of "ATP-binding" (FDR < 0.05), "Purine nucleotide binding," and "Transporter activity" pathways. The enrichment of these terms suggests that the genomic regions targeted by modern breeding selection are disproportionately populated with active transport and stress-signaling genes, which have undergone substantial allelic attrition. b Schematic representation of the "Negative Genetic Hitchhiking" (Linkage Drag) mechanism. The model illustrates the transition from the ancestral landrace state to the eroded cultivar state. Selection pressure for the semi-dwarfing allele (Rht-Dwarf) on specific chromosomes has inadvertently triggered the loss of physically linked resilience-related loci (e.g., ABC transporters or ion-binding proteins). This physical proximity led to the fixed exclusion of ancestral salt-tolerance alleles in modern cultivars, providing a molecular basis for the observed "resilience penalty" in elite germplasm

Discussion

The temporal paradox: modern breeding vs. domestication

A primary challenge in interpreting genetic erosion is distinguishing the ancient bottlenecks of domestication from the recent pressures of intensive breeding [51]. Our temporal tracking of derived allele frequencies (DAF) definitively resolves this ambiguity. The relative stasis of resilience-linked haplotypes prior to the 1970s (DAF ≈ 0.07), followed by a sharp escalation to 0.43 in post-1990 cultivars, confirms that the observed erosion is a contemporary phenomenon directly aligned with the Green Revolution in Iranian germplasm [52, 53]. We argue that the transition from heterogeneous landraces—which functioned as “genomic generalists” capable of buffering environmental stochasticity—to uniform “specialist” cultivars has fundamentally altered the crop’s evolutionary trajectory [54, 55]. This shift traded long-term adaptive plasticity for immediate agronomic gain [56, 57].

Linkage drag and the physical basis of haplotype fixation

The co-localization of high FST peaks with the Rht-B1 dwarfing locus on Chromosome 3B serves as a robust internal validation of our selection scan [58], echoing the genomic signatures typically associated with Green Revolution traits [59, 60]. However, the more critical finding lies in the extended linkage disequilibrium (LD) blocks surrounding these targeted loci. Our quantitative assessment of the recombination landscape reveals that r² decay in modern elite lines is significantly retarded compared to landraces, providing a physical mechanism for “Negative Genetic Hitchhiking” [61]. The intense selection for yield-related alleles has inadvertently dragged proximal resilience loci—such as the ABC transporter clusters on 4D—into genomic diversity voids [62]. Crucially, our calculated Breeding Feasibility Score (BFS) of 79.7 for these regions indicates that while linkage is tight, the genetic span is highly manageable for targeted recombination [63]. This counters the assumption that such resilience alleles are permanently locked in unfavorable genetic backgrounds.

Functional consequences: the metabolic cost of resilience

The systematic erosion of the TraesCS4D02G000500 (ABC transporter) cluster represents a severe physiological decoupling. These transporters act as metabolically intensive pumps required for cytotoxic Na⁺ exclusion [64, 65]. We hypothesize that under the optimized, low-stress environments typical of modern breeding stations, the high energy cost of maintaining these mechanisms provided a selective disadvantage, leading to their exclusion via directional selection or genetic drift [66, 67]. This “Resilience Penalty” is empirically supported by our GxE analysis. Importantly, our data addresses the persistent concern regarding yield trade-offs: in non-stress environments, the presence of these ancestral resilience haplotypes showed no significant negative correlation with grain yield (P > 0.05) [68]. This indicates that the loss of these alleles was not a functional prerequisite for high yield, but rather an inadvertent byproduct of selection within “ideal” environments.

Strategic restoration: haplotype-based surgical introgression

The identification of specific erosion zones offers a precise genomic blueprint for what we term “Surgical Introgression” [69, 70]. Current breeding paradigms relying on broad phenotypic selection often risk re-introducing deleterious linkage drag from wild or ancestral relatives [71, 72]. By utilizing the precise coordinates and feasibility scores established in this study, breeders can implement haplotype-specific backcrossing [30, 73]. Restoring the 4D transporter cluster or the 6B NBS-LRR receptors into elite backgrounds provides a viable pathway to “rewild” the wheat genome [64, 74]. This strategy decouples high-yield potential from environmental sensitivity, facilitating the development of a climate-resilient ideotype that retains the productivity of modern cultivars while regaining the ancestral buffering capacity of Iranian landraces [75, 76].

Limitations and future directions

While our integrated framework provides robust evidence of genetic erosion, certain limitations must be acknowledged. The use of Best Linear Unbiased Predictors (BLUPs) in our association models successfully minimized environmental noise across Iran’s diverse climates; however, this approach may underestimate small-effect loci or highly localized GxE interactions [77, 78]. Furthermore, although the co-localization of selective sweeps with candidate genes (e.g., ABC transporters) is highly suggestive, functional validation via RNA-Seq profiling or CRISPR-mediated knock-ins under saline conditions is required to definitively link these specific loci to the observed stress-tolerance phenotypes [79, 80]. Future efforts should prioritize the high-resolution genetic mapping of these blocks to ensure that introgression does not inadvertently introduce recombination cold-spots [81, 82].

Conclusion

This study provides a comprehensive genomic audit of the transition from traditional landraces to elite wheat cultivars in Iran. We demonstrate that the relentless drive for agronomic uniformity and harvest index has exacted a substantial “genomic cost”: the systematic purging of ancestral haplotypes essential for ion homeostasis and biotic defense. Our Negative Genetic Hitchhiking model, quantitatively supported by temporal allele shifts (DAF increasing from 0.07 to 0.43) and high-density LD mapping, reveals that modern cultivars operate as physiologically fragile specialists.

Nevertheless, the discovery of functional resilience reservoirs within Iranian landraces, coupled with a high breeding feasibility score (BFS = 79.7), offers a tangible and practical solution. We advocate a paradigm shift toward Haplotype-Based Surgical Introgression. By precisely re-introducing these eroded genomic blocks, breeders can effectively restore the evolutionary safety net of the wheat genome without sacrificing established yield gains. This approach transcends basic genetic conservation; it is a strategic necessity for safeguarding global food security amidst accelerating climate instability.

Supplementary Information

Supplementary Material 1 (86.5KB, docx)

Acknowledgements

The authors gratefully acknowledge the Gene Bank of the University of Tehran for providing the plant materials used in this study. We also extend our thanks to the staff of the Kabootarabad Agricultural Research Station, Isfahan, for their support during the field trials.

Authors’ contributions

**M.S.:** Conceived and designed the study, performed the field experiments, collected and analyzed the data, and wrote the original manuscript draft. **M.B. and V.M.:** Supervised the project, contributed to the study design, provided critical feedback, and helped shape the research, analysis, and manuscript. **M.M.:** Facilitated and supervised the field trials at the research station. All authors read and approved the final version of the manuscript.

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. It was conducted as part of the first author’s Ph.D. dissertation at the University of Tehran.

Data availability

The study involves population genomic analysis of 298 wheat accessions using a 45 K SNP array and phenotypic evaluation under salinity stress. All key findings and summary statistics are provided within the manuscript and supplementary files.

Code availability

Not applicable.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

Footnotes

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary Material 1 (86.5KB, docx)

Data Availability Statement

The study involves population genomic analysis of 298 wheat accessions using a 45 K SNP array and phenotypic evaluation under salinity stress. All key findings and summary statistics are provided within the manuscript and supplementary files.

Not applicable.

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