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Background <p>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.</p> Results <p>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 (<i>P</i> &lt; 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&#xa0;A, 4D, and 6B. While selection on chromosome 3B successfully fixed Rht dwarfing alleles (<i>d</i> = -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 (<i>P</i> &lt; 0.05). A Breeding Feasibility Score (BFS) of 79.7 identifies these regions as viable targets for recombination-based recovery.</p> Conclusions <p>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.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年6月22日

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  • Sayed Mujtaba Sadaat,
  • Mohammadreza Bihamta,
  • Valiollah Mohammadi,
  • Mehrdad Mahlooji

摘要

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.