Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.

中文翻译：

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野生大麦基因组结构和基因组分化的分化选择塑造模式

在对比环境中对种群的不同选择导致功能基因组差异。然而，异质基因组分化背后的基因组结构仍然知之甚少。在这里，我们从头组装了两种优质野生大麦（Hordeum spontaneumK. Koch）基因组，并检测了两个种群在非生物胁迫下的基因组分化和基因表达模式。这两个种群具有共同的血统，起源于非常接近的地理区域，但由于截然不同的微环境，它们经历了不同的选择压力。我们确定了结构变异可能在影响可能与分化良好的表型相关的基因方面发挥重要作用，例如两个野生大麦基因组之间的开花时间和干旱反应。其中，启动子区域的 29 bp 插入在HvWRKY45基因中形成顺式调控元件，这可能有助于增强对干旱的耐受性。启动子区域的单个 SNP 突变可能影响HvCO5表达并推定与当地开花时间适应有关。我们还揭示了具有持续基因流动的两个群体之间显着的基因组差异。我们的结果表明，SNP 和小型 SV 通过局部适应在基因水平上与遗传分化相关联，并通过发散选择得以维持。相反，大的染色体倒位可能通过抑制染色体重组和基因流动，塑造了染色体上基因组分化的异质模式。我们的研究为当地适应的基因组基础提供了新的见解，并为栽培大麦的遗传改良提供了宝贵的资源。