Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.

中文翻译：

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大麦泛基因组揭示了突变育种的隐藏遗产

遗传多样性是作物改良的关键。由于普遍的基因组结构变异，单个参考基因组组装无法捕获作物物种的完整序列多样性（称为“泛基因组”1）。多个高质量序列组装是泛基因组基础设施不可或缺的组成部分。大麦 (Hordeum vulgare L.) 是一种重要的谷类作物，具有悠久的种植历史，适应广泛的农业气候条件2。在这里，我们报告了 20 个大麦品种（包括地方品种、栽培品种和野生大麦）基因型的染色体规模序列组装的构建，这些品种被选为全球大麦多样性的代表。我们对基因组存在/缺失变异进行了编目，并通过对 300 个基因库加入的全基因组鸟枪法测序探索了使用结构变异进行定量遗传分析。我们发现了丰富的大倒位多态性，并详细分析了目前优良大麦种质中常见的两种倒位；一个可能是突变育种的产物，另一个与涉及地理范围扩大的基因座密切相关。这种第一代大麦泛基因组使以前隐藏的遗传变异可用于遗传研究和育种。一个可能是突变育种的产物，另一个与涉及地理范围扩大的基因座密切相关。这种第一代大麦泛基因组使以前隐藏的遗传变异可用于遗传研究和育种。一个可能是突变育种的产物，另一个与涉及地理范围扩大的基因座密切相关。这种第一代大麦泛基因组使以前隐藏的遗传变异可用于遗传研究和育种。