The barley pan-genome reveals the hidden legacy of mutation breeding

第一作者：Murukarthick Jayakodi

第一单位：莱布尼兹植物遗传与作物研究所

通讯作者：Nils Stein

 Abstract 

研究背景：Genetic diversity is key to crop improvement.

存在问题：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’). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure.

研究物种：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 conditions.

主要研究：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.

结果1-PAV鉴定：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.

结果2-倒位：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.

结论：This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.

 摘  要 

遗传多态性是作物改良的关键。由于广泛存在的基因组结构变异，单一的参考基因组根本不可能获得作物物种所有的完整序列多样性信息，这种信息又称之为泛基因组。多个高质量的序列组装是泛基因组研究不可或缺的组成部分。大麦是一种重要的谷类作物，具有较长的栽培历史，适应于广泛的农业气候条件。本文中，作者构建了20个大麦栽培种基因型的染色体水平序列组装，这些大麦包括地方品种、栽培种以及野生大麦，作为全球大麦多样性的代表种质资源。作者鉴定了PAV变异，并且基于大麦基因库300份材料的全基因组鸟枪法测序结果探索了利用结构变异来进行数量遗传分析。作者发现了丰富的大片段倒位多态性，并详细分析了其中两个频繁出现在优质大麦种质资源中的倒位，其中一个可能是突变育种产生的，而另外一个则与参与大麦地理范围扩张相关的位点连锁。本文所报道的大麦泛基因组揭示了先前未知的遗传变异，有助于未来大麦的遗传研究和育种实践。

 通讯作者 

doi: 10.1038/s41586-020-2947-8

Journal: Nature

Published date: Nov 25, 2020