De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
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大豆野生近缘种的从头组装，用于多样性和农艺性状的全基因组分析
DOI：
10.1038/nbt.2979
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发表时间：
2014-10-01
影响因子：
46.9
通讯作者：
Qiu, Li-juan
中科院分区：
文献类型：
--
作者：
Li, Ying-hui;Zhou, Guangyu;Qiu, Li-juan
作物的野生近缘是农业遗传多样性的重要来源，但它们的基因库在很大程度上仍未被探索。我们报道了栽培大豆的野生近缘种大豆的泛基因组的建立和分析，通过对7个具有系统发育和地理代表性的种质进行测序和重新组装。基因组间比较发现了谱系特有的基因和具有拷贝数变异或大效应突变的基因，其中一些显示出正选择的证据，并可能导致生物抗性、种子组成、开花和成熟时间、器官大小和最终生物量等农艺性状的变异。约80%的泛基因组存在于所有七个材料(核心)中，而其余的是可有可无的，表现出比核心基因组更大的变异，可能反映了对不同环境的适应作用。这项工作将有助于利用野生大豆未开发的遗传多样性来改良优良品种。
Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.