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第一作者:Peng Qin
第一单位:四川农业大学
通讯作者:Shigui Li
Abstract
背景回顾:Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement.
主要研究:Here, we assembled 31 high-quality genomes of genetically diverse rice accessions.
结果1-泛基因组:Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations.
结果2-结构变异和基因拷贝数变异检测:Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population.
结果3-结构变异形成机制及对基因表达的影响:Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication.
结果4-利用结构变异做GWAS:Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly.
结论:Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.
摘 要
结构变异(SV)和基因拷贝数变异(gCNV)作用于作物的演化、驯化和改良。本文中,作者组装了31个不同水稻种质材料的高质量基因组。与现有的两个水稻基因组组装一起,作者开发出了一套水稻的泛基因组遗传资源,包括一个图形结构基因组(graph-based genome),为水稻广泛的基因组变异鉴定提供了可能。作者共鉴定了171,072个SVs和25,549个gCNVs,并利用非洲栽培稻的基因组组装作为参考,推断亚洲栽培稻群体中SVs的起源。作者对SVs形成机制、及其对基因表达的影响,以及亚群体间分布的分析,阐明了可以利用这些资源,帮助我们进一步理解SVs和gCNVs是如何影响水稻环境适应和驯化的。本文所报道的图形结构基因组,可以帮助我们通过全基因组关联研究(GWAS),来鉴定那些仅通过SNPs和单个参考基因组所无法检测的、与表型相关的遗传变异。本文的工作提供了水稻群体级别的基因组资源,同时配套开发了在线网站便于用户获取相关资源,有助于促进水稻育种以及植物功能基因组学和进化生物学研究。
通讯作者
** 李仕贵 **
个人简介:
1983年,四川农业大学,学士;
1990年,四川农业大学,硕士;
1995-1998年,四川农业大学,博士。
研究方向:水稻遗传育种及应用基础研究。
doi: https://doi.org/10.1016/j.cell.2021.04.046
Journal: Cell
Published date: May 28, 2021
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