Qin Peng, Lu Hongwei, Du Huilong, Wang Hao, Chen Weilan, Chen Zhuo, He Qiang, Ou Shujun, Zhang Hongyu, Li Xuanzhao, Li Xiuxiu, Li Yan, Liao Yi, Gao Qiang, Tu Bin, Yuan Hua, Ma Bingtian, Wang Yuping, Qian Yangwen, Fan Shijun, Li Weitao, Wang Jing, He Min, Yin Junjie, Li Ting, Jiang Ning, Chen Xuewei, Liang Chengzhi, Li Shigui
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
Cell. 2021 Jun 24;184(13):3542-3558.e16. doi: 10.1016/j.cell.2021.04.046. Epub 2021 May 28.
Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. 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. 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. 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. 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.
结构变异（SVs）和基因拷贝数变异（gCNVs）推动了作物的进化、驯化和改良。在此，我们组装了31个遗传多样性丰富的水稻品种的高质量基因组。结合另外两个已有的组装结果，我们开发了泛基因组规模的基因组资源，包括一个基于图的基因组，用于获取水稻基因组变异信息。具体而言，我们发现了171,072个SVs和25,549个gCNVs，并利用一个光稃稻组装结果推断了栽培稻群体中SVs的衍生状态。我们对SV形成机制、对基因表达的影响以及在亚群体中的分布进行的分析，阐明了这些资源在理解SVs和gCNVs如何塑造水稻环境适应性和驯化过程中的作用。我们基于图的基因组使得基于全基因组关联研究（GWAS）能够鉴定出仅使用单核苷酸多态性（SNPs）和单个参考组装时无法检测到的与表型相关的遗传变异。我们的工作提供了丰富的群体规模资源以及易于使用的工具，以促进水稻育种以及植物功能基因组学和进化生物学研究。
