Analysis of 427 genomes reveals moso bamboo population structure and genetic basis of property traits

• Published in: Nature communications Vol. 12; no. 1; p. 5466
• Main Authors: Zhao, Hansheng, Sun, Shuai, Ding, Yulong, Wang, Yue, Yue, Xianghua, Du, Xiao, Wei, Qiang, Fan, Guangyi, Sun, Huayu, Lou, Yongfeng, Yang, Huanming, Wang, Jian, Xu, Xun, Li, Lichao, Yang, Kebin, Xu, Hao, Wang, Jiongliang, Zhu, Chenglei, Wang, Sining, Shan, Xuemeng, Hou, Yinguang, Wang, Yu, Fei, Benhua, Liu, Xin, Jiang, Zehui, Gao, Zhimin
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 15.09.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 45/23; 45/43; 631/208/205/2138; 631/208/514/1948; 631/449/1870; 631/449/2669; Adaptation; Adaptation, Physiological - genetics; Association analysis; Balancing; Bamboo; Carbohydrate metabolism; Carbohydrates; Cell walls; China; Demography; Economic analysis; Evolution; Evolution, Molecular; Exome Sequencing - methods; Forestry; Gene Expression Regulation, Plant; Genes; Genetic diversity; Genetic Variation; Genetics, Population - methods; Genome, Plant - genetics; Genome-Wide Association Study - methods; Genomes; Genomics - methods; Geography; Heterozygosity; Humanities and Social Sciences; multidisciplinary; Nucleotides; Phyllostachys edulis; Phylogeny; Plant Proteins - genetics; Poaceae - classification; Poaceae - genetics; Poaceae - metabolism; Polymorphism, Single Nucleotide; Population; Population genetics; Population structure; Science; Science (multidisciplinary); Single-nucleotide polymorphism; Species; Transcriptome; China
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-25795-x

Moso bamboo ( Phyllostachys edulis ) is an economically and ecologically important nontimber forestry species. Further development of this species as a sustainable bamboo resource has been hindered by a lack of population genome information. Here, we report a moso bamboo genomic variation atlas of 5.45 million single-nucleotide polymorphisms (SNPs) from whole-genome resequencing of 427 individuals covering 15 representative geographic areas. We uncover low genetic diversity, high genotype heterozygosity, and genes under balancing selection underlying moso bamboo population adaptation. We infer its demographic history with one bottleneck and its recently small population without a rebound. We define five phylogenetic groups and infer that one group probably originated by a single-origin event from East China. Finally, we conduct genome-wide association analysis of nine important property-related traits to identify candidate genes, many of which are involved in cell wall, carbohydrate metabolism, and environmental adaptation. These results provide a foundation and resources for understanding moso bamboo evolution and the genetic mechanisms of agriculturally important traits. Moso bamboo is an economically and ecologically important nontimber forestry species. Here, the authors analyze 427 genomes collected from 15 representative geographic areas, and identify genes under balancing selection, putative patterns of historic demography, and candidate genes associated with important traits.