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

Hansheng Zhao,Yue Wang,Jian Wang,Lichao Li,Huayu Sun,Kebin Yang,Xiao Du,Shuai Sun,Baowei Fei ,Xin Liu,Guangyi Fan,Yulong Ding,Xianghua Yue,Hao Xu,Qiang Wei,Yu Wang,Sining Wang,Yinguang Hou,Chenglei Zhu,Xuemeng Shan,Yonggen Lou ,Jiongliang Wang,Huanming Yang,Zehui Jiang,Xun Xu,Zhimin Gao

doi:10.1038/s41467-021-25795-x

Abstract

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.

Highlights

Moso bamboo (Phyllostachys edulis) is an economically and ecologically important nontimber forestry species
We found that approximately 93.97% of these single-nucleotide polymorphisms (SNPs) are located in intergenic regions, compared to 3.18% in intronic regions and 2.85% in coding regions (Supplementary Table 4)
We found relatively low whole-genome diversity in the moso bamboo population, indicating a possible low effective population size and small genetic pool to be used for future breeding purposes

Summary

Introduction

Moso bamboo (Phyllostachys edulis) is an economically and ecologically important nontimber forestry species. 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. We sequence 427 moso bamboo individuals from 15 representative geographic distribution areas of moso bamboo in China to identify genome-wide variations, including singlenucleotide polymorphisms (SNPs), small insertions, and deletions (InDels), structural variations (SVs), and copy number variations (CNVs). These variations are further analyzed to understand genome features and population structure to aid in further research and applications. The identified variations provide insight into the origin and evolutionary history of moso bamboo and reveal possible genetic loci related to the agronomic traits of moso bamboo

Methods

Results

Conclusion