Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations

Yinguang Hou; Junwei Gan; Zeyu Fan; Lei Sun; Vanika Garg; Yu Wang; Shanying Li; Pengfei Bao; Bingchen Cao; Rajeev K Varshney; Hansheng Zhao

doi:10.1038/s41467-024-52376-5

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Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations

Journal article

Open access

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Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations

Yinguang Hou, Junwei Gan, Zeyu Fan, Lei Sun, Vanika Garg, Yu Wang, Shanying Li, Pengfei Bao, Bingchen Cao, Rajeev K Varshney, …

Nature communications, Vol.15(1), 8085

2024

DOI: https://doi.org/10.1038/s41467-024-52376-5

PMID: 39278956

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Abstract

Acclimatization - genetics

Adaptation, Physiological - genetics

China

Climate Change

Genetic Variation

Genome, Plant

Haplotypes

Poaceae - genetics

Moso bamboo (Phyllostachys edulis), an ecologically and economically important forest species in East Asia, plays vital roles in carbon sequestration and climate change mitigation. However, intensifying climate change threatens moso bamboo survival. Here we generate high-quality haplotype-based pangenome assemblies for 16 representative moso bamboo accessions and integrated these assemblies with 427 previously resequenced accessions. Characterization of the haplotype-based pangenome reveals extensive genetic variation, predominantly between haplotypes rather than within accessions. Many genes with allele-specific expression patterns are implicated in climate responses. Integrating spatiotemporal climate data reveals more than 1050 variations associated with pivotal climate factors, including temperature and precipitation. Climate-associated variations enable the prediction of increased genetic risk across the northern and western regions of China under future emissions scenarios, underscoring the threats posed by rising temperatures. Our integrated haplotype-based pangenome elucidates moso bamboo's local climate adaptation mechanisms and provides critical genomic resources for addressing intensifying climate pressures on this essential bamboo. More broadly, this study demonstrates the power of long-read sequencing in dissecting adaptive traits in climate-sensitive species, advancing evolutionary knowledge to support conservation.

Details

Title: Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations
Authors/Creators: Yinguang Hou - Zhejiang A & F University
Junwei Gan - Zhejiang A & F University
Zeyu Fan - Zhejiang A & F University
Lei Sun - State Forestry and Grassland Administration
Vanika Garg - Murdoch University, Centre for Crop and Food Innovation
Yu Wang - Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing, 100102, China
Shanying Li - Zhejiang A & F University
Pengfei Bao - Zhejiang A & F University
Bingchen Cao - Zhejiang A & F University
Rajeev K Varshney - Murdoch University, Food Futures Institute
Hansheng Zhao - Zhejiang A & F University
Publication Details: Nature communications, Vol.15(1), 8085
Publisher: Springer Nature
Number of pages: 15
Grant note: 32271975 / National Natural Science Foundation of China (National Science Foundation of China)
Identifiers: 991005707269807891
Murdoch Affiliation: State Agricultural Biotechnology Centre; Centre for Crop and Food Innovation
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.54 Molecular & Cell Biology - Genetics; 1.54.1543 Flow Cytometry
Web Of Science research areas: Biotechnology & Applied Microbiology
ESI research areas: Biology & Biochemistry