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Published (Version of Record)CC BY V4.0, Open Access
Journal article
A pangenome analysis pipeline provides insights into functional gene identification in rice
Genome Biology, Vol.24(1), pp.19-19
2023
PMID: 36703158
Abstract
Background: A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, bioinformatics analysis tools for graph format genomes are lacking.
Results: To overcome this problem, we develop a novel strategy for pangenome construction and a downstream pangenome analysis pipeline (PSVCP) that captures genetic variants' position information while maintaining a linearized layout. Using PSVCP, we construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 diverse accessions using the pangenome as the reference. We show that PSVCP successfully identifies causal structural variations for rice grain weight and plant height. Our results provide insights into rice population structure and genomic diversity. We characterize a new locus (qPH8-1) associated with plant height on chromosome 8 undetected by the SNP-based genome-wide association study (GWAS).
Conclusions: Our results demonstrate that the pangenome constructed by our pipeline combined with a presence and absence variation-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and the associated genome sequence and genetic variants data provide valuable genomic resources for rice genomics research and improvement in future.
Details
- Title
- A pangenome analysis pipeline provides insights into functional gene identification in rice
- Authors/Creators
- Jian Wang - Guangzhou, 510640 ChinaWu Yang - Guangzhou, 510640 ChinaShaohong Zhang - Guangzhou, 510640 ChinaHaifei Hu - Guangzhou, 510640 China Murdoch, Western Australia 6150 AustraliaYuxuan Yuan - Hong Kong, SAR ChinaJingfang Dong - Guangzhou, 510640 ChinaLuo Chen - Guangzhou, 510640 ChinaYamei Ma - Guangzhou, 510640 ChinaTifeng Yang - Guangzhou, 510640 ChinaLian Zhou - Guangzhou, 510640 ChinaJiansong Chen - Guangzhou, 510640 ChinaBin Liu - Guangzhou, 510640 ChinaChengdao Li - Murdoch, Western Australia 6150 AustraliaDavid Edwards - Perth, WA AustraliaJunliang Zhao - Guangzhou, 510640 China
- Publication Details
- Genome Biology, Vol.24(1), pp.19-19
- Publisher
- BioMed Central
- Grant note
- 2022KJ106 / ; R2019PY-JX001 / ; 2021A0505030048 / ; 2020A1515111025 / ; 2020B1212060047 / ; 2021YG001 / ; R2019YJ-YB3006 / ;
- Identifiers
- 991005570077607891
- Copyright
- © The Author(s) 2023
- Murdoch Affiliation
- Centre for Crop and Food Innovation
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics