Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice

Yong Zhou; Zhichao Yu; Dmytro Chebotarov; Kapeel Chougule; Zhenyuan Lu; Luis F Rivera; Nagarajan Kathiresan; Noor Al-Bader; Nahed Mohammed; Aseel Alsantely; Saule Mussurova; João Santos; Manjula Thimma; Maxim Troukhan; Alice Fornasiero; Carl D Green; Dario Copetti; David Kudrna; Victor Llaca; Mathias Lorieux; Andrea Zuccolo; Doreen Ware; Kenneth McNally; Jianwei Zhang; Rod A Wing

doi:10.1038/s41467-023-37004-y

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Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice

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Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice

Yong Zhou, Zhichao Yu, Dmytro Chebotarov, Kapeel Chougule, Zhenyuan Lu, Luis F Rivera, Nagarajan Kathiresan, Noor Al-Bader, Nahed Mohammed, Aseel Alsantely, …

Nature communications, Vol.14(1), pp.1567-14

21/03/2023

DOI: https://doi.org/10.1038/s41467-023-37004-y

PMID: 36944612

Résumé

Biological Evolution

Genome, Plant - genetics

Oryza - genetics

Phylogeny

Sequence Analysis, DNA

Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogon and O. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of the O. sativa cv. Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance.

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Titre: Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
Créateurs - sans rôle: Yong Zhou - Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
Zhichao Yu - National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
Dmytro Chebotarov - International Rice Research Institute (IRRI), Los Baños, 4031, Laguna, Philippines
Kapeel Chougule - Cold Spring Harbor Laboratory
Zhenyuan Lu - Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
Luis F Rivera - Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
Nagarajan Kathiresan - King Abdullah University of Science and Technology
Noor Al-Bader - Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
Nahed Mohammed - King Abdullah University of Science and Technology
Aseel Alsantely - Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
Saule Mussurova - Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
João Santos - Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
Manjula Thimma - Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
Maxim Troukhan - Persephone Software, LLC, Agoura Hills, CA, 91301, USA
Alice Fornasiero - Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
Carl D Green - Information Technology Department, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
Dario Copetti - University of Arizona
David Kudrna - University of Arizona
Victor Llaca - Research and Development, Corteva Agriscience, Johnston, IA, 50131, USA
Mathias Lorieux - DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
Andrea Zuccolo - Crop Science Research Center (CSRC), Scuola Superiore Sant'Anna, Pisa, 56127, Italy. andrea.zuccolo@kaust.edu.sa
Doreen Ware - Plant
Kenneth McNally - International Rice Research Institute (IRRI), Los Baños, 4031, Laguna, Philippines. k.mcnally@irri.org
Jianwei Zhang - National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. jzhang@mail.hzau.edu.cn
Rod A Wing - International Rice Research Institute (IRRI), Los Baños, 4031, Laguna, Philippines. rod.wing@kaust.edu.sa
Détails de publication: Nature communications, Vol.14(1), pp.1567-14
Note de subvention: S10 OD028621 / NIH HHS
Identifiants: 99136526409311
Unité académique: Diversité, Adaptation et Développement des plantes - DIADE
Langue: English
Type de ressource: Journal article