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 () and Rod A. Wing ()
Additional contact information
Yong Zhou: King Abdullah University of Science and Technology (KAUST)
Zhichao Yu: Huazhong Agricultural University
Dmytro Chebotarov: International Rice Research Institute (IRRI), Los Baños
Kapeel Chougule: Cold Spring Harbor Laboratory
Zhenyuan Lu: Cold Spring Harbor Laboratory
Luis F. Rivera: King Abdullah University of Science and Technology (KAUST)
Nagarajan Kathiresan: King Abdullah University of Science and Technology (KAUST)
Noor Al-Bader: King Abdullah University of Science and Technology (KAUST)
Nahed Mohammed: King Abdullah University of Science and Technology (KAUST)
Aseel Alsantely: King Abdullah University of Science and Technology (KAUST)
Saule Mussurova: King Abdullah University of Science and Technology (KAUST)
João Santos: King Abdullah University of Science and Technology (KAUST)
Manjula Thimma: King Abdullah University of Science and Technology (KAUST)
Maxim Troukhan: Persephone Software, LLC
Alice Fornasiero: King Abdullah University of Science and Technology (KAUST)
Carl D. Green: King Abdullah University of Science and Technology (KAUST)
Dario Copetti: University of Arizona
David Kudrna: University of Arizona
Victor Llaca: Research and Development, Corteva Agriscience
Mathias Lorieux: DIADE, University of Montpellier, CIRAD, IRD
Andrea Zuccolo: King Abdullah University of Science and Technology (KAUST)
Doreen Ware: Cold Spring Harbor Laboratory
Kenneth McNally: International Rice Research Institute (IRRI), Los Baños
Jianwei Zhang: University of Arizona
Rod A. Wing: King Abdullah University of Science and Technology (KAUST)

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: Abstract 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.

Date: 2023
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DOI: 10.1038/s41467-023-37004-y

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