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

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dc.creatorZhou, Yong
dc.creatorYu, Zhichao
dc.creatorChebotarov, Dmytro
dc.creatorChougule, Kapeel
dc.creatorLu, Zhenyuan
dc.creatorRivera, Luis F.
dc.creatorKathiresan, Nagarajan
dc.creatorAl-Bader, Noor
dc.creatorMohammed, Nahed
dc.creatorAlsantely, Aseel
dc.creatorMussurova, Saule
dc.creatorSantos, João
dc.creatorThimma, Manjula
dc.creatorTroukhan, Maxim
dc.creatorFornasiero, Alice
dc.creatorGreen, Carl D.
dc.creatorCopetti, Dario
dc.creatorKudrna, David
dc.creatorLlaca, Victor
dc.creatorLorieux, Mathias
dc.creatorZuccolo, Andrea
dc.creatorWare, Doreen
dc.creatorMcNally, Kenneth
dc.creatorZhang, Jianwei
dc.creatorWing, Rod A.
dc.date2023-03-21
dc.date2024-12-19T12:53:14Z
dc.date2024-12-19T12:53:14Z
dc.date.accessioned2026-06-27T04:15:48Z
dc.descriptionUnderstanding 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. rufipogonandO. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of theO. sativacv. 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.
dc.identifierhttps://hdl.handle.net/10568/163971
dc.identifier.urihttp://hdl.handle.net/123456789/26979
dc.languageen
dc.publisherSpringer
dc.rightsOpen Access
dc.sourceZhou, Yong; Yu, Zhichao; Chebotarov, Dmytro; Chougule, Kapeel; Lu, Zhenyuan; Rivera, Luis F.; Kathiresan, Nagarajan; Al-Bader, Noor; Mohammed, Nahed; Alsantely, Aseel; Mussurova, Saule; Santos, João; Thimma, Manjula; Troukhan, Maxim; Fornasiero, Alice; Green, Carl D.; Copetti, Dario; Kudrna, David; Llaca, Victor; Lorieux, Mathias; Zuccolo, Andrea; Ware, Doreen; McNally, Kenneth; Zhang, Jianwei and Wing, Rod A. 2023. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nat Commun, Volume 14, no. 1
dc.subjectgenetic diversity
dc.subjectoryza sativa
dc.subjectwild relatives
dc.subjectplants
dc.subjectgene expression
dc.subjectlinkage disequilibrium
dc.subjectcrop performance
dc.titlePan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)