TY - JOUR
T1 - Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
AU - Zhou, Yong
AU - Yu, Zhichao
AU - Chebotarov, Dmytro
AU - Chougule, Kapeel
AU - Lu, Zhenyuan
AU - Rivera, Luis F.
AU - Kathiresan, Nagarajan
AU - Al-Bader, Noor
AU - Mohammed, Nahed
AU - Alsantely, Aseel
AU - Mussurova, Saule
AU - Santos, João
AU - Thimma, Manjula
AU - Troukhan, Maxim
AU - Fornasiero, Alice
AU - Green, Carl D.
AU - Copetti, Dario
AU - Kudrna, David
AU - Llaca, Victor
AU - Lorieux, Mathias
AU - Zuccolo, Andrea
AU - Ware, Doreen
AU - McNally, Kenneth
AU - Zhang, Jianwei
AU - Wing, Rod A.
N1 - Publisher Copyright:
© 2023, The Author(s).
PY - 2023/12
Y1 - 2023/12
N2 - 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.
AB - 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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U2 - 10.1038/s41467-023-37004-y
DO - 10.1038/s41467-023-37004-y
M3 - Article
C2 - 36944612
AN - SCOPUS:85150669133
SN - 2041-1723
VL - 14
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 1567
ER -