Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (Oryza sativa)

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; Dave Kudrna; Victor Llaca; Mathias Lorieux; Andrea Zuccolo; Doreen Ware; Kenneth McNally; Jianwei Zhang; Rod A. Wing

doi:10.1101/2022.06.11.495682

Abstract

Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Utilizing 16 high-quality genomes that represent the subpopulation structure of Asian rice (O. sativa), plus the genomes of two close relatives (O. rufipogon and O. punctata), we built a pan-genome inversion index of 1,054 non-redundant inversions that span an average of ∼ 14% of the O. sativa cv. Nipponbare reference genome sequence. Using this index we estimated an inversion rate of 1,100 inversions per million years in Asian rice, which is 37 to 73 times higher than previously estimated for plants. Detailed analyses of these inversions showed evidence of their effects on gene regulation, recombination rate, linkage disequilibrium and agronomic trait performance. Our study uncovers the prevalence and scale of large inversions (≥ 100 kb) across the pan-genome of Asian rice, and hints at their largely unexplored role in functional biology and crop performance.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

Yong Zhou^1a, yong.zhou{at}kaust.edu.sa,
Zhichao Yu^2a, proyu{at}webmail.hzau.edu.cn,
Dmytro Chebotarov^3a, d.chebotarov{at}irri.org,
Kapeel Chougule^4a, kchougul{at}cshl.edu,
Zhenyuan Lu⁴, luj{at}cshl.edu,
Luis F. Rivera¹, luis.riveraserna{at}kaust.edu.sa,
Nagarajan Kathiresan⁵, nagarajan.kathiresan{at}kaust.edu.sa,
Noor Al-Bader¹, noor.albader{at}kaust.edu.sa,
Nahed Mohammed¹, nahed.mohammed{at}kaust.edu.sa,
Aseel Alsantely¹, aseel.alsantely{at}kaust.edu.sa,
Saule Mussurova¹, saule.mussurova{at}kaust.edu.sa,
João Santos¹, dourado.jns{at}gmail.com,
Manjula Thimma¹, manjula.thimma{at}kaust.edu.sa,
Maxim Troukhan⁶, mtroukhan{at}persephonesoft.com,
Alice Fornasiero¹, alice.fornasiero{at}kaust.edu.sa,
Carl D. Green⁷, carl.green{at}kaust.edu.sa,
Dario Copetti⁸, dcopetti{at}email.arizona.edu,
Dave Kudrna⁸, dkudrna{at}email.arizona.edu,
Victor Llaca⁹, victor.llaca{at}corteva.com,
Mathias Lorieux¹⁰, mathias.lorieux{at}ird.fr,
Andrea Zuccolo^1,11*, andrea.zuccolo{at}kaust.edu.sa,
Doreen Ware^4,12*, Doreen.ware{at}usda.gov,
Kenneth McNally^3*, k.mcnally{at}irri.org,
Jianwei Zhang^2,8*, jzhang{at}mail.hzau.edu.cn,
Rod A. Wing^1,3,8*, rod.wing{at}kaust.edu.sa, rwing{at}ag.arizona.edu,

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