A platinum standard pan-genome resource that represents the population structure of Asian rice

Yong Zhou, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, Noor Al-Bader, Chandler Sobel-Sorenson, Praveena Parakkal, Lady Johanna Arbelaez, Natalia Franco, Nickolai Alexandrov, N. Ruaraidh Sackville Hamilton, Hei Leung, Ramil Mauleon, Mathias Lorieux, Andrea Zuccolo, Kenneth McNally, Jianwei ZhangRod A. Wing

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

As the human population grows from 7.8 billion to 10 billion over the next 30 years, breeders must do everything possible to create crops that are highly productive and nutritious, while simultaneously having less of an environmental footprint. Rice will play a critical role in meeting this demand and thus, knowledge of the full repertoire of genetic diversity that exists in germplasm banks across the globe is required. To meet this demand, we describe the generation, validation and preliminary analyses of transposable element and long-range structural variation content of 12 near-gap-free reference genome sequences (RefSeqs) from representatives of 12 of 15 subpopulations of cultivated Asian rice. When combined with 4 existing RefSeqs, that represent the 3 remaining rice subpopulations and the largest admixed population, this collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to map resequencing data to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice.

Original languageEnglish (US)
Article number113
JournalScientific Data
Volume7
Issue number1
DOIs
StatePublished - Dec 1 2020

ASJC Scopus subject areas

  • Statistics and Probability
  • Information Systems
  • Education
  • Computer Science Applications
  • Statistics, Probability and Uncertainty
  • Library and Information Sciences

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    Zhou, Y., Chebotarov, D., Kudrna, D., Llaca, V., Lee, S., Rajasekar, S., Mohammed, N., Al-Bader, N., Sobel-Sorenson, C., Parakkal, P., Arbelaez, L. J., Franco, N., Alexandrov, N., Hamilton, N. R. S., Leung, H., Mauleon, R., Lorieux, M., Zuccolo, A., McNally, K., ... Wing, R. A. (2020). A platinum standard pan-genome resource that represents the population structure of Asian rice. Scientific Data, 7(1), [113]. https://doi.org/10.1038/s41597-020-0438-2