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 Abdullah 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 Zhang; Rod Anthony Wing

doi:10.1038/s41597-020-0438-2

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 Abdullah 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 Anthony Wing

Research output: Contribution to journal › Article › peer-review

78 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 language	English (US)
Journal	Scientific data
Volume	7
Issue number	1
DOIs	https://doi.org/10.1038/s41597-020-0438-2
State	Published - Apr 7 2020

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10.1038/s41597-020-0438-2

https://repository.kaust.edu.sa/bitstream/10754/662480/1/Articlefile1.pdf

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Zhou, Y., Chebotarov, D., Kudrna, D., Llaca, V., Lee, S., Rajasekar, S., Mohammed, N. A., 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). https://doi.org/10.1038/s41597-020-0438-2

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title = "A platinum standard pan-genome resource that represents the population structure of Asian rice",

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.",

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

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: This research was supported by the AXA Research Fund (International Rice Research Institute), the King Abdullah University of Science & Technology, and the Bud Antle Endowed Chair for Excellence in Agriculture (University of Arizona) to R.A.W., the Start-up Fund of Huazhong Agricultural University to J.Z., and funding from the Taiwan Council of Agriculture to K.M.. The BUSCO analysis data for maize was kindly provided by Dr. Wu and Dr. Li from the Institute of Plant Physiology and Ecology, and Dr. Wang from Shanghai Jiao Tong University. One of two TE libraries used for repeat analysis was provided by Dr. Eric Laserre (University of Perpignan, France).",

year = "2020",

month = apr,

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doi = "10.1038/s41597-020-0438-2",

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Zhou, Y, Chebotarov, D, Kudrna, D, Llaca, V, Lee, S, Rajasekar, S, Mohammed, NA, Al-Bader, N, Sobel-Sorenson, C, Parakkal, P, Arbelaez, LJ, Franco, N, Alexandrov, N, Hamilton, NRS, Leung, H, Mauleon, R, Lorieux, M, Zuccolo, A, McNally, K, Zhang, J & Wing, RA 2020, 'A platinum standard pan-genome resource that represents the population structure of Asian rice', Scientific data, vol. 7, no. 1. https://doi.org/10.1038/s41597-020-0438-2

TY - JOUR

T1 - A platinum standard pan-genome resource that represents the population structure of Asian rice

AU - Zhou, Yong

AU - Chebotarov, Dmytro

AU - Kudrna, Dave

AU - Llaca, Victor

AU - Lee, Seunghee

AU - Rajasekar, Shanmugam

AU - Mohammed, Nahed Abdullah

AU - Al-Bader, Noor

AU - Sobel-Sorenson, Chandler

AU - Parakkal, Praveena

AU - Arbelaez, Lady Johanna

AU - Franco, Natalia

AU - Alexandrov, Nickolai

AU - Hamilton, N. Ruaraidh Sackville

AU - Leung, Hei

AU - Mauleon, Ramil

AU - Lorieux, Mathias

AU - Zuccolo, Andrea

AU - McNally, Kenneth

AU - Zhang, Jianwei

AU - Wing, Rod Anthony

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: This research was supported by the AXA Research Fund (International Rice Research Institute), the King Abdullah University of Science & Technology, and the Bud Antle Endowed Chair for Excellence in Agriculture (University of Arizona) to R.A.W., the Start-up Fund of Huazhong Agricultural University to J.Z., and funding from the Taiwan Council of Agriculture to K.M.. The BUSCO analysis data for maize was kindly provided by Dr. Wu and Dr. Li from the Institute of Plant Physiology and Ecology, and Dr. Wang from Shanghai Jiao Tong University. One of two TE libraries used for repeat analysis was provided by Dr. Eric Laserre (University of Perpignan, France).

PY - 2020/4/7

Y1 - 2020/4/7

N2 - 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.

AB - 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.

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DO - 10.1038/s41597-020-0438-2

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SN - 2052-4463

VL - 7

JO - Scientific data

JF - Scientific data

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ER -

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

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