A platinum standard pan-genome resource that represents the population structure of Asian rice
Type
ArticleAuthors
Zhou, Yong
Chebotarov, Dmytro

Kudrna, Dave

Llaca, Victor

Lee, Seunghee
Rajasekar, Shanmugam
Mohammed, Nahed Abdullah

Al-Bader, Noor

Sobel-Sorenson, Chandler
Parakkal, Praveena
Arbelaez, Lady Johanna
Franco, Natalia
Alexandrov, Nickolai

Hamilton, N. Ruaraidh Sackville

Leung, Hei
Mauleon, Ramil

Lorieux, Mathias

Zuccolo, Andrea

McNally, Kenneth

Zhang, Jianwei

Wing, Rod Anthony

KAUST Department
Biological and Environmental Science and Engineering (BESE) DivisionCenter for Desert Agriculture
Plant Science
Date
2020-04-07Online Publication Date
2020-04-07Print Publication Date
2020-12Submitted Date
2020-01-27Permanent link to this record
http://hdl.handle.net/10754/662480
Metadata
Show full item recordAbstract
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.Citation
Zhou, Y., Chebotarov, D., Kudrna, D., Llaca, V., Lee, S., Rajasekar, S., … Wing, R. A. (2020). A platinum standard pan-genome resource that represents the population structure of Asian rice. Scientific Data, 7(1). doi:10.1038/s41597-020-0438-2Sponsors
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).Publisher
Springer NatureJournal
Scientific DataPubMed ID
32265447Additional Links
http://www.nature.com/articles/s41597-020-0438-2https://www.nature.com/articles/s41597-020-0438-2.pdf
Relations
Is Supplemented By:- [Dataset]
Zhou, Y., Chebotarov, D., Kudrna, D., Llaca, V., Seunghee Lee, Rajasekar, S., Mohammed, N., Al-Bader, N., Sobel-Sorenson, C., Praveena Parakkal, Lady Johanna Arbelaez, Franco, N., Nickolai Alexandrov, N. Ruaraidh Sackville Hamilton, Leung, H., Mauleon, R., Lorieux, M., Zuccolo, A., McNally, K. L., … Wing, R. A. (2020). A platinum standard pan-genome resource that represents the population structure of Asian rice. figshare. https://doi.org/10.6084/M9.FIGSHARE.C.4816266.V1. DOI: 10.6084/m9.figshare.c.4816266.v1 Handle: 10754/664963
ae974a485f413a2113503eed53cd6c53
10.1038/s41597-020-0438-2
Scopus Count
Except where otherwise noted, this item's license is described as Archived with thanks to Scientific Data
Related articles
- Genomic variation in 3,010 diverse accessions of Asian cultivated rice.
- Authors: Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang F, Mansueto L, Copetti D, Sanciangco M, Palis KC, Xu J, Sun C, Fu B, Zhang H, Gao Y, Zhao X, Shen F, Cui X, Yu H, Li Z, Chen M, Detras J, Zhou Y, Zhang X, Zhao Y, Kudrna D, Wang C, Li R, Jia B, Lu J, He X, Dong Z, Xu J, Li Y, Wang M, Shi J, Li J, Zhang D, Lee S, Hu W, Poliakov A, Dubchak I, Ulat VJ, Borja FN, Mendoza JR, Ali J, Li J, Gao Q, Niu Y, Yue Z, Naredo MEB, Talag J, Wang X, Li J, Fang X, Yin Y, Glaszmann JC, Zhang J, Li J, Hamilton RS, Wing RA, Ruan J, Zhang G, Wei C, Alexandrov N, McNally KL, Li Z, Leung H
- Issue date: 2018 May
- Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.
- Authors: Zhao Q, Feng Q, Lu H, Li Y, Wang A, Tian Q, Zhan Q, Lu Y, Zhang L, Huang T, Wang Y, Fan D, Zhao Y, Wang Z, Zhou C, Chen J, Zhu C, Li W, Weng Q, Xu Q, Wang ZX, Wei X, Han B, Huang X
- Issue date: 2018 Feb
- Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication.
- Authors: Zhang F, Xu T, Mao L, Yan S, Chen X, Wu Z, Chen R, Luo X, Xie J, Gao S
- Issue date: 2016 Apr 26
- The rice genome revolution: from an ancient grain to Green Super Rice.
- Authors: Wing RA, Purugganan MD, Zhang Q
- Issue date: 2018 Aug
- Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era.
- Authors: Kim TS, He Q, Kim KW, Yoon MY, Ra WH, Li FP, Tong W, Yu J, Oo WH, Choi B, Heo EB, Yun BK, Kwon SJ, Kwon SW, Cho YH, Lee CY, Park BS, Park YJ
- Issue date: 2016 May 26