A platinum standard pan-genome resource that represents the population structure of Asian rice
Mohammed, Nahed Abdullah
Arbelaez, Lady Johanna
Hamilton, N. Ruaraidh Sackville
Wing, Rod Anthony
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Desert Agriculture Initiative
Online Publication Date2020-04-07
Print Publication Date2020-12
Permanent link to this recordhttp://hdl.handle.net/10754/662480
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AbstractAs 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.
CitationZhou, 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/s41597-020-0438-2
SponsorsThis 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).
RelationsIs Supplemented By:
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
Except where otherwise noted, this item's license is described as Archived with thanks to Scientific Data
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