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dc.contributor.authorZhou, Yong
dc.contributor.authorChebotarov, Dmytro
dc.contributor.authorKudrna, Dave
dc.contributor.authorLlaca, Victor
dc.contributor.authorLee, Seunghee
dc.contributor.authorRajasekar, Shanmugam
dc.contributor.authorMohammed, Nahed Abdullah
dc.contributor.authorAl-Bader, Noor
dc.contributor.authorSobel-Sorenson, Chandler
dc.contributor.authorParakkal, Praveena
dc.contributor.authorArbelaez, Lady Johanna
dc.contributor.authorFranco, Natalia
dc.contributor.authorAlexandrov, Nickolai
dc.contributor.authorHamilton, N. Ruaraidh Sackville
dc.contributor.authorLeung, Hei
dc.contributor.authorMauleon, Ramil
dc.contributor.authorLorieux, Mathias
dc.contributor.authorZuccolo, Andrea
dc.contributor.authorMcNally, Kenneth
dc.contributor.authorZhang, Jianwei
dc.contributor.authorWing, Rod Anthony
dc.date.accessioned2020-04-12T06:51:10Z
dc.date.available2020-04-12T06:51:10Z
dc.date.issued2020-04-07
dc.date.submitted2020-01-27
dc.identifier.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
dc.identifier.issn2052-4463
dc.identifier.pmid32265447
dc.identifier.doi10.1038/s41597-020-0438-2
dc.identifier.urihttp://hdl.handle.net/10754/662480
dc.description.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.
dc.description.sponsorshipThis 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).
dc.publisherSpringer Nature
dc.relation.urlhttp://www.nature.com/articles/s41597-020-0438-2
dc.relation.urlhttps://www.nature.com/articles/s41597-020-0438-2.pdf
dc.rightsArchived with thanks to Scientific Data
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleA platinum standard pan-genome resource that represents the population structure of Asian rice
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentDesert Agriculture Initiative
dc.contributor.departmentPlant Science
dc.identifier.journalScientific Data
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionInternational Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031, Laguna, Philippines.
dc.contributor.institutionArizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA.
dc.contributor.institutionGenomics Technologies, Applied Science and Technology, Corteva AgriscienceTM, Iowa, IA, 50131, USA.
dc.contributor.institutionRice Genetics and Genomics Lab, International Center for Tropical Agriculture (CIAT), Cali, Colombia.
dc.identifier.volume7
dc.identifier.issue1
kaust.personZhou, Yong
kaust.personMohammed, Nahed Abdullah
kaust.personAl-Bader, Noor
kaust.personZuccolo, Andrea
kaust.personWing, Rod Anthony
dc.date.accepted2020-03-05
dc.relation.issupplementedbyDOI:10.6084/m9.figshare.c.4816266.v1
refterms.dateFOA2020-04-12T06:51:59Z
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Dataset]</i> <br/> 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). <i>A platinum standard pan-genome resource that represents the population structure of Asian rice</i>. figshare. https://doi.org/10.6084/M9.FIGSHARE.C.4816266.V1. DOI: <a href="https://doi.org/10.6084/m9.figshare.c.4816266.v1" >10.6084/m9.figshare.c.4816266.v1</a> Handle: <a href="http://hdl.handle.net/10754/664963" >10754/664963</a></a></li></ul>
dc.date.published-online2020-04-07
dc.date.published-print2020-12


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