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
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 A.
N1 - Funding Information:
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 Copyright:
© 2020, The Author(s).
PY - 2020/12/1
Y1 - 2020/12/1
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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U2 - 10.1038/s41597-020-0438-2
DO - 10.1038/s41597-020-0438-2
M3 - Article
C2 - 32265447
AN - SCOPUS:85083171909
VL - 7
JO - Scientific data
JF - Scientific data
SN - 2052-4463
IS - 1
M1 - 113
ER -