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Published (Version of record)CC BY V4.0, Open
Journal article
Genomic variation in 3,010 diverse accessions of Asian cultivated rice
Nature, Vol.557(7703), pp.43-49
2018
PMCID: PMC6784863
PMID: 29695866
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Source: InCites
Abstract
Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.
Details
- Title
- Genomic variation in 3,010 diverse accessions of Asian cultivated rice
- Creators
- Wensheng Wang (Author) - Chinese Academy of Agricultural SciencesRamil Mauleon (Author) - International Rice Research Institute (Phillipines)Zhiqiang Hu (Author) - Shanghai Jiao Tong UniversityDmytro Chebotarov (Author) - International Rice Research InstituteShuaishuai Tai (Author) - BGI Genomics (China)Zhichao Wu (Author) - Chinese Academy of Agricultural SciencesMin Li (Author) - Anhui UniversityTianqing Zheng (Author) - Chinese Academy of Agricultural SciencesRoven Rommel Fuentes (Author) - International Rice Research InstituteFan Zhang (Author) - Chinese Academy of Agricultural SciencesLocedie Mansueto (Author) - Southern Cross University, Faculty of Science and EngineeringDario Copetti (Author) - University of ArizonaMillicent Sanciangco (Author) - International Rice Research InstituteKevin Christian Palis (Author) - International Rice Research InstituteJianlong Xu (Author) - Chinese Academy of Agricultural SciencesChen Sun (Author) - Shanghai Jiao Tong UniversityBinying Fu (Author) - Chinese Academy of Agricultural SciencesHongliang Zhang (Author) - China Agricultural UniversityYongming Gao (Author) - Chinese Academy of Agricultural SciencesXiuqin Zhao (Author) - Chinese Academy of Agricultural SciencesFei Shen (Author) - China Agricultural UniversityXiao Cui (Author) - Shanghai Jiao Tong UniversityHong Yu (Author) - Chinese Academy of Agricultural SciencesZichao Li (Author) - China Agricultural UniversityMiaolin Chen (Author) - Shanghai Jiao Tong UniversityJeffrey Detras (Author) - International Rice Research InstituteYongli Zhou (Author) - Chinese Academy of Agricultural SciencesXinyuan Zhang (Author) - Chinese Academy of Agricultural SciencesYue Zhao (Author) - Shanghai Jiao Tong UniversityDave Kudrna (Author) - University of ArizonaChunchao Wang (Author) - Chinese Academy of Agricultural SciencesRui Li (Author) - Shanghai Jiao Tong UniversityBen Jia (Author) - Shanghai Jiao Tong UniversityJinyuan Lu (Author) - Shanghai Jiao Tong UniversityXianchang He (Author) - Shanghai Jiao Tong UniversityZhaotong Dong (Author) - Shanghai Jiao Tong UniversityJiabao Xu (Author) - Chinese Academy of Agricultural SciencesYanhong Li (Author) - BGI Genomics (China)Miao Wang (Author) - BGI Genomics (China)Jianxin Shi (Author) - Shanghai Jiao Tong UniversityJing Li (Author) - Shanghai Jiao Tong UniversityDabing Zhang (Author) - Shanghai Jiao Tong UniversitySeunghee Lee (Author) - University of ArizonaWushu Hu (Author) - BGI Genomics (China)Alexander Poliakov (Author) - DOE Joint Genome Institute, Walnut Creek, CA, USAInna Dubchak (Author) - Lawrence Berkeley National LaboratoryVictor Jun Ulat (Author) - International Rice Research Institute (Phillipines)Frances Nikki Borja (Author) - International Rice Research Institute (Phillipines)John Robert Mendoza (Author) - Advanced Science and Technology InstituteJauhar Ali (Author) - International Rice Research Institute (Phillipines)Qiang Gao (Author) - BGI Genomics (China)Yongchao Niu (Author) - BGI Genomics (China)Zhen Yue (Author) - BGI Genomics (China)Ma Elizabeth B Naredo (Author) - International Rice Research Institute (Phillipines)Jayson Talag (Author) - University of ArizonaXueqiang Wang (Author) - China Agricultural UniversityJinjie Li (Author) - China Agricultural UniversityXiaodong Fang (Author) - BGI Genomics (China)Ye Yin (Author) - BGI Genomics (China)Jean-Christophe Glaszmann (Author) - Universite de MontpellierJianwei Zhang (Author) - University of ArizonaRuaraidh Sackville Hamilton (Author) - International Rice Research Institute (Phillipines)Rod A Wing (Author) - University of ArizonaJiayang Li (Author)Jue Ruan (Author) - Chinese Academy of Agricultural SciencesGengyun Zhang (Author) - Chinese Academy of Agricultural SciencesChaochun Wei (Author) - Shanghai Center For Bioinformation TechnologyNickolai Alexandrov (Author) - International Rice Research Institute (Phillipines)Kenneth L McNally (Author) - International Rice Research Institute (Phillipines)Zhikang Li (Author)Hei Leung (Author) - International Rice Research Institute (Phillipines)
- Publication Details
- Nature, Vol.557(7703), pp.43-49
- Publisher
- England
- Identifiers
- 991012917300302368
- Academic Unit
- Faculty of Science and Engineering; Science; Southern Cross Plant Science
- Language
- English
- Resource Type
- Journal article