Genomic variation in 3,010 diverse accessions of Asian cultivated rice

Wang Wensheng, Mauleon Ramil P., Hu Zhiqiang, Chebotarov Dmytro, Tai Shuaishuai, Wu Zhi-Chao, Li Min, Zheng Tianqing, Fuentes Roven Rommel, Zhang Fan, Mansueto Locedie, Copetti Dario, Sanciangco Millicent, Palis Kevin Christian, Xu Jianlong, Sun Chen, Fu Binying, Zhang Hongliang, Gao Yongming, Zhao Xiuqin, Shen Fei, Cui Xiao, Yu Hong, Li Zichao, Chen Miaolin, Detras Jeffrey, Zhou Yong-Li, Zhang Xinyuan, Zhao Yue, Kudrna Dave, Wang Chunchao, Li Rui, Jia Ben, Lu Jinyuan, He Xianchang, Dong Zhaotong, Xu Jiabao, Li Yanhong, Wang Miao, Shi Jianxin, Li Jing, Zhang Dabing, Lee Seunghee, Hu Wushu, Poliakov Alexander, Dubchak Inna, Ulat Victor Jun, Borja Borja Nikki Frances, Mendoza John Robert, Ali Jauhar, Li Jing, Gao Qiang, Niu Yongchao, Yue Zhen, Naredo Ma. Elizabeth B., Talag Jayson, Wang Xueqiang, Li Jinjie, Fang Xiaodong, Yin Ye, Glaszmann Jean-Christophe, et al.. 2018. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557:7703 : pp. 43-49.

Journal article ; Article de revue à facteur d'impact
Published version - Anglais
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Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Economie-gestion; Psychologie-éthologie-ergonomie

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.

Mots-clés Agrovoc : riz, Variation génétique, Sélection, Provenance

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Wang Wensheng, CAAS (CHN)
  • Mauleon Ramil P., IRRI (PHL)
  • Hu Zhiqiang, CAAS (CHN)
  • Chebotarov Dmytro, IRRI (PHL)
  • Tai Shuaishuai, BGI-Shenzhen (CHN)
  • Wu Zhi-Chao, CAAS (CHN)
  • Li Min, CAAS (CHN)
  • Zheng Tianqing, CAAS (CHN)
  • Fuentes Roven Rommel, IRRI (PHL)
  • Zhang Fan, CAAS (CHN)
  • Mansueto Locedie, IRRI (PHL)
  • Copetti Dario, University of Arizona (USA)
  • Sanciangco Millicent, IRRI (PHL)
  • Palis Kevin Christian, IRRI (PHL)
  • Xu Jianlong, CAAS (CHN)
  • Sun Chen, Shanghai Jiaotong University (CHN)
  • Fu Binying, IRRI (PHL)
  • Zhang Hongliang, CAU [China Agricultural University] (CHN)
  • Gao Yongming, CAAS (CHN)
  • Zhao Xiuqin, CAAS (CHN)
  • Shen Fei, CAU [China Agricultural University] (CHN)
  • Cui Xiao, Shanghai Jiaotong University (CHN)
  • Yu Hong, CAAS (CHN)
  • Li Zichao, CAU [China Agricultural University] (CHN)
  • Chen Miaolin, Shanghai Jiaotong University (CHN)
  • Detras Jeffrey, IRRI (PHL)
  • Zhou Yong-Li, CAAS (CHN)
  • Zhang Xinyuan, CAAS (CHN)
  • Zhao Yue, Shanghai Jiaotong University (CHN)
  • Kudrna Dave, University of Arizona (USA)
  • Wang Chunchao, CAAS (CHN)
  • Li Rui, Shanghai Jiaotong University (CHN)
  • Jia Ben, Shanghai Jiaotong University (CHN)
  • Lu Jinyuan, Shanghai Jiaotong University (CHN)
  • He Xianchang, Shanghai Jiaotong University (CHN)
  • Dong Zhaotong, Shanghai Jiaotong University (CHN)
  • Xu Jiabao, BGI-Shenzhen (CHN)
  • Li Yanhong, BGI-Shenzhen (CHN)
  • Wang Miao, BGI-Shenzhen (CHN)
  • Shi Jianxin, Shanghai Jiaotong University (CHN)
  • Li Jing, Shanghai Jiaotong University (CHN)
  • Zhang Dabing, Shanghai Jiaotong University (CHN)
  • Lee Seunghee, University of Arizona (USA)
  • Hu Wushu, BGI-Shenzhen (CHN)
  • Poliakov Alexander, DOE-JGI (USA)
  • Dubchak Inna, DOE-JGI (USA)
  • Ulat Victor Jun, IRRI (PHL)
  • Borja Borja Nikki Frances, IRRI (PHL)
  • Mendoza John Robert, Advanced Science and Technology Institute (PHL)
  • Ali Jauhar, IRRI (PHL)
  • Li Jing, Shanghai Jiaotong University (CHN)
  • Gao Qiang, BGI-Shenzhen (CHN)
  • Niu Yongchao, BGI-Shenzhen (CHN)
  • Yue Zhen, BGI-Shenzhen (CHN)
  • Naredo Ma. Elizabeth B., IRRI (PHL)
  • Talag Jayson, University of Arizona (USA)
  • Wang Xueqiang, CAU [China Agricultural University] (CHN)
  • Li Jinjie, CAU [China Agricultural University] (CHN)
  • Fang Xiaodong, BGI-Shenzhen (CHN)
  • Yin Ye, BGI-Shenzhen (CHN)
  • Glaszmann Jean-Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-9918-875X
  • et al.

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