, Volume 240, Issue 6, pp 1353–1363 | Cite as

Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China

  • Jie Qiu
  • Jinwen Zhu
  • Fei Fu
  • Chu-Yu Ye
  • Weidi Wang
  • Linfeng Mao
  • Zhangxiang Lin
  • Li Chen
  • Haiqiang Zhang
  • Longbiao Guo
  • Shen Qiang
  • Yongliang LuEmail author
  • Longjiang FanEmail author
Original Article


Main conclusion

Whole-genome re-sequencing of weedy rice from southern China reveals that weedy rice can originate from hybridization of domesticated indica and japonica rice.


Weedy rice (Oryza sativa f. spontanea Rosh.), which harbors phenotypes of both wild and domesticated rice, has become one of the most notorious weeds in rice fields worldwide. While its formation is poorly understood, massive amounts of rice genomic data may provide new insights into this issue. In this study, we determined genomes of three weedy rice samples from the lower Yangtze region, China, and investigated their phylogenetics, population structure and chromosomal admixture patterns. The phylogenetic tree and principle component analysis based on 46,005 SNPs with 126 other Oryza accessions suggested that the three weedy rice accessions were intermediate between japonica and indica rice. An ancestry inference study further demonstrated that weedy rice had two dominant genomic components (temperate japonica and indica). This strongly suggests that weedy rice originated from indica-japonica hybridization. Furthermore, 22,443 novel fixed single nucleotide polymorphisms were detected in the weedy genomes and could have been generated after indica-japonica hybridization for environmental adaptation.


Weedy rice (Oryza sativa f. spontanea Rosh.) Whole-genome re-sequencing Population structure Hybridization origin 



We thank Xunbin Guo and Junsen Jiao for collecting the weedy rice samples. This work was financially supported in part by grants from the China Agriculture Research System (CARS-01-02A) and the Natural Science Foundation of China (31171863).

Conflict of interest

We declare that we have no financial or personal relationships with other people or organizations that may have inappropriately influenced our work, and there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in or the review of the manuscript.

Ethical standard

This manuscript has not been published previously and there is no prior interaction with Planta. We confirm that there are no known conflicts of interest associated with the publication. The manuscript has been read and approved by all of the authors.

Supplementary material

425_2014_2159_MOESM1_ESM.pdf (956 kb)
Fig. S1 StepPCO plots for all chromosomes of the three weedy rice samples. Indica (blue) and japonica (orange) were treated as ancestral groups. Chromosomal regions of the admixed genome are attributed to either the “orange” or “blue” ancestry with admixed regions in the middle (YG02: yellow; YJ06: green; YJ07: red). The mean PC1 coordinates for each parental population are centered at 1 and -1, and the progressively lighter shading surrounding the mean of each parental group indicates ±1, ±2 or ±3 SDs from the mean. Supplementary material 1 (PDF 955 kb)
425_2014_2159_MOESM2_ESM.pdf (397 kb)
Supplementary material 2 (PDF 397 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Jie Qiu
    • 1
  • Jinwen Zhu
    • 2
  • Fei Fu
    • 1
  • Chu-Yu Ye
    • 1
  • Weidi Wang
    • 1
  • Linfeng Mao
    • 1
  • Zhangxiang Lin
    • 1
  • Li Chen
    • 1
  • Haiqiang Zhang
    • 1
  • Longbiao Guo
    • 3
  • Shen Qiang
    • 4
  • Yongliang Lu
    • 3
    Email author
  • Longjiang Fan
    • 1
    Email author
  1. 1.Department of Agronomy, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
  2. 2.Department of Plant Protection, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
  3. 3.China National Rice Research Institute, Chinese Academy of Agricultural SciencesHangzhouChina
  4. 4.Weed Research LaboratoryNanjing Agricultural UniversityNanjingChina

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