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

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Abstract

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.

Abstract

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.

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Acknowledgments

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.

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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.

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Authors and Affiliations

  1. Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China

    Jie Qiu, Fei Fu, Chu-Yu Ye, Weidi Wang, Linfeng Mao, Zhangxiang Lin, Li Chen, Haiqiang Zhang & Longjiang Fan

  2. Department of Plant Protection, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China

    Jinwen Zhu

  3. China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China

    Longbiao Guo & Yongliang Lu

  4. Weed Research Laboratory, Nanjing Agricultural University, Nanjing, 210095, China

    Shen Qiang

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  1. Jie Qiu
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  2. Jinwen Zhu
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  3. Fei Fu
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  4. Chu-Yu Ye
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Corresponding authors

Correspondence to Yongliang Lu or Longjiang Fan.

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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)

Supplementary material 2 (PDF 397 kb)

Table S1 Rice accessions used in this study.

Table S2 Summary of the genomic distribution of SNPs of weedy rice relative to two reference rice genomes.

Table S3 GO and plant metabolic pathway enrichment analysis of genes with fixed novel SNPs that cause moderate effects in weedy rice.

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Qiu, J., Zhu, J., Fu, F. et al. Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China. Planta 240, 1353–1363 (2014). https://doi.org/10.1007/s00425-014-2159-2

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