Planta

, 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 Lu
  • Longjiang Fan
Original Article

Abstract

Main conclusion

Whole-genome re-sequencing of weedy rice from southern China reveals that weedy rice can originate from hybridization of domesticatedindicaandjaponicarice.

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.

Keywords

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

Supplementary material

425_2014_2159_MOESM1_ESM.pdf (956 kb)
Fig. S1StepPCO 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
  • Longjiang Fan
    • 1
  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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