Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice

Hyun Jung Kim, Janelle Jung, Namrata Singh, Anthony Greenberg, Jeff J. Doyle, Wricha Tyagi, Jong Wook Chung, Jennifer Kimball, Ruaraidh Sackville Hamilton, Susan R. McCouch

Research output: Contribution to journalArticlepeer-review

38 Scopus citations


Background: Understanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites). Results: Six wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the O. sativa subpopulations, indica, aus and japonica, and carried O. sativa introgressions; the other three wild groups were genetically divergent, had unique chloroplast haplotypes, and were located at the geographical extremes of the species range. The genetic subpopulations were significantly correlated (r2 = 0.562) with traditional species designations, O. rufipogon (perennial) and O. nivara (annual), differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies. Conclusions: Our results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations.

Original languageEnglish (US)
Article number56
Issue number1
StatePublished - Dec 1 2016
Externally publishedYes

Bibliographical note

Funding Information:
We gratefully acknowledge Sandra Harrington for managing tissue and seed stocks of the wild Oryza germplasm, Yuxin Shi for submission of data to NCBI, Genevieve DeClerck and Sandra Harrington for developing the Laboratory Information Management System (LIMS) for the McCouch lab, Fumio Onishi for greenhouse support, Namrata Singh for designing the primers used in the Bh4 and RC gene indel analysis, Kyeong Oh Kim for Python and R consulting, Diane Wang, and Margaret Smith for constructive comments and help editing the manuscript, Sang-Nag Ahn for historical interpretation of population structure in the ORSC, and Jeanne Kisacky for help with formatting. The wild rice accessions used in this study were distributed from the International Rice Genebank at the International Rice Research Institute in the Philippines and from the National Institute of Genetics supported by the National Bioresource Project, MEXT, Japan. This project was supported by the National Science Foundation (NSF) with a grant from the Plant Genome Research Program, Award #0606461 and #1026555 to SMc, and a grant from the Government of Norway entitled ‘Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives’ implemented in partnership with the Global Crop Diversity Trust, the Millennium Seed Bank of the Royal Botanic Gardens, Kew Gardens, national and international gene banks (SMc & RSH).

Publisher Copyright:
© 2016, The Author(s).


  • Annual-Perennial
  • Chloroplast Diversity
  • Domestication
  • Phylogeography
  • Population Structure


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