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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 ( r   2  = 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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-016-0119-0) contains supplementary material, which is available to authorized users.

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