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The history of the domestication of rice is controversial, as it remains unknown whether domestication processes occurred once or multiple times. To date, genetic architecture and phylogenetic studies based on the rice nuclear genome have been extensively studied, but the results are quite different. Here, we found interesting results for different selections in  Oryza sativa  based on comprehensive studies of the rice mitochondrial (mt) genome. In detail, 412 rice germplasms were collected from around the world for variant architecture studies. A total of 10632 variants were detected in the mt genome, including 7277 SNPs and 3355 InDels. Selection signal ( π   w  / π   c  ) indicated that the selection sites in  Oryza sativa  L. ssp.  japonica  were different from those of  Oryza sativa  L.  indica  rice. The fixation index ( F  ST ) was higher between  indica  and  japonica  than between  indica  and wild rice. Moreover, haplotype and phylogenetic analyses also revealed  indica  clusters and  japonica  clusters that were well separated from wild rice. As mentioned above, our studies indicate that the selection sites of the  indica  type were different from those of the  japonica  type. This means that  indica  and  japonica  have experienced different domestication processes. We also found that  japonica  may have experienced a bottleneck event during domestication.

Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice