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Background  Three-line  Oryza sativa  (ssp.  japonica ) hybrids have been developed mainly using Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS). The  Rf1  gene restores the fertility of BT-type CMS lines, and is the only fertility restorer gene ( Rf ) that has been used to produce three-line  japonica  hybrids. Using more  Rf  genes to breed BT-type restorer lines may broaden the genetic diversity of the restorer lines, and represents a viable approach to improve the heterosis level of BT-type  japonica  hybrids.    Results  We identified two major  Rf  genes from ‘93-11’ that are involved in restoring the fertility of BT-type CMS plants. These genes were identified from resequenced chromosome segment substitution lines derived from a cross between the  japonica  variety ‘Nipponbare’ and the  indica  variety ‘93-11’. Molecular mapping results revealed that these genes were  Rf5  and  Rf6 , which are the  Rf  genes that restore fertility to Honglian-type CMS lines. The BT-type F 1  hybrids with either  Rf5  or  Rf6  exhibited normal seed setting rates, but F 1  plants carrying  Rf6  showed more stable seed setting rates than those of plants carrying  Rf5  under heat-stress conditions. Furthermore, the seed setting rates of F 1  hybrids carrying both  Rf5  and  Rf6  were more stable than that of F 1  plants carrying only one  Rf  gene.    Conclusion    Rf6  is an important genetic resource for the breeding of BT-type  japonica  restorer lines. Our findings may be useful for breeders interested in developing BT-type  japonica  hybrids.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-017-0142-9) contains supplementary material, which is available to authorized users.

Ability of Rf5 and Rf6 to Restore Fertility of Chinsurah Boro II-type Cytoplasmic Male Sterile Oryza Sativa (ssp. Japonica) Lines