A fertility restorer gene, Rf4, widely used for hybrid rice breeding encodes a pentatricopeptide repeat protein

BACKGROUND: Uncontrolled expression of a certain mitochondrial gene often causes cytoplasmic male sterility (CMS) in plants. This phenotype is prevented by the presence of a fertility restorer (Rf) gene in the nuclear genome. Such CMS/Rf systems have been successfully used for breedings of F(1) hybrid cultivars. In rice, approximately 99% of F(1) hybrid cultivars have been developed using a wild abortive type of CMS (WA-CMS) and its Rf genes. Recently, a newly identified mitochondrial gene, orf352, was reported as a WA-CMS-causing gene. FINDINGS: We cloned and functionally characterized Rf4, a major Rf gene for WA-CMS. We revealed that Rf4 encoded a pentatricopeptide repeat-containing protein and reduced the orf352-containing transcripts, thereby restoring pollen fertility. CONCLUSIONS: Through a map-based cloning, we have independently identified an allele of a recently reported Rf4 gene and demonstrated that the fertility restoration is controlled sporophytically. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12284-014-0028-z) contains supplementary material, which is available to authorized users.