Cryptic cytoplasmic male sterility‐causing gene in the mitochondrial genome of common japonica rice

SUMMARY Cytoplasmic male sterility (CMS) is an agronomically significant trait that causes dysfunction in pollen and anther development. It is often observed during successive backcrossing between distantly related species. Here, we show that Asian japonica cultivars (Oryza sativa) exhibit CMS when the nucleus is replaced with that of the African rice Oryza glaberrima. The CMS line produced stunted anthers and did not set any seeds. Mitochondrial orf288 RNA was detected in the anthers of CMS lines but not in fertility restorer lines. The mitochondrial genome‐edited japonica rice that was depleted of orf288 did not exhibit male sterility when backcrossed with O. glaberrima. These results demonstrate that orf288 is a CMS‐causing gene. As orf288 commonly occurs in the mitochondrial genomes of japonica rice, these results indicate that common japonica rice cultivars possess a cryptic CMS‐causing gene hidden in their mitochondrial genomes. Significance Statement Cytoplasmic male sterility (CMS) is caused by the expression of a mitochondrial gene. Here, deletion of the mitochondrial orf288 gene by mitochondria‐targeted TALEN restored fertility in CMS rice and uncovered that orf288 was a CMS‐causing gene hidden in the mitochondrial genome of standard japonica rice. The mitochondrial orf288 gene in japonica rice is a cytoplasmic male sterility‐causing gene.